Molecular markers for reduced pyruvate level traits in onions

Abstract

The present invention relates to genetic markers for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in an Allium cepa plant or plant part, wherein the markers are selected from the group consisting of markers linked to a QTL conferring reduced pyruvate located on chromosome 2, markers linked to a QTL conferring reduced pyruvate located on chromosome 1 and markers linked to a QTL conferring reduced pyruvate located on chromosome 7. The present invention also relates to the use of the markers of the present invention for determining the presence or absence of one or more QTLs conferring reduced pyruvates levels in an Allium cepa plant or plant part. The present invention also relates to a method for identifying and / or selecting an Allium cepa plant or plant part comprising determining the presence or absence of one or more markers of the present invention in said plant or plant part. The present invention relates to the use of isolated nucleic acids and the nucleotide sequences provided herein for marker assisted selection of Allium cepa plants or plant parts.

Description

Technical Field

[0001] This invention relates to the field of plant breeding. The invention provides genetic markers for determining the presence or absence of one or more quantitative trait loci (QTLs) conferring reduced pyruvate levels in onion (Allium cepa) plants or plant parts, wherein said markers are selected from: markers linked to a QTL conferring reduced pyruvate levels located on chromosome 2, markers linked to a QTL conferring reduced pyruvate levels located on chromosome 1, and markers linked to a QTL conferring reduced pyruvate levels located on chromosome 7. The invention also relates to the use of the markers of the invention for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts. The invention further relates to methods for identifying and / or selecting onion plants or plant parts, including determining the presence or absence of one or more markers of the invention in said plant or plant part. This invention relates to the use of isolated nucleic acids and the nucleotide sequences provided herein for marker-assisted selection of onion plants or plant parts. Background Technology

[0002] The onion plant is believed to have originated in West or Central Asia. In Europe, it has been known since the Bronze Age. The bulb of the onion plant—the “onion bulb”—is used in many dishes and enjoys a very healthy reputation. Plant breeding has always focused on yield, appearance, harvestability, storability, flavor, and content, because onions contain a variety of compounds that have beneficial health effects. Some of these compounds are most effective when onions are eaten fresh, and their concentrations are generally related to the onion's solids level. Mild and sweet enough to be eaten without cooking, high-solids onions provide more health-promoting compounds in the diet.

[0003] Pungent flavor is a typical characteristic of onions, caused by the enzyme alliinase converting the sulfur-containing flavor precursor alkyl(enyl)-L-cysteine ​​sulfoxide (ACSO) into thiosulfonate when onion cells are cut or damaged. The byproduct of this enzymatic process, pyruvate, is measured as an indicator of pungent flavor (Schwimmer and Weston 1961, J. of Agric. Food Chem. 9:301-4). The amount of pyruvate produced is directly correlated with the pungent flavor of onions as determined by a tasting panel (Schwimmer and Guadagni, 1962, J. Food Sc. 27:94-97).

[0004] Pungent flavor is an important commercial trait because consumers prefer fresh onions with low pungentness and a sweet taste. The pungent flavor masks the sweetness of sugar, which exists in onions as a water-soluble solid or part of carbohydrates. The spiciness is strongly influenced by the presence or absence of sulfur in the soil or plant nutrients (Randle 1992, Euhytica 59:151-156 and Randle and Bussard 1993, J.Amer.Soc.Hort.Sci.118:766-770), but there is also a clear genetic component, as shown by Lin (1995, J.Americ.Soc.Hort.Sci.120:119-122), Simon (1995, Euhytica 82:1-8), Wall et al. (1996, Euhytica 87:133-139) and Wall and Corgan (1999, Euhytica106:7-13).

[0005] According to some reports (Shock et al. 2004: “Pungency of Selected Onion Varieties Before and After Storage”, Oregon State University, Malheur Experiment Station Special Report 1055:45-46), pungency may increase significantly during storage. Therefore, onions with reduced pungency at harvest, where the pungency does not increase significantly during storage, are desired. Specifically, onions with reduced pungency after storage for at least approximately 2, 3, 4, 5, 6, 7, 8 months or more are desired. Long-day onions can be stored, while short-day onions are typically consumed after a short period of storage or without storage. Long-day onions with reduced pungency are particularly desirable, where the pungency does not increase during storage but rather remains unchanged or decreases (compared to harvest levels), i.e., lower than harvest levels after storage for at least approximately 2, 3, 4, 5, 6, 7, 8 months or more. Therefore, "reduction during storage" refers to a level that is lower than the level at harvest after a specific storage period (e.g., after about 2, 3, 4, 5, 6, 7, 8 months or more of storage).

[0006] Previously documented onion plants producing bulbs with reduced spiciness. WO2007011857A2 describes a long-day onion plant containing bulbs with low spiciness. WO 2009 / 092560 A1 describes a long-day onion plant capable of producing onion bulbs, containing increased soluble solids content and reduced spiciness. EP 2 992756 A1 describes an onion plant in which alliinase gene expression is reduced, resulting in reduced amounts of spiciness and lachrymatory components produced when onion cells break down. A common problem with onion varieties with reduced spiciness is the potential for reduced consistency in spiciness characteristics. One reason for this is the often large genotype resulting from environmental interactions, which is difficult to genetically fix through phenotypic selection. Further exacerbating this problem is that onion breeding lines are often inbred to the F4 or F5 level before being “aggregated” and maintained as a population rather than through appropriate individual seeds. This resulted in a residual heterozygosity level of up to 12.5%. Consequently, segregation was found in onion lines at the genetic loci of the desired trait (including the locus controlling the pungent trait). Therefore, the development of reliable genetic markers to determine the presence of reduced pungent alleles has not yet been successful. With molecular markers for the pungent trait in onion plants, it is possible to increase the genetic stability of low-pungent lines by immobilizing these loci in breeding lines, thereby producing a more coherent pungent trait in the resulting onion varieties. The availability of reliable molecular markers will further allow for faster breeding of new low-pungent varieties, as more individual plants can be screened using molecular markers compared to the more laborious pyruvate phenotypic screening. Summary of the Invention

[0007] In this invention, a method for identifying and / or selecting onion plants or plant parts is provided, comprising determining the presence or absence of one or more markers adapted to determine the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, wherein the markers are selected from: markers linked to a QTL conferring reduced pyruvate between markers isotig30225_1454 and isotig32865_1404 on chromosome 2; markers linked to a QTL conferring reduced pyruvate between markers isotig32772_1413 and isotig33099_885 on chromosome 1; and markers linked to a QTL conferring reduced pyruvate between markers isotig28625_2789 and isotig41937_218 on chromosome 7. The order of SNP markers identified in the context of this invention may be derived from Table 7 provided below.

[0008] This document also provides an isolated nucleic acid comprising a nucleotide sequence selected from the following: SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:15; SEQ ID SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:17; SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:21; SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:27; SEQ ID NO:29 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:17; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 1 A fragment consisting of at least 15 nucleotides of nucleotide 51 of SEQ ID NO:33; or a fragment of SEQ ID NO:35 or thereof consisting of at least 15 nucleotides of SEQ ID NO:35 containing nucleotide 51 of SEQ ID NO:35;SEQ ID NO:37 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:37; SEQ ID NO:39 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:39; SEQ ID NO:41 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:41; SEQ ID NO:43 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:43; SEQ ID NO:45 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:45; SEQ ID NO:47 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:47; and SEQ ID NO:49 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:49, or containing their complementary nucleotide sequences.

[0009] This document also provides the use of one or more nucleotide sequences selected from SEQ ID NO:1-50 or fragments thereof for marker-assisted selection of onion plants or plant parts, wherein the fragments consist of at least 15 nucleotides, the nucleotides comprising the 51st nucleotide of the nucleotide sequence selected from SEQ ID NO:1-50, or a complementary sequence of the one or more nucleotide sequences.

[0010] This document also provides markers for identifying onion plants that produce bulbs with reduced pyruvate levels, said markers comprising one or more SNPs selected from the following: SNP_01, which contains thymine at nucleotide 51 of SEQ ID NO:1 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, which contains adenine at nucleotide 51 of SEQ ID NO:3 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_03, which contains adenine at nucleotide 51 of SEQ ID NO:5 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; NO:5 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains cytosine at the 51st nucleotide of SEQ ID NO:11 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:11 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 contains thymine at the 51st nucleotide of SEQ ID NO:15 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15.SNP_09, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; SNP_10, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19; SNP_11, which contains adenine at nucleotide 51 of SEQ ID NO:21 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_23 contains cytosine at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 contains adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_15 contains adenine at nucleotide 51 of SEQ ID NO:29 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; NO:29 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33.SNP_18, comprising thymine at nucleotide 51 of SEQ ID NO:35 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, comprising thymine at nucleotide 51 of SEQ ID NO:37 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1; SNP_22 contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; SNP_23 contains thymine at the 51st nucleotide of SEQ ID NO:45 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_24 contains thymine at the 51st nucleotide of SEQ ID NO:47 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; NO:47 contains cytosine at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_25 contains guanine at nucleotide 51 of SEQ ID NO:49 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49.

[0011] Brief description of sequence lists

[0012] SEQ ID NO:1 shows a reduced pungent genotype of SNP_01.

[0013] SEQ ID NO:2 shows the high spiciness genotype of SNP_01.

[0014] SEQ ID NO:3 shows a reduced pungent genotype of SNP_02.

[0015] SEQ ID NO:4 shows the high spiciness genotype of SNP_02.

[0016] SEQ ID NO:5 shows a reduced pungent genotype of SNP_03.

[0017] SEQ ID NO:6 shows the high spiciness genotype of SNP_03.

[0018] SEQ ID NO:7 shows a reduced pungent genotype of SNP_04.

[0019] SEQ ID NO:8 shows the high spiciness genotype of SNP_04.

[0020] SEQ ID NO:9 shows a reduced pungent genotype of SNP_05.

[0021] SEQ ID NO:10 shows the high spiciness genotype of SNP_05.

[0022] SEQ ID NO:11 shows a reduced pungent genotype of SNP_06.

[0023] SEQ ID NO:12 shows the high spiciness genotype of SNP_06.

[0024] SEQ ID NO:13 shows a reduced pungent genotype of SNP_07.

[0025] SEQ ID NO:14 shows the high spiciness genotype of SNP_07.

[0026] SEQ ID NO:15 shows a reduced pungent genotype of SNP_08.

[0027] SEQ ID NO:16 shows the high spiciness genotype of SNP_08.

[0028] SEQ ID NO:17 shows a reduced pungent genotype of SNP_09.

[0029] SEQ ID NO:18 shows the high spiciness genotype of SNP_09.

[0030] SEQ ID NO:19 shows a reduced pungent genotype of SNP_10.

[0031] SEQ ID NO:20 shows the high spiciness genotype of SNP_10.

[0032] SEQ ID NO:21 shows a reduced pungent genotype of SNP_11.

[0033] SEQ ID NO:22 shows the high spiciness genotype of SNP_11.

[0034] SEQ ID NO:23 shows a reduced pungent genotype of SNP_12.

[0035] SEQ ID NO:24 shows the high spiciness genotype of SNP_12.

[0036] SEQ ID NO:25 shows a reduced pungent genotype of SNP_13.

[0037] SEQ ID NO:26 shows the high spiciness genotype of SNP_13.

[0038] SEQ ID NO:27 shows a reduced pungent genotype of SNP_14.

[0039] SEQ ID NO:28 shows the high spiciness genotype of SNP_14.

[0040] SEQ ID NO:29 shows a reduced pungent genotype of SNP_15.

[0041] SEQ ID NO:30 shows the high spiciness genotype of SNP_15.

[0042] SEQ ID NO:31 shows a reduced pungent genotype of SNP_16.

[0043] SEQ ID NO:32 shows the high spiciness genotype of SNP_16.

[0044] SEQ ID NO:33 shows a reduced pungent genotype of SNP_17.

[0045] SEQ ID NO:34 shows the high spiciness genotype of SNP_17.

[0046] SEQ ID NO:35 shows a reduced pungent genotype of SNP_18.

[0047] SEQ ID NO:36 shows the high spiciness genotype of SNP_18.

[0048] SEQ ID NO:37 shows a reduced pungent genotype of SNP_19.

[0049] SEQ ID NO:38 shows the high spiciness genotype of SNP_19.

[0050] SEQ ID NO:39 shows a reduced pungent genotype of SNP_20.

[0051] SEQ ID NO:40 shows the high spiciness genotype of SNP_20.

[0052] SEQ ID NO:41 shows a reduced pungent genotype of SNP_21.

[0053] SEQ ID NO:42 shows the high spiciness genotype of SNP_21.

[0054] SEQ ID NO:43 shows a reduced pungent genotype of SNP_22.

[0055] SEQ ID NO:44 shows the high spiciness genotype of SNP_22.

[0056] SEQ ID NO:45 shows a reduced pungent genotype of SNP_23.

[0057] SEQ ID NO:46 shows the high spiciness genotype of SNP_23.

[0058] SEQ ID NO:47 shows a reduced pungent genotype of SNP_24.

[0059] SEQ ID NO:48 shows the high spiciness genotype of SNP_24.

[0060] SEQ ID NO:49 shows a reduced pungent genotype of SNP_25.

[0061] SEQ ID NO:50 shows the high spiciness genotype of SNP_25.

[0062] SEQ ID NO:51 shows a reduced spiciness genotype of isottig30225_1454.

[0063] SEQ ID NO:52 shows the high spiciness genotype of isotig30225_1454.

[0064] SEQ ID NO:53 shows a reduced spiciness genotype of isottig32865_1404.

[0065] SEQ ID NO:54 shows the high spiciness genotype of isotig32865_1404.

[0066] SEQ ID NO:55 shows a reduced spiciness genotype of isotig32772_1413.

[0067] SEQ ID NO:56 shows the high spiciness genotype of isotig32772_1413.

[0068] SEQ ID NO:57 shows a reduced spiciness genotype of isottig33099_885.

[0069] SEQ ID NO:58 shows the high spiciness genotype of isottig33099_885.

[0070] SEQ ID NO:59 shows a reduced spiciness genotype of isottig28625_2789.

[0071] SEQ ID NO:60 shows the high spiciness genotype of isottig28625_2789.

[0072] SEQ ID NO:61 shows a reduced spiciness genotype of isottig41937_218.

[0073] SEQ ID NO:62 shows the high spiciness genotype of isottig41937_218. Detailed Implementation

[0074] General definition

[0075] The term "genome" refers to the genetic material of an organism. It is composed of DNA. The genome includes genes and non-coding sequences of DNA.

[0076] The term "genetic determinant cluster" refers to the genetic information in a plant's genome that causes a specific trait in the plant. Therefore, a genetic determinant cluster contains the genetic information (genes, loci, or introgressions) that confer a particular trait. Generally, a genetic determinant cluster can contain a single gene (or a quantitative trait locus (QTL)) or more than one gene.

[0077] "Phenotype" is the observable external and / or physiological appearance of a plant, which is the result of the interaction between its genotype and its environment. It includes all observable morphological and physiological characteristics, and therefore includes phenotypes such as pungent taste, PAD measurements, and the soluble solids content of onion bulbs.

[0078] In the context of this application, the term "trait" refers to the phenotype of a plant. When a plant exhibits the trait of the present invention, its genome contains at least one reduced pungent flavor allele associated with the trait of the present invention, particularly when the reduced pungent flavor allele is homozygous. Therefore, the plant possesses the genetic determinants of the present invention. It should be understood that when referring to a plant containing the trait of the plant of the present invention, it means an onion plant containing the reduced pungent flavor trait further described herein.

[0079] "Genome" is the sum of heritable genetic information of a plant, which is partly influenced by environmental factors and is expressed in its phenotype.

[0080] As used herein, “onion plant” or “onion” refers to the plant species *Allium cepa* L. or a part thereof, such as the (harvested) bulb, seeds, etc. “Bulb” is the harvested, edible part of the plant. Onion bulbs can be developing or mature. Mature bulbs, which are ready for harvest or have already been harvested, are preferred herein.

[0081] When the light (day length) is at least about 14 consecutive hours or longer, such as at least about 14, 15 or 16 hours, "long-day" onion plants will begin to form bulbs. Preferably, such continuous light (several hours per day) is provided for 2, 4, 7, 14, 21, 25 or more days to initiate bulb formation.

[0082] "Storage conditions" and "storage" include typical conditions for storing (preferably fresh) onions, such as darkness, cool temperatures (as used herein, cool temperatures mean preferably below 12°C, for example about 3-12°C, 3-10°C, 5-10°C, or about 3-5°C, preferably about 3, 4, or 5°C) and relative humidity (RH) of about 60-80%, preferably about 70-80%, most preferably about 70%. Controlled ventilation is also preferred.

[0083] "Soluble solids" or "soluble solids content" (referred to as "SSC" in this article) is the percentage (%) of water-soluble compounds in onion bulbs as measured by a refractometer according to the methods of Mann and Hoyle, 1945 (Proc.Americ.Soc.Hort.Sci.46:285-292) or Foskett and Peterson, 1949 (Proc.Americ.Soc.Hort.Sci.55:314-318).

[0084] “High SSC” in this document refers to an average SSC of at least 7.0% or 7.5% for a representative number of onion bulbs (e.g., at least 5, 6, 10, 15, 20, 30, 40, 50, 50, 60, 70, 80, 90 or more bulbs), or even at least 8%, 9%, 10%, 11%, 12%, 15%, 20%, 25%, 30% or more. Therefore, this document includes average SSCs of 7.0–30%, 7.5–30%, or even 7.0–20%, 8.0–20%, 7.0–15%, 8.0–15%, 7.0–10%, etc.

[0085] "Pungency" is the typical strong flavor of onions when the onion bulb tissue disintegrates due to crushing. It is preferably determined by measuring the enzymatic development of pyruvate according to the method of Schwimmer and Weston (1961, J. of Agric. Food Chemistry 9:301-304), which is closely related to the taste perception of the test group (Schwimmer 1962, J. Food Sci. 27:94-97; Wall and Corgan, 1992, Hort. Science 27:1029-1030). Alternatively, pyruvate (also known as pyruvate) can be measured using a colorimetric method as described in Anthon and Barrett (2003) Science of Food and Agriculture (83) 1210-1213. Pungency is expressed as μMol (micromoles, also μM or μmol) of pyruvate per gram of fresh weight of bulb material (μMol / g FW). This article also refers to it as “PAD measurement” (PAD from which pyruvate occurs) or “pyruvate measurement” or “pyruvate level”.

[0086] Therefore, the term "reduced spiciness" as used herein refers to a reduced spiciness level compared to the spiciness level of a reference variety. Preferably, a reduced spiciness level corresponds to a spiciness level reduced to such a degree that the reduced spiciness level corresponds to a low spiciness level. "Low spiciness" herein refers to an average spiciness of less than 5.5 μMol / g FW pyruvate, or even less than 5.0, 4.5, or 4.0 μMol / g FW pyruvate, equal to or less than 3.8 or 3.75 μMol / g FW pyruvate, or equal to or less than 3.5, 3.0, 2.5, 2.3, 2.0, 1.8, 1.5, or 1.3 μMol / g FW pyruvate, as determined by PAD measurements. In this document, "high spiciness" refers to an average spiciness level higher than that defined herein by a representative number of (mature) onion bulbs, preferably greater than 5.5 μMol / g FW pyruvate, or even greater than 6.0, 6.5, or 7.0 μMol / g FW pyruvate. Spiciness can be measured at harvest and / or after 2, 3, 4, 5, 6, 7, 8 months or more of storage.

[0087] "Narrow spiciness range" refers to a narrow difference in spiciness between individual bulbs from multiple bulbs obtained from a plant strain. Specifically, the difference in spiciness level between the spiciest bulb (maximum) and the least spicy bulb (minimum) is preferably less than or at most 5 μMol / g FW pyruvate, more preferably less than or at most 4 μMol / g FW pyruvate or less than or at most 3.5 μMol / g FW pyruvate, more preferably less than or at most 3.0, 2.5, 2.0, 1.5, or 1.0 μMol / g FW pyruvate. Preferably, the maximum spiciness (of the spiciest bulb produced by the plant) is equal to or less than 5 μMol / g FW pyruvate, more preferably equal to or less than 4.9, 4.8, 4.75, 4.7, 4.5, 4.0 or 3.8, 3.7, 3.5, or 3.0 μMol / g FW pyruvate. Preferably, the minimum spiciness level (i.e., the least pungent bulb produced by the plant) is equal to or less than 3.0, 2.5, more preferably equal to or less than 2.0, 1.3, or 1.2 μMol / g FW pyruvate. Therefore, the preferred range of spiciness within the plant line is that all bulbs have a spiciness level of 0 (minimum) to 5 (maximum) μMol / g FW pyruvate, preferably 1 (minimum) to 5 (maximum) μMol / g FW pyruvate, more preferably 1 (minimum) to 4 (maximum) μMol / g FW pyruvate. Furthermore, in one embodiment of the invention, all bulbs have a pungent flavor with a range of 0 (minimum) to 5 (maximum) μMol / g FW pyruvate, preferably 1 (minimum) to 5 (maximum) μMol / g FW pyruvate, more preferably 1 or 1.2 (minimum) to 4.9, 4.8, 4.7 or 4.5 (maximum) μMol / g FW pyruvate, and even more preferably 1 (minimum) to 4 (maximum) μMol / g FW pyruvate. For consumers, a narrow pungent flavor range is an important quality characteristic. It can be measured at harvest and / or preferably after a certain storage period (e.g., after at least about 2, 3, 4, 5, 6, 7, 8 months or more of storage).

[0088] "High spiciness allele" in this document refers to the allele associated with the high spiciness trait as further defined herein. In one implementation, the high spiciness allele is a wild-type allele.

[0089] "Reduced spiciness allele" in this document refers to an allele associated with the reduced spiciness trait as further defined herein. In one embodiment, the reduced spiciness allele is a mutant allele.

[0090] “Wild-type plant” in this paper refers to a plant that produces onion bulbs with high spiciness as defined herein. Such a plant is, for example, a suitable control in phenotypic studies, especially if the control plant has the same genetic background as the plant undergoing phenotypic testing (e.g., a low-spiciness plant).

[0091] "Long-term storage" herein refers to a storage length of at least 2, 3, 4, 5, 6, 7 months or more. Preferably, during the storage period, i.e., when comparing the average spiciness and / or SSC at harvest (or shortly after harvest) with the spiciness and / or SSC levels after 2, 3, 4, 5, 6, 7 months or more of storage, there is no significant increase in spiciness and / or no significant decrease in SSC. "No significant increase in spiciness" herein means that, compared with the measurement at harvest (or shortly after harvest), the spiciness measurement (i.e., pyruvic acid) increases by less than 10% after the storage period, more preferably less than 5%, even more preferably less than 3%, 2%, or 1%, more preferably no increase at all, and in one embodiment, the spiciness decreases. "No significant decrease in SSC" herein means that, compared with the SSC level at harvest (or shortly after harvest), the SSC level decreases by less than 5%, 4%, 3%, or 2% after the storage period, preferably less than 1% or 0.5%, more preferably unchanged. In one embodiment, the average SSC level after storage for 2, 3, 4, 5, 6, 7 months or more is at least about 80%, 85%, 87%, 88%, 89%, 90%, 95%, or 98% of the level at harvest, more preferably at least about 100%, or 101%, 102%, 103%, 105%, or more of the level at harvest.

[0092] Genetic determinants can be inherited in a recessive, intermediate, or dominant manner. When intermediate or dominant inheritance is involved, selection of the phenotypic trait is easier because a larger proportion of the offspring from the cross reveals the trait. Generally, genetic determinants can also contain combinations of recessive and / or intermediate and / or dominant genes or QTLs.

[0093] Selection for genetic determinants (e.g., reduced spiciness alleles) can be made on the phenotype (observable traits). Selection can also be made using molecular genotyping methods, such as one or more molecular markers genetically linked to the reduced spiciness allele, or preferably using the gene or allele sequence itself, for example, by molecular methods capable of distinguishing the presence of the reduced spiciness allele from the wild-type allele or its products (e.g., mRNA or protein encoded by the allele). Using molecular genotyping methods in breeding (such as "marker-assisted selection" using genetically linked markers, or other genotyping methods such as SNP genotyping) requires smaller populations for screening (compared to phenotypic selection) and can be done at a very early stage. Another advantage of molecular genotyping methods is that homozygous plants or seeds without copies of any of the high spiciness alleles described herein can be easily distinguished from plants having one or more copies of one or more of the said high spiciness alleles, even before seed germination or in early plant development, such as before onion bulb development.

[0094] “Plant line” or “breeding line” refers to a plant and its offspring. As used herein, the term “inbred line” refers to a plant line that has undergone repeated self-pollination and is nearly homozygous for each trait. Thus, “inbred line” or “parental line” refers to a plant that has undergone several (e.g., at least 4, 5, 6, 7 or more) generations of inbreeding, resulting in a plant line with high uniformity.

[0095] The term "allele" refers to any one or more alternative forms of the DNA sequence at a specific locus, all of which are associated with a trait or characteristic at that locus. In the diploid cells of an organism, the alleles of a given gene are located at specific locations or loci (multiple loci) on a chromosome. One allele is present on each of the pair of homologous chromosomes. Diploid plant species can contain a large number of different alleles at a given locus. These can be the same allele of the gene (homozygote) or two different alleles (heterozygote).

[0096] The term "locus" (multiple loci) refers to one or more specific locations or sites on a chromosome, such as the locations or sites where genes or genetic markers are found. Therefore, the reduced spiciness locus described herein is the location in the onion genome where a reduced spiciness allele is found.

[0097] As used herein, the term "linkage group" is defined as a group of loci physically linked together on a single DNA molecule (chromosome) and passed on together to offspring more frequently than expected according to the law of independent assortment. In this invention, eight linkage groups were identified. Preferably, each of the eight linkage groups used herein corresponds to one of the eight chromosomes of the onion genome. Preferably, the term "linkage group 3" used herein corresponds to chromosome 3 (of the onion). Preferably, the term "linkage group 4" used herein corresponds to chromosome 1 (of the onion). Preferably, the term "linkage group 6" used herein corresponds to chromosome 7 (of the onion).

[0098] The term "gene" refers to a (genomic) DNA sequence containing a region (transcribed region) transcribed into messenger RNA molecules (mRNA) in a cell and an operablely linked regulatory region (e.g., a promoter). Thus, a gene can contain several operablely linked sequences, such as a promoter, a 5' leader sequence containing, for example, sequences involved in translation initiation, a (protein) coding region (cDNA or genomic DNA), and a 3' untranslated sequence containing, for example, a transcription termination site. Therefore, different alleles of a gene are different alternative forms of the gene, which can be, for example, one or more nucleotides of a genomic DNA sequence (e.g., promoter sequence, exon sequence, intron sequence, etc.), differences in the amino acid sequence of mRNA and / or encoded protein. Genes can be endogenous genes (in the species of origin) or chimeric genes (e.g., transgenic or cis-genes). A "promoter" of a gene sequence is defined as the DNA region that initiates the transcription of a specific gene. Promoters are located near the gene they transcribe, on the same strand, and upstream of the DNA. Promoters can be approximately 100–1000 base pairs long. In one respect, a promoter is defined as a region approximately 1,000 or more (e.g., approximately 1,500 or 2,000 base pairs) upstream of the start codon (ATG) of a protein encoded by a gene.

[0099] "Transgenic" or "chimeric gene" refers to a genetic locus containing a DNA sequence (such as a recombinant gene) that has been introduced into a plant genome through transformation (such as Agrobacterium-mediated transformation). Plants containing transgenes stably integrated into their genome are called "transgenic plants."

[0100] "Gene expression" refers to the process in which a region of DNA operatively linked to an appropriate regulatory region (particularly a promoter) is transcribed into biologically active RNA, meaning it can be translated into a biologically active protein or peptide (or an active peptide fragment) or is itself active (e.g., in post-transcriptional gene silencing or RNAi). The coding sequence can be sense-oriented and encodes the desired biologically active protein or peptide, or an active peptide fragment.

[0101] A quantitative trait locus (QTL) is a chromosomal locus that encodes one or more alleles that affect the phenotypic expression of a continuously distributed (quantitative) phenotype.

[0102] The "physical distance" between loci on the same chromosome (e.g., between molecular markers and / or between phenotypic markers) is the actual physical distance, expressed in bases or base pairs (bp), kilobases or kilobase pairs (kb), or megabases or megabase pairs (Mb).

[0103] Genetic distance, expressed in centimorgans (cM), is measured by crossover frequency or recombination frequency (RF) between loci on the same chromosome (such as between molecular markers and / or phenotypic markers). One cM corresponds to a recombination frequency of 1%. If no recombinants are found, the RF is zero, and the loci are physically very close together or they are identical. The greater the distance between two loci, the higher the RF.

[0104] "Introgression fragment," "introgression section," or "introgression region" refers to a segment (or part or region) of chromosome that has been introduced into another plant of the same or closely related species through hybridization or conventional breeding techniques (such as backcrossing). In other words, introgression fragments are the result of breeding methods (such as backcrossing) expressed by the verb "de-introgression." It should be understood that the term "introgression fragment" never includes an entire chromosome, but only a portion of it. The introgressed gene fragment can be large, for example, even three-quarters or half of a chromosome, but is preferably small, for example, about 15 Mb or less, for example, about 10 Mb or less, about 9 Mb or less, about 8 Mb or less, about 7 Mb or less, about 6 Mb or less, about 5 Mb or less, about 4 Mb or less, about 3 Mb or less, about 2.5 Mb or 2 Mb or less, about 1 Mb (equal to 1,000,000 base pairs) or less, or about 0.5 Mb (equal to 500,000 base pairs) or less, for example, about 200,000 bp (equal to 200 kilobase pairs) or less, about 100,000 bp (100 kb) or less, about 50,000 bp (50 kb) or less, about 25,000 bp (25 kb) or less.

[0105] The term "syngenetic plants" refers to two plants that are genetically identical except for the reduced spiciness allele of this invention. To study the effect of the reduced spiciness trait, a target plant line (or variety) can be crossed with a plant containing the reduced spiciness allele and expressing the desired trait in the offspring. Optionally, self-crossing may be necessary once or multiple times to identify the genetic determinant of the reduced spiciness trait in the plant phenotype. These offspring can then be backcrossed with the target plant line (or variety) (at least twice, for example three or four times, or preferably five or six times), while selecting offspring with the same phenotype as the target plant line (or variety) and expressing the genetic determinant of the reduced spiciness trait. The effect of the reduced spiciness can then be compared between the target plant line (variety) and its syngenetic lines that do not contain the genetic determinant of the reduced spiciness trait.

[0106] The terms “nucleic acid,” “nucleic acid sequence,” “nucleic acid molecule,” or “polynucleotide” are used interchangeably to refer to DNA or RNA molecules in single-stranded or double-stranded form, particularly DNA encoding the protein or protein fragment of this invention. “Isolated nucleic acid” refers to nucleic acid that is no longer in the natural environment from which it was isolated, such as nucleic acid in the genome of a bacterial host cell or plant cell nucleus or plastid.

[0107] The terms “protein,” “peptide sequence,” “amino acid sequence,” or “polypeptide” are used interchangeably to refer to a molecule composed of chains of amino acids, without specifying a particular mode of action, size, three-dimensional structure, or origin. Therefore, a “fragment” or “part” of a protein can still be called a “protein.” “Isolated protein” is used to refer to a protein that is no longer in its native environment, such as in vitro or in recombinant bacterial or plant host cells.

[0108] "Active protein" or "functional protein" is a protein that has measurable protein activity in vitro (e.g., by in vitro activity assay) and / or in vivo (e.g., by the phenotype conferred by the protein). A "wild-type" protein is a fully functional protein found in wild-type plants. A "mutant protein," as used herein, is a protein whose nucleic acid sequence encoding the protein contains one or more mutations, wherein said mutations result in (the mutant nucleic acid molecule encoding) a protein with altered activity, preferably with reduced activity, and most preferably with no activity.

[0109] As described herein, a “functional derivative” of a protein is a fragment, variant, analog, or chemical derivative of that protein that retains at least a portion of its activity or immune cross-reactivity with antibodies that specifically target the mutant protein.

[0110] A fragment of a mutant protein refers to any subset of the molecule.

[0111] Variant peptides can be prepared by direct chemical synthesis, for example, using methods well known in the art.

[0112] Mutant protein analogs are non-natural proteins that are substantially similar to the whole protein or a fragment thereof.

[0113] A "mutation" in a nucleic acid molecule is a change in one or more nucleotides compared to the wild-type sequence, such as by substitution, deletion, or insertion of one or more nucleotides.

[0114] A "mutation" in the amino acid molecule that makes up a protein is a change in one or more amino acids compared to the wild-type sequence, such as by substitution, deletion, or insertion of one or more amino acids. Such a protein is also called a "mutant protein".

[0115] A point mutation is a substitution of a single nucleotide, or the insertion or deletion of a single nucleotide.

[0116] A nonsense mutation is a point mutation in the nucleic acid sequence that encodes a protein, in which a codon in the nucleic acid molecule is changed to a stop codon. This results in a premature stop codon in the mRNA and leads to the translation of a truncated protein. The truncated protein may have reduced or lost function.

[0117] "Missense or nonsynonymous mutations" are point mutations in the nucleic acid sequence that encodes a protein, in which a codon is changed to encode a different amino acid. The resulting protein may have reduced or lost function.

[0118] A "splicing site mutation" is a mutation in the nucleic acid sequence that encodes a protein, in which the RNA splicing of the pre-mRNA is altered, resulting in an mRNA with a different nucleotide sequence and a protein with a different amino acid sequence than the wild type. The resulting protein may have reduced or lost function.

[0119] A frameshift mutation is a mutation in the nucleic acid sequence that encodes a protein. This mutation alters the reading frame of the mRNA, resulting in a different amino acid sequence. The resulting protein may have reduced or lost function.

[0120] In the context of this invention, "deletion" refers to any place in a given nucleic acid sequence where at least one nucleotide is missing compared to the corresponding wild-type sequence, or any place in a given amino acid sequence where at least one amino acid is missing compared to the corresponding (wild-type) sequence.

[0121] "Truncation" should be understood as meaning that, compared to the corresponding wild-type nucleic acid sequence, at least one nucleotide is missing at the 3' or 5' end of the nucleotide sequence, or at least one amino acid is missing at the N-terminus or C-terminus of the protein compared to the corresponding wild-type protein sequence. In 3' or C-terminal truncation, at least the first nucleotide at the 5' end or the first amino acid at the N-terminus remains, and in 5' or N-terminal truncation, at least the last nucleotide at the 3' end or the last amino acid at the C-terminus remains. The 5' end is determined by the ATG codon used as the start codon in the translation of the corresponding wild-type nucleic acid sequence.

[0122] "Replacement" should refer to a difference in at least one nucleotide in a nucleic acid sequence or an amino acid in a protein sequence compared to the corresponding wild-type nucleic acid sequence or the corresponding wild-type amino acid sequence, due to the exchange of nucleotides in the coding sequence of the corresponding protein.

[0123] "Insertion" should refer to the fact that, compared with the corresponding wild-type nucleic acid sequence or the corresponding wild-type amino acid sequence, the nucleic acid sequence or amino acid sequence of the protein contains at least one additional nucleotide or amino acid.

[0124] In the context of this invention, "early stop codon" refers to a stop codon that exists in the coding sequence (cds) and is closer to the start codon at the 5' end than the stop codon of the corresponding wild-type coding sequence.

[0125] A “mutation in a regulatory sequence” (e.g., in a gene’s promoter or enhancer) is a change of one or more nucleotides compared to the wild-type sequence, such as by substitution, deletion, or insertion of one or more nucleotides, resulting in, for example, a reduction or absence of the formation of the gene’s mRNA transcript. Therefore, a “promoter of a gene sequence” is defined as a DNA region that initiates transcription of a specific gene. Promoters are located near the gene they transcribe, on the same strand, and upstream of the DNA. Promoters can be approximately 100-1000 base pairs long. In one aspect, a promoter is defined as a region approximately 2000 base pairs or more upstream of the start codon (i.e., ATG) of the protein encoded by the gene; preferably, the promoter is a region approximately 1500 base pairs upstream of the start codon; more preferably, the promoter is a region approximately 1000 base pairs upstream of the start codon.

[0126] As used herein, the term "operably linked" refers to the linking of polynucleotide elements in a functional relationship. A nucleic acid is "operably linked" when it is in a functional relationship with another nucleic acid sequence. For example, if a promoter, or more precisely, a transcriptional regulatory sequence, influences the transcription of a coding sequence, then it is operably linked to the coding sequence. Operable linking means that the linked nucleic acid sequences are typically contiguous.

[0127] "Sequence identity" and "sequence similarity" can be determined by aligning two peptide or two nucleotide sequences using global or local alignment algorithms. Then, when sequences are optimally aligned using programs such as GAP, BESTFIT, or the Emboss program "Needle" (using default parameters, see below), they can be described as "substantially identical" if they share at least one minimum percentage of sequence identity (as further defined below). These programs use the Needleman and Wunsch global alignment algorithms to align two sequences across their full length, maximizing the number of matches and minimizing the number of gaps. Typically, default parameters are used, where the gap generation penalty = 10 and the gap extension penalty = 0.5 (this applies to both nucleotide and protein alignments). For nucleotides, the default scoring matrix used is DNAFULL, and for proteins, the default scoring matrix is ​​Blosum62 (Henikoff & Henikoff, 1992, PNAS 89, 10915-10919). Sequence alignment and percentage sequence identity scoring can be determined, for example, using a computer program such as EMBOSS (available online at http: / / www.ebi.ac.ukunder / Tools / psa / emboss_needle / ). Alternatively, sequence similarity or identity can be determined by searching databases such as FASTA, BLAST, etc., but hits should be retrieved and paired for comparison of sequence identity. If the percentage sequence identity is at least 95%, 96%, 97%, 98%, 98.3%, 98.7%, 99.0%, or 99.3%, or more preferably 99.7% (determined by using the default parameters (i.e., void generation penalty = 10, void extension penalty = 0.5) with the scoring matrix DNAFULL (for nucleic acids) and the scoring matrix Blosum62 (for proteins) with Emboss "Needle"), then two proteins, two protein domains, or two nucleic acid sequences have "basic sequence identity". Such sequences are also referred to herein as “variants”. For example, in addition to the specific nucleic acid and amino acid sequences disclosed herein, other variants of the alleles that cause the reduced pungent trait of the present invention and proteins that have the same effect on pungent taste as the plants of the present invention can be identified.

[0128] As used herein, the term "hybridization" generally refers to the hybridization of nucleic acids under appropriate stringent conditions (stringent hybridization conditions), which will be apparent to those skilled in the art and depends on the nature of the probe and target sequences. Hybridization and washing conditions are well known in the art and can be readily adjusted according to the required stringency by varying the incubation time, temperature, and / or the ionic strength of the solution. See, for example, Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, 2nd edition, Cold Spring Harbor Press, Cold Spring Harbor, New York, 1989. The choice of conditions depends on the length of the sequences being hybridized, particularly the length of the probe sequence, the relative GC content of the nucleic acid, and the permissible amount of mismatches. Low stringent conditions are preferred when partial hybridization between strands with low complementarity is required. High stringent conditions are preferred when complete or near-complete complementarity is required. For typical high stringent conditions, the hybridization solution contains 6X SSC, 0.01M EDTA, 1X Denhardt's solution, and 0.5% SOS. For cloned DNA fragments, hybridization is performed at approximately 68°C for about 3 to 4 hours, and for total eukaryotic DNA for about 12 to 16 hours. For lower stringency, the hybridization temperature is lowered to the denaturation temperature of the double helix (T0). M The temperature is approximately 42℃ below. Given T... M It is a function of GC content, double strand length, and solution ionic strength.

[0129] As used herein, the phrase “hybridize” with a DNA or RNA molecule means that a molecule hybridizing with, for example, an oligonucleotide, polynucleotide, or any nucleotide sequence (sense or antisense direction) recognizes and hybridizes with a sequence in another nucleic acid molecule that is substantially the same size and has sufficient sequence similarity to achieve hybridization under suitable conditions. For example, a 100-nucleotide-long molecule from the 3' coding or non-coding region of a gene will recognize and hybridize with a portion of about 100 nucleotides of the nucleotide sequence within the 3' coding or non-coding region of that gene or any other plant gene, provided that there is about 70% or more sequence similarity between the two sequences. It should be understood that the size of the corresponding portion will allow for some mismatches in hybridization, such that the corresponding portion can be smaller or larger than the molecule it hybridizes with, for example, by 20-30%, preferably no more than about 12-15%.

[0130] As used herein, the phrases “sequence containing at least 95% sequence identity” or “sequence containing at least 95% amino acid sequence identity” or “sequence containing at least 95% nucleotide sequence identity” mean a sequence having at least 95%, such as at least 96%, 97%, 98%, 98.3%, 98.7%, 99.0%, or 99.3%, or more preferably 99.7%, sequence identity compared to an indicated reference sequence. Sequence identity can be determined according to the methods described herein.

[0131] A “fragment” of a gene or DNA sequence refers to any subset of that molecule, such as a shorter polynucleotide or oligonucleotide. In one aspect, said fragment contains a mutation as defined in this invention.

[0132] A "variant" of a gene or DNA is a molecule that is substantially similar to the whole gene or a segment thereof, such as a nucleotide substitution variant having one or more substituted nucleotides, but retaining its ability to hybridize with a particular gene or encode an mRNA transcript that hybridizes with native DNA. Preferably, the variant contains a reduced pungent flavor allele as defined in this invention.

[0133] As used herein, the term "plant" includes the whole plant or any part or derivative thereof, such as plant organs (e.g., harvested or unharvested flowers, leaves, bulbs, etc.), plant cells, plant protoplasts, plant cell or tissue cultures from which a whole plant can be regenerated, regenerable or non-regenerable plant cells, plant callus, plant cell clumps, and intact plant cells in a plant or plant part, such as embryos, pollen, ovules, ovaries (e.g., harvested tissues or organs), flowers, leaves, seeds, bulbs, asexually reproduced plants, roots, stems, cotyledons, hypocotyls, root tips, etc. It also includes any developmental stage, such as seedlings, immature and mature seedlings, etc. Preferably, the plant part or derivative contains a gene or locus as defined in this invention.

[0134] "Plant line" or "breeding line" refers to a plant and its offspring.

[0135] A "plant variety" or "variety" is a group of plants within the same plant taxonomic group at the lowest known level. These plants (whether or not they meet the criteria recognized by the Plant Breeders' Rights) can be defined based on the expression of characteristics derived from a certain genotype or combination of genotypes, can be distinguished from plants in any other group by the expression of at least one of those characteristics, and can be considered a single entity because it can reproduce without any alteration. Therefore, if a group of plants is characterized entirely by the presence of a single locus or gene (or a series of phenotypic characteristics produced by that single locus or gene), but may be distinctly different from each other in terms of other loci or genes, then even if they are of the same species, the term "plant variety" cannot be used to refer to them. "F1, F2, etc." refers to successive generations of hybridization between two parent plants or parent lines. Plants grown from seeds produced by hybridization of two plants or lines are called the F1 generation. F1 plants self-pollinate to produce the F2 generation, etc. "F1 hybrid" plants (or F1 seeds or hybrids) are generations obtained by hybridization of two inbred parent lines. Therefore, "self-pollination" refers to the self-pollination of plants, that is, the combination of gametes from the same plant.

[0136] "Backcrossing" refers to a breeding method by which a (single) trait (e.g., the ability to induce reduced spiciness) is transferred from one genetic background (also called a "donor," usually but not necessarily an inferior genetic background) to another genetic background (also called a "recurrent parent," usually but not necessarily a superior genetic background). The offspring of the hybridization (e.g., F1 plants, obtained by crossing a first plant of a plant species containing the reduced spiciness allele of the present invention with a second plant of the same plant species or a second plant of a different plant species that can be hybridized with the first plant species, wherein the second plant species does not contain the reduced spiciness allele of the present invention; or F2 or F3 plants obtained through self-pollination of F1, etc.) are "backcrossed" with a parent plant of the second plant species. After repeated backcrossing, the trait of the donor genetic background (e.g., the reduced spiciness allele conferring the reduced spiciness trait of the present invention) is integrated into the recurrent genetic background. In this paper, the terms "transformed gene," "transformed plant," or "single-locus transformation" refer to plants developed through backcrossing, in which substantially all the desired morphological and / or physiological characteristics of the recurrent parent are recovered, in addition to one or more genes transferred from the donor parent. Plants grown from seeds produced by backcrossing F1 plants with a second parental plant line are referred to as the "BC1 generation." Plants from the BC1 population can self-pollinate to produce the BC1F2 generation, or be backcrossed again with cultivated parental plant lines to provide the BC2 generation. The "M1 population" refers to multiple mutagenized seeds / plants of a particular plant line. "M2, M3, M4, etc." refer to successive generations obtained after self-pollination of the first mutagenized seed / plant (M1).

[0137] The term "cultivated plant" or "cultivar" refers to a plant of a given species, such as a variety, breeding line, or cultivar of that species, which is cultivated by humans and possesses favorable agronomic traits. So-called heirloom varieties or cultivars, that is, open-pollinating varieties or cultivars that were widely cultivated in earlier periods of human history and often modified to adapt to specific geographical regions, are included herein as cultivated plants in one aspect of this invention. The term "cultivated plant" does not include wild plants. "Wild plants" include, for example, wild accession.

[0138] The term "food" is any substance that is consumed to provide nutrition to the body. It is typically of plant or animal origin and contains essential nutrients such as carbohydrates, fats, proteins, vitamins, or minerals. This substance is ingested by an organism and absorbed by its cells to produce energy, sustain life, or stimulate growth. The term food includes substances consumed to provide nutritional support to humans and animals.

[0139] Throughout this article, "average" and "mean" are used interchangeably, both referring to the arithmetic mean.

[0140] It should be understood that comparisons between different plant lines involve growing many plants of a lineage (or variety) under the same conditions as one or more control plant lines (preferably wild-type plants) (e.g., at least 5 plants of each line, preferably at least 10 plants), and determining the differences between plant lines when grown under the same environmental conditions, preferably statistically significant differences. Preferably, the plants are of the same lineage or variety.

[0141] In this document and its claims, the verb "comprising" and its variations are used in their non-limiting sense to indicate items included following the word, but not excluding items not specifically mentioned. Furthermore, referring to an element by the indefinite article "a" or "an" does not preclude the possibility of more than one of the stated elements, unless the context explicitly requires the presence of one and only one stated element. Therefore, the indefinite article "a" or "an" generally means "at least one". It should also be understood that when "sequence" is referred to herein, it generally refers to an actual physical molecule having a sequence of subunits (e.g., amino acids or nucleic acids).

[0142] Markers and their uses

[0143] This invention provides markers for identifying onion plants that produce bulbs with reduced pyruvate levels, comprising markers selected from: markers linked to a QTL conferring reduced pyruvate between markers isotig30225_1454 and isotig32865_1404 on chromosome 2; markers linked to a QTL conferring reduced pyruvate between markers isotig32772_1413 and isotig33099_885 on chromosome 1; and markers linked to a QTL conferring reduced pyruvate between markers isotig28625_2789 and isotig41937_218 on chromosome 7. The markers of this invention are particularly suitable for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts as described in WO 2009 / 092560 A1. Therefore, in one embodiment, the present invention provides markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, wherein one or more QTLs conferring reduced pyruvate levels are present in plants whose seeds are deposited with accession number PTA-9053, plants whose seeds are deposited with accession number PTA-9054, or plants whose seeds are deposited with accession number PTA-9055. Therefore, in one embodiment, the present invention provides markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts obtained by crossing plants whose seeds are deposited with accession number PTA-9053, plants whose seeds are deposited with accession number PTA-9054, or plants whose seeds are deposited with accession number PTA-9055 with another onion plant, wherein the marker is selected from: the marker isotig30225_1 located on chromosome 2. The markers linked to the QTLs conferring reduced pyruvate between 454 and isotig32865_1404; the markers linked to the QTLs conferring reduced pyruvate between isotig32772_1413 and isotig33099_885 on chromosome 1; and the markers linked to the QTLs conferring reduced pyruvate between isotig28625_2789 and isotig41937_218 on chromosome 7.

[0144] The publicly available genetic markers isotig30225_1454 and isotig32865_1404, located on chromosome 2 at map B9885 x B8667, are well known in the art and described in more detail in Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72. The publicly available genetic markers isotig32772_1413 and isotig33099_885, located on chromosome 1 at map Char x B5351, are well known in the art and described in more detail in Havey (2000) J. Amer. Soc. Hort. Sci., 145(2), 110-119. The publicly available genetic markers isotig28625_2789 and isotig41937_218, located on chromosome 7 at map B9885 x B8667, are well known in the art and described in more detail in Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72. All publicly available genetic markers cited herein are further detailed in Duangjit et al. (2013) Theor Appl Genet 126, 2093–2101. The nucleotide sequences of these publicly available genetic markers are further described in Table 5.

[0145] Preferably, the present invention provides a marker for identifying onion plants that produce bulbs with reduced pyruvate levels, said marker comprising one or more SNPs selected from the following: SNP_01, which contains thymine at nucleotide 51 of SEQ ID NO:1 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, which contains adenine at nucleotide 51 of SEQ ID NO:3 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_03, which contains adenine at nucleotide 51 of SEQ ID NO:5 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; NO:5 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains cytosine at the 51st nucleotide of SEQ ID NO:11 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:11 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 contains thymine at the 51st nucleotide of SEQ ID NO:15 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15.SNP_09, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; SNP_10, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19; SNP_11, which contains adenine at nucleotide 51 of SEQ ID NO:21 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_23 contains cytosine at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 contains adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_15 contains adenine at nucleotide 51 of SEQ ID NO:29 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; NO:29 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33.SNP_18, comprising thymine at nucleotide 51 of SEQ ID NO:35 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, comprising thymine at nucleotide 51 of SEQ ID NO:37 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1; SNP_22 contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; SNP_23 contains thymine at the 51st nucleotide of SEQ ID NO:45 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_24 contains thymine at the 51st nucleotide of SEQ ID NO:47 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; NO:47 contains cytosine at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_25 contains guanine at nucleotide 51 of SEQ ID NO:49 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49.

[0146] A “marker” or “genetic marker” is a DNA segment located at a known position on a chromosome that is polymorphic among individuals (e.g., individual plants forming part of a plant population) and can be used to distinguish and / or identify an individual from other individuals. In one embodiment, the QTL conferring reduced pyruvate is located between SNP_11 and SNP_04, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7. Those skilled in the art can readily identify one or more suitable genetic markers using conventional methods that are linked to a QTL conferring reduced pyruvate at a locus defined herein on chromosome 2 (i.e., between marker isotig30225_1454 and marker isotig32865_1404 and / or between marker SNP_11 and SNP_4, which are further defined herein). In one embodiment, the QTL conferring reduced pyruvate is located between SNP_16 and SNP_20, wherein SNP_16 is located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, and SNP_20 is located at the 51st nucleotide of SEQ ID NO:39 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39. Those skilled in the art can readily identify one or more suitable genetic markers using conventional methods that are linked to a QTL conferring reduced pyruvate at a locus defined herein on chromosome 1 (i.e., between marker isotig32772_1413 and marker isotig33099_885 and / or between SNP_16 and SNP_20 as further defined herein).In one embodiment, the QTL conferring reduced pyruvate is located between SNP_22 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19. Those skilled in the art can readily identify one or more suitable genetic markers linked to a QTL conferring reduced pyruvate at a locus defined herein on chromosome 7 (i.e., between marker isotig28625_2789 and marker isotig41937_218 and / or between SNP_22, further defined herein, and the distal end of chromosome 7 containing SNP_10). As used herein, when referring to the term "linked marker," it specifically means "the marker is genetically linked."

[0147] Therefore, the present invention provides markers for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, wherein the markers are selected from: markers linked to a QTL conferring reduced pyruvate between SNP_11 and SNP_04 located on chromosome 2, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; and markers linked to a QTL conferring reduced pyruvate between SNP_16 and SNP_20 located on chromosome 1, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:21. SNP_20 is located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, or at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; and a marker conferring reduced pyruvate QTL linkage between SNP_22 located on chromosome 7 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at the 51st nucleotide of SEQ ID NO:43 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, or at the 51st nucleotide of SEQ ID NO:43, or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of SEQ ID NO:31. The 51st nucleotide of NO:19 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0148] Despite residual heterozygosity in the initially available low-spiciness onion lines, the inventors successfully identified three significant QTLs that confer reduced pyruvate levels in the bulbs produced by the onion plants. Various technical difficulties had to be overcome before the QTLs according to the invention could be identified. The construction of multiple mapping populations required careful planning, and the parent plants of the populations had grown for nearly six years before materials for QTL analysis were available. Several hybridizations were performed because the mechanism of low pyruvate in the low-pyruvate donor was unknown. The results showed that the low-pyruvate trait is a complex trait controlled by at least three genetic loci, necessitating the construction and analysis of multiple mapping populations to identify the three QTLs of the invention, as no redundant QTLs were detected in two populations. QTL validation also required an unconventional approach, also due to the long generation time of onions. In addition to the challenges associated with actual mapping and validation, extensive work was required prior to these efforts to develop genome-wide molecular markers for genetic mapping and to develop low-pyruvate donor lines through phenotypic selection, requiring decades of targeted breeding. A QTL conferring reduced pyruvate was identified between SNP_11 and SNP_04 on linkage group 3, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7. Another QTL conferring reduced pyruvate was identified between SNP_16 and SNP_20 on linkage group 4, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, and SNP_20 is located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39.Another QTL conferring reduced pyruvate was identified between SNP_22 on linkage group 6 and the distal end of linkage group 6 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0149] Linkage group 3 was found to correspond to chromosome 2 of onions, linkage group 4 to chromosome 1, and linkage group 6 to chromosome 7. Therefore, the term "linkage group 3" used in this paper corresponds to the term "chromosome 2." Similarly, the term "linkage group 4" corresponds to the term "chromosome 1." Finally, the term "linkage group 6" corresponds to the term "chromosome 7." Therefore, the present invention provides markers for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, wherein the markers are selected from: markers linked to a QTL conferring reduced pyruvate between SNP_11 and SNP_04 located on chromosome 2, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, wherein SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; and markers linked to a QTL conferring reduced pyruvate between SNP_16 and SNP_20 located on chromosome 1, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:21. SNP_20 is located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; and a marker conferring reduced pyruvate QTL linkage between SNP_22 located on chromosome 7 and the distal end of a chromosome containing SNP_10, wherein SNP_22 is located at the 51st nucleotide of SEQ ID NO:43 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at the 51st nucleotide of SEQ ID NO:39. The 51st nucleotide of SEQ ID NO:19 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0150] Preferably, the present invention provides a marker for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in an onion plant or plant part, wherein the marker is selected from: a marker linked to a QTL conferring reduced pyruvate between SNP_01 and SNP_04 located on chromosome 2, wherein SNP_01 is located at nucleotide 51 of SEQ ID NO:1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1, wherein SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (at least 98%, or at least 99%) identity with SEQ ID NO:7; and a marker linked to a QTL conferring reduced pyruvate between SNP_16 and SNP_20 located on chromosome 1, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of SEQ ID NO:30. SNP_20 is located at nucleotide 51 of a sequence having at least 95% (at least 98% or at least 99%) identity with SEQ ID NO:31, or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; and a marker conferring QTL linkage of reduced pyruvate between SNP_22 located on chromosome 7 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of SEQ ID NO:39. NO:19 has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity at nucleotide 51. Therefore, the present invention provides a marker for determining the presence or absence of one or more said QTLs conferring reduced pyruvate levels in onion plants or plant parts. Such a marker, also referred to herein as a "molecular marker," can be any measurable indicator linked to the genetics of the desired trait, and thus, in the context of the present invention, is the reduced pungent allele.In the context of this invention, DNA-based markers are particularly preferred, including but not limited to: restriction fragment length polymorphism (RFLP) markers, enzyme-amplified polymorphic sequence (CPAS) markers, microsatellite markers (also known as short tandem repeats (STRs) or simple sequence repeats (SSRs), restriction fragment length polymorphism (RFLP) markers, random amplified polymorphic DNA (RAPD) markers, amplified fragment length polymorphism (AFLP) markers, and single nucleotide polymorphism (SNP) markers. Preferably, the markers according to the invention are SNP markers.

[0151] In the context of this invention, distinct specific SNP markers linked to QTLs that confer reduced pyruvate on chromosome 2 were also identified. The specific SNP markers linked to the QTL conferring reduced pyruvate on chromosome 2 are selected from: SNP_11, located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (at least 98% or at least 99%) identity with SEQ ID NO:21; SNP_12, located at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13, located at nucleotide 51 of SEQ ID NO:25 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14, located at nucleotide 51 of SEQ ID NO:27 or at nucleotide 51 of SEQ ID NO:25. NO:27 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_01 is located at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02 is located at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_3 is located at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; SNP_04 is located at the 51st nucleotide of SEQ ID NO:5. The 51st nucleotide of NO:7 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7;And SNP_15, which is located at the 51st nucleotide of SEQ ID NO:29 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity with SEQ ID NO:29. Therefore, a specific example of an SNP marker suitable for determining the presence or absence of a QTL conferring reduced pyruvate between SNP_11 and SNP_04 located on chromosome 2 (where SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21) is the following SNP marker: SNP_11, which is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21. NO:21 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_12 is located at the 51st nucleotide of SEQ ID NO:23 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 is located at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 is located at the 51st nucleotide of SEQ ID NO:27 or at the 51st nucleotide of SEQ ID NO:25. NO:27 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_01 is located at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02 is located at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3;SNP_3, located at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; SNP_04, located at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; and SNP_15, located at the 51st nucleotide of SEQ ID NO:29 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:29. Preferably, the specific SNP marker linked to the QTL conferring reduced pyruvate on chromosome 2 is selected from: SNP_11, located at the 51st nucleotide of SEQ ID NO:21 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, located at the 51st nucleotide of SEQ ID NO:23 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13, located at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14, located at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of SEQ ID NO:25; SNP_14, located at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of SEQ ID NO:25; SNP_15 ...; SNP_16, located at the 51st nucleotide of SEQ ID NO:25; SNP_17, located at the 51st nucleotide of SEQ ID NO:25; SNP_18, located at the 51st nucleotide of SEQ ID NO:25; SNP_19, located at the 51st nucleotide of SEQ ID NO The 51st nucleotide of SEQ ID NO:27 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_01, located at the 51st nucleotide of SEQ ID NO:1 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, located at the 51st nucleotide of SEQ ID NO:3 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3;SNP_3, located at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; and SNP_04, located at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7. Therefore, a specific example of an SNP marker suitable for determining the presence or absence of a QTL conferring reduced pyruvate between marker isotig30225_1454 and marker isotig32865_1404 located on chromosome 2 (preferably between SNP_11 and SNP_04, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7) is: SNP_11, which is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7. NO:21 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_12 is located at the 51st nucleotide of SEQ ID NO:23 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 is located at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 is located at the 51st nucleotide of SEQ ID NO:27 or at the 51st nucleotide of SEQ ID NO:25. NO:27 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_01 is located at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1;SNP_02, located at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_3, located at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; and SNP_04, located at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7. Therefore, SNP markers linked to QTLs conferring reduced pyruvate levels located on chromosome 2 can be used to determine the presence of QTLs conferring reduced pyruvate levels, wherein: SNP_11 contains adenine at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12 contains cytosine at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains cytosine at nucleotide 51 of SEQ ID NO:25 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; NO:25 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_14 contains adenine at the 51st nucleotide of SEQ ID NO:27 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_01 contains thymine at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02 contains thymine at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; NO:3 contains adenine at nucleotide position 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity;SNP_03 contains cytosine at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; and SNP_15 contains guanine at the 51st nucleotide of SEQ ID NO:29 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:29. Preferably, SNP markers linked to the QTL conferring reduced pyruvate levels located on chromosome 2 can be used to determine the presence of the QTL conferring reduced pyruvate levels, wherein: SNP_11 contains adenine at the 51st nucleotide of SEQ ID NO:21 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12 contains cytosine at the 51st nucleotide of SEQ ID NO:23 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains cytosine at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of SEQ ID NO:23. NO:25 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_14 contains adenine at the 51st nucleotide of SEQ ID NO:27 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_01 contains thymine at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02 contains thymine at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; NO:3 contains adenine at nucleotide position 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity;SNP_03 contains cytosine at nucleotide 51 of SEQ ID NO:5 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; and SNP_04 contains thymine at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7.

[0152] In the context of this invention, distinct specific SNP markers linked to QTLs that confer reduced pyruvate located on chromosome 1 were also identified. This SNP marker linked to the QTL conferring reduced pyruvate on chromosome 1 is selected from: SNP_16, located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17, located at nucleotide 51 of SEQ ID NO:33 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_05, located at nucleotide 51 of SEQ ID NO:9 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06, located at nucleotide 51 of SEQ ID NO:11 or at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of SEQ ID NO:33. NO:11 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_7 is located at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 is located at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15; SNP_18 is located at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of SEQ ID NO:15. NO:35 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_19 is located at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20 is located at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39;And SNP_21, which is located at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity with SEQ ID NO:51. Therefore, a specific example of an SNP marker suitable for determining the presence or absence of a QTL conferring reduced pyruvate between marker isotig32772_1413 and marker isotig33099_885 located on chromosome 1 (preferably between SNP_16 and SNP_20, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, and SNP_20 is located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39) is: SNP_16, which is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39. NO:31 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_17 is located at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_05 is located at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 is located at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:11; SNP_7 is located at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:11; The 51st nucleotide of SEQ ID NO:13 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08, which is located at the 51st nucleotide of SEQ ID NO:15 or the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15;SNP_18, located at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, located at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, located at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; and SNP_21, located at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of SEQ ID NO:35. NO:41 is the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity. Preferably, the SNP marker linked to the QTL conferring reduced pyruvate on chromosome 1 is selected from: SNP_16, located at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17, located at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_05, located at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06, located at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of SEQ ID NO:33. NO:11 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_7 is located at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13;SNP_08, located at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15; SNP_18, located at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, located at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, located at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of SEQ ID NO:15. NO:39 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_21 is located at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41. Therefore, a specific example of an SNP marker suitable for determining the presence or absence of a QTL conferring reduced pyruvate between SNP_16 and SNP_20 located on chromosome 1 (where SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, and SNP_20 is located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39) is as follows: SNP_16, which is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39. NO:31 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_17 is located at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33;SNP_05, located at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06, located at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:11; SNP_7, located at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08, located at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of SEQ ID NO:9. NO:15 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_18 is located at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_19 is located at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_20 is located at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity. Therefore, SNP markers linked to QTLs conferring reduced pyruvate levels located on chromosome 1 can be used to determine the presence of QTLs conferring reduced pyruvate levels, wherein: SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33;SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains adenine at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:11; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 contains cytosine at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:15 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_18 contains thymine at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19 contains thymine at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20 contains thymine at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; NO:39 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_21 contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41. Preferably, therefore, SNP markers linked to QTLs conferring reduced pyruvate levels located on chromosome 1 can be used to determine the presence of QTLs conferring reduced pyruvate levels, wherein: SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31;SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_06 contains adenine at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:11; SNP_07 contains adenine at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; NO:13 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_08 contains thymine at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15; SNP_18 contains thymine at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19 contains thymine at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35. NO:37 contains thymine at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_20 contains guanine at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39.

[0153] In the context of this invention, distinct specific SNP markers linked to QTLs conferring reduced pyruvate located on chromosome 7 were also identified. This SNP marker linked to the QTL conferring reduced pyruvate on chromosome 7 is selected from: SNP_22, located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_23, located at nucleotide 51 of SEQ ID NO:45 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; SNP_24, located at nucleotide 51 of SEQ ID NO:47 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:47; SNP_25, located at nucleotide 51 of SEQ ID NO:49 or at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of SEQ ID NO:45. NO:49 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_09 is located at the 51st nucleotide of SEQ ID NO:17 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; and SNP_10 is located at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.Therefore, a specific example of an SNP marker suitable for determining the presence or absence of a QTL conferring reduced pyruvate between marker isotig28625_2789 and marker isotig41937_218 located on chromosome 7 (preferably between SNP_22 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19) is: SNP_22, which is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of SEQ ID NO:19. NO:43 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_23 is located at the 51st nucleotide of SEQ ID NO:45 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_24 is located at the 51st nucleotide of SEQ ID NO:47 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_25 is located at the 51st nucleotide of SEQ ID NO:49 or at the 51st nucleotide of SEQ ID NO:45. NO:49 is located at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_09 is located at the 51st nucleotide of SEQ ID NO:17 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; and SNP_10 is located at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.Therefore, SNP markers linked to QTLs conferring reduced pyruvate levels located on chromosome 7 can be used to determine the presence of QTLs conferring reduced pyruvate levels, wherein: SNP_22 contains thymine at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_23 contains thymine at nucleotide 51 of SEQ ID NO:45 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; SNP_24 contains thymine at nucleotide 51 of SEQ ID NO:47 or at nucleotide 51 of SEQ ID NO:45. NO:47 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_25 contains guanine at the 51st nucleotide of SEQ ID NO:49 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49; SNP_09 contains thymine at the 51st nucleotide of SEQ ID NO:17 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; and SNP_10 contains thymine at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; The 51st nucleotide of the sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity contains guanine.

[0154] The markers according to the invention are preferably selected from: the sequence between marker isotig30225_1454 and marker isotig32865_1404 located on chromosome 2 (preferably between SNP_11 and SNP_04, wherein SNP_11 is located at the 51st nucleotide of SEQ ID NO:21 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of SEQ ID NO:21 or at the 51st nucleotide of SEQ ID NO:21). A QTL-linked marker conferring reduced pyruvate (NO:7) at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; and a marker linked to a QTL conferring reduced pyruvate between marker isotig32772_1413 and marker isotig33099_885 on chromosome 1 (preferably between SNP_16 and SNP_20, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, wherein SNP_20 is located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of SEQ ID NO:32772_1413; A QTL-linked marker conferring reduced pyruvate (at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; and a marker associated with the marker isotig28625_2789 and marker isotig41937_218 located on chromosome 7 (preferably between SNP_22 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, wherein SNP_10 is located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of SEQ ID NO:43). A marker linked to a QTL conferring reduced pyruvate at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with NO:19, is therefore particularly suitable for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts.

[0155] Therefore, the present invention provides a marker for identifying onion plants that produce bulbs with reduced pyruvate levels, the marker comprising one or more SNPs selected from the following: SNP_01, which contains thymine at the 51st nucleotide of SEQ ID NO:1 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, which contains adenine at the 51st nucleotide of SEQ ID NO:3 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_03, which contains adenine at the 51st nucleotide of SEQ ID NO:5 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; NO:5 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains cytosine at the 51st nucleotide of SEQ ID NO:11 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:11 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 contains thymine at the 51st nucleotide of SEQ ID NO:15 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15.SNP_09, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; SNP_10, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19; SNP_11, which contains adenine at nucleotide 51 of SEQ ID NO:21 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_23 contains cytosine at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 contains adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_15 contains adenine at nucleotide 51 of SEQ ID NO:29 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; NO:29 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33.SNP_18, comprising thymine at nucleotide 51 of SEQ ID NO:35 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, comprising thymine at nucleotide 51 of SEQ ID NO:37 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1; SNP_22 contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; SNP_23 contains thymine at the 51st nucleotide of SEQ ID NO:45 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_24 contains thymine at the 51st nucleotide of SEQ ID NO:47 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; NO:47 contains cytosine at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_25 contains guanine at nucleotide 51 of SEQ ID NO:49 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49.

[0156] Methods for identifying and / or selecting plants or plant parts

[0157] This invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers described herein in the plant or plant part. Therefore, this invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers in the plant or plant part, said markers being adapted to determine the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, wherein said markers are selected from: markers linked to a QTL conferring reduced pyruvate between marker isotig30225_1454 and marker isotig32865_1404 located on chromosome 2; markers linked to a QTL conferring reduced pyruvate between marker isotig32772_1413 and marker isotig33099_885 located on chromosome 1; and markers linked to a QTL conferring reduced pyruvate between marker isotig28625_2789 and marker isotig41937_218 located on chromosome 7.

[0158] The method of the present invention for identifying and / or selecting onion plants or plant parts is particularly suitable for determining the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts as described in WO2009 / 092560 A1. Therefore, in one embodiment, the present invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers in the plant or plant part, said markers being suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, wherein the one or more QTLs conferring reduced pyruvate levels are present in plants whose seeds are deposited with Registry No. PTA-9053, plants whose seeds are deposited with Registry No. PTA9054, or plants whose seeds are deposited with Registry No. PTA-9055. Therefore, in one embodiment, the present invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers in the plant or plant part, the markers being adapted to determine the presence of one or more QTLs conferring a reduced pyruvate level in the onion plant or plant part, the onion plant or plant part being obtained by hybridization of a plant whose seeds are deposited with accession number PTA-9053, a plant whose seeds are deposited with accession number PTA-9054, or a plant whose seeds are deposited with accession number PTA-9055, with another onion plant, wherein the markers are selected from... The markers linked to the QTLs conferring reduced pyruvate between isotig30225_1454 and isotig32865_1404 on chromosome 2; the QTLs conferring reduced pyruvate between isotig32772_1413 and isotig33099_885 on chromosome 1; and the QTLs conferring reduced pyruvate between isotig28625_2789 and isotig41937_218 on chromosome 7.

[0159] Preferably, the present invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers in the plant or plant part, the markers being adapted to determine the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, wherein the markers are selected from: markers linked to a QTL conferring reduced pyruvate between SNP_11 and SNP_04 located on chromosome 2, wherein SNP_11 is located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21, and SNP_04 is located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of SEQ ID NO:21. NO:7 is located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; a marker linked to a QTL conferring reduced pyruvate between SNP_16 and SNP_20 located on chromosome 1, wherein SNP_16 is located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31, and SNP_20 is located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of SEQ ID NO:39. NO:39 at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and a marker conferring reduced pyruvate QTL linkage between SNP_22 located on chromosome 7 and the distal end of chromosome 7 containing SNP_10, wherein SNP_22 is located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43, and SNP_10 is located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0160] Preferably, the method includes screening at the DNA, RNA (or cDNA), or protein level using known methods to detect the presence or absence of one or more QTLs conferring reduced pyruvate levels in onion plants or plants as described herein. Numerous methods exist for detecting the presence or absence of the reduced pungent flavor alleles of the present invention.

[0161] For example, single nucleotide polymorphisms (SNPs) may exist between wild-type alleles and reduced pungent alleles. SNP genotyping can be used to detect whether a plant, plant part, or cell contains one or more of the wild-type (high pungent) nucleotides or reduced pungent nucleotides in its genome. For example, one or more SNPs can be easily detected using the KASP assay, which selects 50 base pairs upstream and downstream of the SNP and can design two allele-specific forward primers and one allele-specific reverse primer; see, for example, the KASP assay in Allen et al. (2011) Plant Biotechnology J 9, 1086-1099, especially pp. 1097-1098.

[0162] Similarly, other genotyping assays can be used. For example, TaqMan SNP genotyping assays, high-resolution melting curve (HRM) assays, SNP genotyping arrays (such as Fluidigm, Illumina, etc.), or DNA sequencing can also be used.

[0163] Molecular markers can also be used to help identify plants (or plant parts or nucleic acids derived therefrom) containing a reduced pungent flavor allele. For example, one or more suitable molecular markers can be developed that are genetically (and preferably also physically) closely linked to the reduced pungent flavor allele. Most preferably, causal gene mutations are used as molecular markers for identifying plants (or plant parts or nucleic acids derived therefrom) containing the reduced pungent flavor allele. Suitable molecular markers can be developed by crossing onion plants with the reduced pungent flavor trait with wild-type plants and generating segregating populations (e.g., F2 or backcross populations) from the cross. Phenotyping of the segregating populations can then be performed based on the reduced spiciness phenotype, and genotyping can be performed using, for example, molecular markers (e.g., SNPs (single nucleotide polymorphisms), AFLPs (amplified fragment length polymorphisms; see, for example, EP 534 858) or others). Software analysis can identify molecular markers co-segregating with the reduced spiciness trait in the segregating populations, and can determine their sequence and genetic distance (centimolecular distance, cM) with the QTLs conferring reduced pyruvate on chromosome 2, chromosome 1, and chromosome 7, as further described herein. Molecular markers closely linked to one of the QTLs conferring reduced pyruvate, such as those at a distance of 5 cM or less, can then be used to detect and / or select plants or plant parts containing or retaining the reduced spiciness allele (e.g., in introgression fragments). In breeding procedures, specifically in marker-assisted selection (MAS), such closely linked molecular markers can replace phenotypic selection (or be used in addition to phenotypic selection). Preferably, linked markers are used in MAS. More preferably, flanking markers are used in MAS, i.e., one marker on either side of one or more QTLs described herein that confer a reduced level of pyruvate in the onion plant or plant part.

[0164] As described in this paper, distinct specific SNP markers linked to different QTLs conferring reduced pyruvate were identified, including one QTL conferring reduced pyruvate on chromosome 2, one QTL conferring reduced pyruvate on chromosome 1, and one QTL conferring reduced pyruvate on chromosome 7. Therefore, the method of the present invention for identifying and / or selecting onion plants or plant parts may include determining the presence or absence of one or more (e.g., at least two, three, four, or four) markers in the plant or plant part, said markers being selected from: SNP_01, which contains thymine at the 51st nucleotide of SEQ ID NO:1 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, which contains adenine at the 51st nucleotide of SEQ ID NO:3 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_03, which contains adenine at the 51st nucleotide of SEQ ID NO:5 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; NO:5 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains cytosine at the 51st nucleotide of SEQ ID NO:11 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:11 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13;SNP_08, which contains thymine at nucleotide 51 of SEQ ID NO:15 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15; SNP_09, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; SNP_10, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19; SNP_11, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 2; SNP_21 contains adenine at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12 contains cytosine at nucleotide 51 of SEQ ID NO:23 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13 contains thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; SNP_14 contains thymine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:25; NO:27 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_15 contains guanine at the 51st nucleotide of SEQ ID NO:29 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:29; SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31.SNP_17, comprising adenine at the 51st nucleotide of SEQ ID NO:33 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_18, comprising thymine at the 51st nucleotide of SEQ ID NO:35 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, comprising thymine at the 51st nucleotide of SEQ ID NO:37 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, comprising adenine at the 51st nucleotide of SEQ ID NO:37 on chromosome 1; SNP_21 contains guanine at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21 contains cytosine at nucleotide 51 of SEQ ID NO:41 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; SNP_22 contains thymine at nucleotide 51 of SEQ ID NO:43 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_23 contains thymine at nucleotide 51 of SEQ ID NO:45 on chromosome 7 or at nucleotide 51 of SEQ ID NO:43. NO:45 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_24 contains cytosine at the 51st nucleotide of SEQ ID NO:47 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:47; SNP_25 contains guanine at the 51st nucleotide of SEQ ID NO:49 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49.isotig30225_1454 contains cytosine at nucleotide 61 of SEQ ID NO:51 on chromosome 2 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:51; isotig32865_1404 contains guanine at nucleotide 61 of SEQ ID NO:53 on chromosome 2 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:53; isotig32772_1413 contains guanine at nucleotide 61 of SEQ ID NO:55 on chromosome 1 or at nucleotide 61 of SEQ ID NO:51. NO:55 contains guanine at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; isotig33099_885 contains thymine at nucleotide 61 of SEQ ID NO:57 on chromosome 1 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:57; isotig28625_2789 contains guanine at nucleotide 61 of SEQ ID NO:59 on chromosome 7 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:59; and isotig41937_218 contains guanine at nucleotide 61 of SEQ ID NO:61 on chromosome 7 or at nucleotide 61 of SEQ ID NO:59. NO:61 The 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity contains guanine.

[0165] The method of the present invention for identifying and / or selecting onion plants or plant parts preferably includes determining the presence or absence of one or more (e.g., at least two, three, four, or four) markers in the plant or plant part, said markers being selected from: SNP_01, which contains thymine at the 51st nucleotide of SEQ ID NO:1 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:1; SNP_02, which contains adenine at the 51st nucleotide of SEQ ID NO:3 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; SNP_03, which contains adenine at the 51st nucleotide of SEQ ID NO:5 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:3; NO:5 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 on chromosome 2 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_05 contains cytosine at the 51st nucleotide of SEQ ID NO:9 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; SNP_06 contains cytosine at the 51st nucleotide of SEQ ID NO:11 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:9; NO:11 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13; SNP_08 contains thymine at the 51st nucleotide of SEQ ID NO:15 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:15.SNP_09, which contains thymine at nucleotide 51 of SEQ ID NO:17 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:17; SNP_10, which contains guanine at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19; SNP_11, which contains adenine at nucleotide 51 of SEQ ID NO:21 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, which contains guanine at nucleotide 51 of SEQ ID NO:21 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_13 contains cytosine at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_14 contains adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_15 contains adenine at nucleotide 51 of SEQ ID NO:29 on chromosome 2 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; NO:29 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_16 contains adenine at the 51st nucleotide of SEQ ID NO:31 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17 contains adenine at the 51st nucleotide of SEQ ID NO:33 on chromosome 1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33;SNP_18, comprising thymine at nucleotide 51 of SEQ ID NO:35 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19, comprising thymine at nucleotide 51 of SEQ ID NO:37 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37; SNP_20, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21, comprising guanine at nucleotide 51 of SEQ ID NO:39 on chromosome 1; SNP_22 contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; SNP_23 contains thymine at the 51st nucleotide of SEQ ID NO:45 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_24 contains thymine at the 51st nucleotide of SEQ ID NO:47 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; NO:47 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_25 contains guanine at the 51st nucleotide of SEQ ID NO:49 on chromosome 7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:49;isotig30225_1454 contains cytosine at nucleotide 61 of SEQ ID NO:51 on chromosome 2 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:51; isotig32865_1404 contains guanine at nucleotide 61 of SEQ ID NO:53 on chromosome 2 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:53; isotig32772_1413 contains guanine at nucleotide 61 of SEQ ID NO:55 on chromosome 1 or at nucleotide 61 of SEQ ID NO:51. NO:55 contains guanine at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; isotig33099_885 contains thymine at nucleotide 61 of SEQ ID NO:57 on chromosome 1 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:57; isotig28625_2789 contains guanine at nucleotide 61 of SEQ ID NO:59 on chromosome 7 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:59; and isotig41937_218 contains guanine at nucleotide 61 of SEQ ID NO:61 on chromosome 7 or at nucleotide 61 of SEQ ID NO:59. NO:61 The 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity contains guanine.

[0166] Preferably, the markers used in the method according to the invention are fragment length polymorphism (RFLP) markers, enzyme digestion amplification polymorphism (CPAS) markers, microsatellite markers, restriction fragment length polymorphism (RFLP) markers, random amplification polymorphic DNA (RAPD) markers, amplified fragment length polymorphism (AFLP) markers, or single nucleotide polymorphism (SNP) markers, with SNP markers being preferred.

[0167] Preferably, the marker used in the method according to the invention that is linked to the QTL conferring reduced pyruvate on chromosome 2 is a SNP marker selected from the following: SNP_11, which contains adenine at the 51st nucleotide of SEQ ID NO:21 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:21; SNP_12, which contains cytosine at the 51st nucleotide of SEQ ID NO:23 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:23; SNP_13, which contains cytosine at the 51st nucleotide of SEQ ID NO:25 or at the 51st nucleotide of SEQ ID NO:23. NO:25 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_14 contains adenine at the 51st nucleotide of SEQ ID NO:27 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27; SNP_01 contains thymine at the 51st nucleotide of SEQ ID NO:1 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:01; SNP_02 contains thymine at the 51st nucleotide of SEQ ID NO:3 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:27. NO:3 contains adenine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_03 contains cytosine at the 51st nucleotide of SEQ ID NO:5 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; SNP_04 contains thymine at the 51st nucleotide of SEQ ID NO:7 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; SNP_15 contains thymine at the 51st nucleotide of SEQ ID NO:29 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:7; NO:29 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity;isotig30225_1454, which contains cytosine at the 61st nucleotide of SEQ ID NO:51 or at the 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:51; and isotig32865_1404, which contains guanine at the 61st nucleotide of SEQ ID NO:53 or at the 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:53.

[0168] Preferably, the marker used in the method according to the invention that is linked to the QTL conferring reduced pyruvate on chromosome 1 is a SNP marker selected from the following: SNP_16, which contains adenine at the 51st nucleotide of SEQ ID NO:31 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:31; SNP_17, which contains adenine at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:33; SNP_05, which contains adenine at the 51st nucleotide of SEQ ID NO:9 or at the 51st nucleotide of SEQ ID NO:33 or at the 51st nucleotide of SEQ ID NO:33; NO:9 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_06 contains adenine at the 51st nucleotide of SEQ ID NO:11 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_07 contains cytosine at the 51st nucleotide of SEQ ID NO:13 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_08 contains cytosine at the 51st nucleotide of SEQ ID NO:15 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; NO:15 contains thymine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_18 contains thymine at the 51st nucleotide of SEQ ID NO:35 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:35; SNP_19 contains thymine at the 51st nucleotide of SEQ ID NO:37 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:37.SNP_20, which contains guanine at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:39; SNP_21, which contains cytosine at the 51st nucleotide of SEQ ID NO:41 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:41; isotig32772_1413, which contains guanine at the 61st nucleotide of SEQ ID NO:55 or at the 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:55; and isotig33099_885, which contains guanine at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:55; and isotig33099_885, which contains guanine at the 51st nucleotide of SEQ ID NO:39 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:55; Thymine is contained at nucleotide 61 of NO:57 or at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:57.

[0169] Preferably, the marker linked to the QTL conferring reduced pyruvate on chromosome 7 used in the method according to the invention is a SNP marker selected from the following: SNP_22, which contains thymine at the 51st nucleotide of SEQ ID NO:43 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:43; SNP_23, which contains thymine at the 51st nucleotide of SEQ ID NO:45 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:45; SNP_24, which contains thymine at the 51st nucleotide of SEQ ID NO:47 or at the 51st nucleotide of SEQ ID NO:45. NO:47 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_25 contains guanine at the 51st nucleotide of SEQ ID NO:49 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_09 contains thymine at the 51st nucleotide of SEQ ID NO:17 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_10 contains thymine at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity. NO:19 contains guanine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; isotig28625_2789 contains guanine at the 61st nucleotide of SEQ ID NO:59 or at the 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:59; and isotig41937_218 contains guanine at the 61st nucleotide of SEQ ID NO:61 or at the 61st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:61.

[0170] Preferably, the method for identifying and / or selecting onion plants or plant parts according to the present invention includes determining the presence or absence of one or more markers in the plant or plant part. Therefore, the method for identifying and / or selecting onion plants or plant parts according to the present invention may include determining the presence or absence of at least one (e.g., at least 2, 3, 4, or 4) QTL-linked markers of reduced pyruvate located on chromosome 2 and at least one (e.g., at least 2, 3, 4, or 4) QTL-linked markers of reduced pyruvate located on chromosome 1. The method for identifying and / or selecting onion plants or plant parts according to the present invention may further include determining the presence or absence of at least one (e.g., at least 2, 3, 4, or 4) QTL-linked markers of reduced pyruvate located on chromosome 2 and at least one (e.g., at least 2, 3, 4, or 4) QTL-linked markers of reduced pyruvate located on chromosome 7. The method for identifying and / or selecting onion plants or plant parts according to the present invention may further include determining the presence or absence of at least one (e.g., at least two, three, four, or four) QTL-linked markers of reduced pyruvate-conferred on chromosome 1 and at least one (e.g., at least two, three, four, or four) QTL-linked markers of reduced pyruvate-conferred on chromosome 7. Even more preferably, the method for identifying and / or selecting onion plants or plant parts according to the present invention includes determining the presence or absence of at least one (e.g., at least two, three, four, or four) QTL-linked markers of reduced pyruvate-conferred on chromosome 2, at least one (e.g., at least two, three, four, or four) QTL-linked markers of reduced pyruvate-conferred on chromosome 1, and at least one (e.g., at least two, three, four, or four) QTL-linked markers of reduced pyruvate-conferred on chromosome 7.

[0171] Preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts includes determining the presence or absence of at least one marker linked to a QTL conferring reduced pyruvate on chromosome 2, at least one marker linked to a QTL conferring reduced pyruvate on chromosome 1, and at least one marker linked to a QTL conferring reduced pyruvate on chromosome 7.

[0172] Preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts includes determining the presence or absence of one or more (e.g., two or three) peak markers in the plant or plant part, preferably one or more (e.g., two or three) peak markers as described in Table 2. As used herein, the term "peak marker" describes a marker that is found to be as accurate as possible, preferably with a false positive and / or false negative rate of 0%.

[0173] Therefore, the marker linked to the QTL conferring reduced pyruvate on chromosome 2 is preferably SNP_03, which contains cytosine at nucleotide 51 of SEQ ID NO:5 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5. The marker linked to the QTL conferring reduced pyruvate on chromosome 1 is preferably SNP_07, which contains cytosine at nucleotide 51 of SEQ ID NO:13 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:13. The marker linked to the QTL conferring reduced pyruvate located on chromosome 7 is preferably SNP_10, which contains guanine at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0174] Therefore, the method according to the invention for identifying and / or selecting onion plants or plant parts preferably includes determining the presence or absence of: at least one (e.g., at least two, three, four, or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 2, wherein the marker on chromosome 2 is SNP_03, which contains cytosine at nucleotide 51 of SEQ ID NO:5 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:5; at least one (e.g., at least two, three, four, or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 1, wherein the marker on chromosome 1 is SNP_07, which contains cytosine at nucleotide 51 of SEQ ID NO:5 or at nucleotide 51 of SEQ ID NO:5. NO:14 contains cytosine at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and at least one (e.g., at least two, three, four, or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 7, wherein the marker on chromosome 7 is SNP_10, which contains guanine at the 51st nucleotide of SEQ ID NO:19 or at the 51st nucleotide of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO:19.

[0175] Nucleic acids and their uses

[0176] The present invention also provides an isolated nucleic acid comprising a nucleotide sequence selected from the following: SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:15; SEQ ID NO:11; SEQ ID NO:13; SEQ ID NO:14; SEQ ID NO:15 ... SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:17; SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:21; SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:27; SEQ ID NO:29 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:3 ...17; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:27; SEQ ID NO:29 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 1 A fragment consisting of at least 15 nucleotides of nucleotide 51 of SEQ ID NO:33; or a fragment of SEQ ID NO:35 or thereof consisting of at least 15 nucleotides of SEQ ID NO:35 containing nucleotide 51 of SEQ ID NO:35;SEQ ID NO:37 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:37; SEQ ID NO:39 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:39; SEQ ID NO:41 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:41; SEQ ID NO:43 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:43; SEQ ID NO:45 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:45; SEQ ID NO:47 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:47; and SEQ ID NO:49 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:49, or containing their complementary nucleotide sequences. The present invention preferably provides an isolated nucleic acid comprising a nucleotide sequence selected from the following: SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising the 51st nucleotide of SEQ ID NO:15; SEQ SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides including the 51st nucleotide of SEQ ID NO:17; SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides including the 51st nucleotide of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides including the 51st nucleotide of SEQ ID NO:21.SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:27; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:33; SEQ ID NO:35 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:35; SEQ ID NO:37 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:37; SEQ ID NO:39 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:39; SEQ ID NO:43 or a fragment thereof consisting of at least 15 nucleotides containing the 51st nucleotide of SEQ ID NO:39; Fragments consisting of at least 15 nucleotides of SEQ ID NO:43 at position 51; SEQ ID NO:45 or a fragment thereof consisting of at least 15 nucleotides containing the nucleotide at position 51 of SEQ ID NO:45; SEQ ID NO:47 or a fragment thereof consisting of at least 15 nucleotides containing the nucleotide at position 51 of SEQ ID NO:47; and SEQ ID NO:49 or a fragment thereof consisting of at least 15 nucleotides containing the nucleotide at position 51 of SEQ ID NO:49, or containing their complementary nucleotide sequences.

[0177] Therefore, the isolated nucleic acid provided herein comprises at least 15 nucleotides, wherein the nucleotides comprise the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO: 1-50. Furthermore, the isolated nucleic acid provided herein comprises a complementary sequence of the isolated nucleic acid, wherein the complementary sequence comprises at least 15 nucleotides, wherein the nucleotides comprise the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO: 1-50. This means that the isolated nucleic acid provided herein comprises a fragment of at least 15 subsequent nucleotides of any nucleotide sequence selected from SEQ ID NO: 1-50, wherein the fragment further comprises the 51st nucleotide selected from the nucleotide sequence of SEQ ID NO: 1-50, or its complementary nucleotide sequence. Preferably, the isolated nucleic acid of the present invention comprises more than 15 nucleotides, including the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO:1-50: for example, at least 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 95, or 100 nucleotides, including the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO:1-50, or a complementary nucleotide sequence thereof.

[0178] The nucleic acids according to the invention are particularly suitable for the use or development of methods for identifying and / or selecting onion plants or plant parts, but also suitable for methods for producing onion plants, the method comprising hybridizing a first onion plant with a second onion plant and selecting onion plants from the offspring of the hybridization based on the presence or absence of one or more markers of the invention. Therefore, the invention provides for the use of one or more nucleotide sequences selected from SEQ ID NO:1-50, preferably composed of SEQ ID NO:1-50, or fragments thereof, for marker-assisted selection of onion plants or plant parts, wherein the fragments consist of at least 15 nucleotides comprising the 51st nucleotide of the nucleotide sequences selected from SEQ ID NO:1-50, or complementary sequences of the one or more nucleotide sequences. Furthermore, the invention provides for the use of one or more nucleotide sequences selected from SEQ ID NO:51-62, preferably composed of SEQ ID NO:51-62, or fragments thereof, for marker-assisted selection of onion plants or plant parts, wherein the fragments consist of at least 15 nucleotides comprising the 61st nucleotide of the nucleotide sequences selected from SEQ ID NO:51-62, or complementary sequences of the one or more nucleotide sequences. Preferably, the nucleotide sequence used according to the present invention can be any of the nucleotide sequences described herein, for example, containing more than 15 nucleotides, said nucleotides containing the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO:1-50, each containing more than 15 nucleotides (the nucleotides containing the 61st nucleotide selected from any nucleotide sequence of SEQ ID NO:51-62), for example at least 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 nucleotides, said nucleotides containing the 51st nucleotide selected from any nucleotide sequence of SEQ ID NO:1-50, each containing the 61st nucleotide selected from SEQ ID NO:51-62, for example, at least 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, The 61st nucleotide of any nucleotide sequence of NO:51-62, or the complementary sequence of the nucleotide sequence.

[0179] Seed preservation

[0180] Representative samples of seeds containing the QTLs conferring reduced pyruvate levels described herein were deposited by Nunhems B.V. on March 13, 2008, under the Budapest Treaty, in accordance with Expert Solution (EPC 2000, Rule 32(1)), at the American Center for Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA20110-2209, USA). The seeds were assigned the following accessions: PTA-9053 (as further described in WO 2009 / 092560 A1 for strain I37853B), PTA-9054 (as further described in WO 2009 / 092560 A1 for strain I37554A), and PTA-9055 (as further described in WO 2009 / 092560 A1 for strain I37554B).

[0181] The applicant requires that samples of the biological material and any material derived therefrom be made available to a designated expert only in accordance with the relevant legislation of a country or treaty with similar rules and regulations, until the reference to the patent is granted, or if the application is rejected, withdrawn or deemed to have been withdrawn, for a period of 20 years from the date of application.

[0182] During the pending period of this application, the deposit may be obtained upon request by a person deemed qualified by the Director of the U.S. Patent and Trademark Office. In accordance with 37 C. FR § 1.808(b), upon patent grant, all restrictions imposed by the depositor regarding the public availability of the deposited material will be permanently removed. The deposit will be held for 30 years, or for 5 years after the most recent request, or until the expiry of the patent, whichever is longer, and will be replaced if the deposit becomes inactive during this period. The applicant does not waive any rights granted by this patent application or the Plant Variety Protection Act (7 USC 2321 et seq.).

[0183] Example

[0184] Example 1

[0185] QTL positioning

[0186] A single low-spiciness (reduced spiciness) line, I37720B, derived from a cross between materials in the I37554B pedigree, was crossed with two spiciness inbred lines, I37977B (“Population 1”) and I37545-7 (“Population 2”). The resulting F1 hybrids were self-pollinated to produce two segregating populations of F2 plants. Under field conditions in Brooks, Oregon, a total of 331 F2 plants were grown in Population 1, and 236 plants were grown in Population 2. Leaf tissue was collected from each F2 individual for DNA extraction. Corms were harvested and stored for 4 months, after which pyruvate levels were measured.

[0187] A set of 283 KASP markers was run on DNA extracted from each F2 individual. Monomorphic markers were discarded, and genetic linkage maps for each population were independently computed using the Kosambi localization function in the JoinMap package. The resulting maps were combined with pyruvate measurements using the spaced localization method in the MapQTL package to identify quantitative trait loci (QTLs). A genome-wide substitution test was used to set a threshold for the log-dominance (LOD) score of a significant association between loci and pyruvate concentration, with a cumulative count of at least 0.95, for 200 iterations of 1,000 substitutions per population.

[0188] In population 1, two significant QTLs exceeding the calculated LOD threshold were detected, one on linkage group 3 (chromosome 2) and one on linkage group 6 (chromosome 7). Population 2 contained a single significant QTL on linkage group 4 (chromosome 1). Peak markers for these three QTLs were identified on the integrated genetic linkage map, and additional neighbor markers were added to the F2 population map. The number of additional markers added is detailed in Table 1. Information on the peak and flanking markers for each significant QTL is shown in Table 2.

[0189] After integrating additional markers, peak markers of QTLs on linkage group 3 (chromosome 2) explained 5.6% of the pyruvate variation, peak markers of QTLs on linkage group 4 (chromosome 1) explained 45.6% of the variation, and peak markers of QTLs on linkage group 6 (chromosome 7) explained 6.5% of the pyruvate variation.

[0190] Table 1. Additional markers added to each of the three significant QTLs

[0191] Chain Group No. 3 19 8 11 1 Chain Group No. 4 5 4 1 1 Chain Group No. 6 12 5 7 4

[0192] Table 2. Names of peak markers and flanking markers for each significant QTL

[0193]

[0194]

[0195] *SNP_10 is the furthest marker on linkage 6, therefore there are no true flanking markers.

[0196] Table 3. Nucleotide sequences of identified peak markers and flanking markers

[0197]

[0198]

[0199] Furthermore, the QTLs of this invention were placed on publicly available onion genetic maps. Duangjit et al. (2013) Theor Appl Genet 126, 2093–2101 describes in detail all the public markers cited herein. Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72 describes in detail the cited “B9885 x B8667” map, and Havey (2000) J. Amer. Soc. Hort. Sci., 145(2), 110-119 describes in detail the cited “Char x B5351” map. By integrating public marker information with internal datasets, the QTLs of this invention were located on these public maps, and the low-spiciness strain I37720B was genotyped using public markers to identify alleles associated with the reduced pyruvate locus. Table 4 below describes publicly available markers for the loci that further define the QTLs of the present invention.

[0200] Table 4. Loci of QTLs for decreased pyruvate defined by publicly available genetic markers

[0201] isotig30225_1454 B9885 x B8667 2 96.7 C isotig32865_1404 B9885x B8667 2 116.1 G isotig32772_1413 Char x B5351 1 60.7 G isotig33099_885 Char x B5351 1 75.2 T isotig28625_2789 B9885x B8667 7 0 G isotig41937_218 B9885x B8667 7 11.2 G

[0202] Table 5. Nucleotide sequences of publicly available genetic markers

[0203]

[0204] Therefore, it can be concluded that the QTL for deprived pyruvate on chromosome 2 lies between the common markers isotig30225_1454 (SEQ ID NO:51) and isotig32865_1404 (SEQ ID NO:53), representing a 19.4 cM interval. The QTL for deprived pyruvate on chromosome 1 lies between the common markers isotig32772_1413 (SEQ ID NO:55) and isotig33099_885 (SEQ ID NO:57), representing a 14.5 cM interval. The QTL for deprived pyruvate on chromosome 7 lies between the common markers isotig28625_2789 (SEQ ID NO:59) and isotig41937_218 (SEQ ID NO:61), representing an 11.2 cM interval.

[0205] Furthermore, the markers described in detail above were also placed on their respective public maps. Because the inventors were unable to obtain the isolated individuals from these maps to calculate precise genetic distances, they placed them at intervals according to the public maps.

[0206] Table 6. Loci of QTLs for decreased pyruvate defined by publicly available genetic markers

[0207]

[0208]

[0209] Example 2

[0210] Validation of QTL markers

[0211] To verify that the identified markers could be used to predict pyruvate levels, the inventors genotyped a group of lines with a range of pyruvate values. Five bulbs from each line were genotyped, and the pyruvate concentration was assigned based on the average value of the bulbs from that line.

[0212] Pyruvate was measured in the bulbs after four months of storage. 5-10 mm thick slices were taken from the mid-latitude of onion bulbs (25-50 g). The slices were quartered, mixed with deionized water (1:10 dilution), and homogenized using an immersion mixer until large clumps disappeared (approximately 45 seconds). One (1) mL of onion juice was centrifuged for 5 minutes (16,000 x g at room temperature). The supernatant was used for pyruvate measurement, which was performed according to the method of Anthon and Barrett (2003) with some modifications. Six (6) mL of onion juice was mixed with 50 mL of 0.025% dinitrophenylhydrazine (DNPH) reagent in a 96-well microplate. The mixture was incubated at 37 °C for 15 min, then mixed with 50 mL of 1.5 N sodium hydroxide (NaOH). The mixture was cooled to room temperature, and the absorbance was read at 515 nm. Pyruvate analysis was repeated three times for each sample. Calibration curves were prepared using 0.4, 0.8, and 1.2 mM pyruvate standard solutions. Results are expressed as μmol pyruvate per gram of fresh tissue (μmol / g).

[0213] The results of this validation confirmed that the reduced pungent haplotype (“B” allele call) was enriched in the reduced pungent lines, and lines with lower mean pyruvate values ​​and smaller pyruvate level variations had lower rates of high pyruvate (“A”) alleles (Table 7). For all reduced pungent materials, the soluble solids content (SSC) measured by Brix was above 7% and was not correlated with pyruvate levels (R). 2 =0.2, slope is negative).

[0214] The linkage groups described above were mapped to known markers to determine which chromosome number corresponded to each linkage group. Thus, linkage group 3 was found to correspond to chromosome 2 of onion, linkage group 4 to chromosome 1 of onion, and linkage group 6 to chromosome 7 of onion.

[0215] Table 7. Validation results of reduced spiciness plant materials. Genotypes were coded in A / H / B format, where A represents the high spiciness allele, H represents heterozygote, and B represents the reduced spiciness allele. Flanking SNP markers are underlined, while peak markers are in bold (see also Table 2 above). The row below the SNP marker name indicates the corresponding base call for the reduced spiciness allele. Entries were first sorted according to mean pyruvate level, and then sorted according to the standard deviation of pyruvate level when the mean levels were similar.

[0216] sequence list <110> Nunhems BV <120> Molecular markers for the trait of reduced pyruvate levels in onions <130> 191252WO01 <150> US 62 / 940667 <151> 2019-11-26 <150> EP 19216666.8 <151> 2019-12-16 <150> EP 20170450.9 <151> 2020-04-20 <160> 62 <170> PatentIn version 3.5 <210> 1 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 1 catggcaaga aaaatgttcc aagcttcttg aaacatctcc agacaattgg tctttcaaaa 60 gtgattccga aacctctact tcgaagtaca ttgcttcttt a 101 <210> 2 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 2 catggcaaga aaaatgttcc aagcttcttg aaacatctcc agacaattgg gctttcaaaa 60 gtgattccga aacctctact tcgaagtaca ttgcttcttt a 101 <210> 3 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 3 ttgataaaag cgatattgtt ggggaagtat cctgcagaat ttttgtggcc atgaaaagga 60 agatgagtgg aagctaaatg cattggaaat tgtgtttggc c 101 <210> 4 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 4 ttgataaaag cgatattgtt ggggaagtat cctgcagaat ttttgtggcc gtgaaaagga 60 agatgagtgg aagctaaatg cattggaaat tgtgtttggc c 101 <210> 5 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 5 gacggataat tcagaacagg gaggaagtaa gcagcatgtg ataatcaaca cagaggatag 60 agcttctgag gtgggtaaag ctgatgcgaa tcgtcccacg c 101 <210> 6 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 6 gacggataat tcagaacagg gaggaagtaa gcagcatgtg ataatcaaca tagaggatag 60 agcttctgag gtgggtaaag ctgatgcgaa tcgtcccacg c 101 <210> 7 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 7 tgatgctatc tggaagatta caaatttata gatggtatgg gatgttggaa tagcagattg 60 gtgctgaatt tagtactacc aaaggacaga tgacgccgct t 101 <210> 8 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 8 tgatgctatc tggaagatta caaatttata gatggtatgg gatgttggaa cagcagattg 60 gtgctgaatt tagtactacc aaaggacaga tgacgccgct t 101 <210> 9 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 9 ctcaggaatg agatttgcat cagcatcctc aggatcaatt tcttgatcat cagattgcat 60 tccataatta aacagcagct cgtgccactt catgtcatca a 101 <210> 10 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 10 ctcaggaatg agatttgcat cagcatcctc aggatcaatt tcttgatcat tagattgcat 60 tccataatta aacagcagct cgtgccactt catgtcatca a 101 <210> 11 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 11 cctgagcgat gtaaaaggaa gagatagagt atgggagttg agaaactgta accatgtttt 60 tcataaagga tgcctggaca aatggttaga gcatgatgag c 101 <210> 12 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 12 cctgagcgat gtaaaaggaa gagatagagt atgggagttg agaaactgta gccatgtttt 60 tcataaagga tgcctggaca aatggttaga gcatgatgag c 101 <210> 13 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 13 gattgtttag acattcgttg tatttcgcga gatctgctca cgggatagct cattttttaa 60 gatttttcga gaaattctac ctggattttt gttagggttt t 101 <210> 14 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 14 gattgtttag acattcgttg tatttcgcga gatctgctca cgggatagct gattttttaa 60 gattttcga gaattctac ctggatttt gttagggttt t <210> 15 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 15 aattacactt tagcaatcaa gagatgattc tcaggagaaa tatccgagga tgtatacttc accatttgtg catccaaccc ctgatccctt agccacgaca t <210> 16 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 16 aattacactt tagcaatcaa gagatgattc tcaggagaaa tatccgagga ggtatacttc accatttgtg catccaaccc ctgatccctt agccacgaca t <210> 17 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 17 60. gatgatggtg gagcgagaag agaatggttc tggtttgtgg tttgattgga tgggtttgtc gatcgaggtc catgaccatt gcttgtggat gcggttccat c <210> 18 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 18 60. gatgatggtg gagcgagaag agaatggttc tggtttgtgg tttgattgga cgggtttgtc gatcgaggtc catgaccatt gcttgtggat gcggttccat c <210> 19 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 19 gagcaagatc agttaagatt cttaaagctc tttgaagaca ccgatgagtt ggatgatgag ttggaacaat tataagttca atctactacg ccatacttta c <210> 20 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 20 gagcaagatc agttaagatt cttaaagctc tttgaagaca ccgatgagtt cgatgatgag ttggaacaat tataagttca atctactacg ccatacttta c <210> 21 <211> 101 <212> DNA <213> Spider(Allium cepa) <400> 21 acttatttgt accagatgct agttcatcat accagatctcga tcaacagctc aaaactgtcc ccacttcatc tgacggcaat atcatggttt cttggaatcc t <210> 22 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 22 acttatttgt accagatgct agttcatcat acgatctcga tcaacagctc gaaactgtcc 60 ccacttcatc tgacggcaat atcatggttt cttggaatcc t 101 <210> 23 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 23 actcttttca aaatggcaat tccaaaactt gaactttaac ttttgttaca cgcttaatca 60 cgtcgataat catgcttagc accactgcca ctttctaaat c 101 <210> 24 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 24 actcttttca aaatggcaat tccaaaactt gaactttaac ttttgttaca tgcttaatca 60 cgtcgataat catgcttagc accactgcca ctttctaaat c 101 <210> 25 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 25 cctgaacatt atgcaaaatg tttagccaca ctttcacgct catcttcact tggaattcga 60 ttgtgttttc gtcagtacag taaaaataaa ttcaagcttt t 101 <210> 26 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 26 cctgaacatt atgcaaaatg tttagccaca ctttcacgct catcttcact aggaattcga 60 ttgtgttttc gtcagtacag taaaaataaa ttcaagcttt t 101 <210> 27 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 27 cgtgaaagtg tggctaaaca ttttgcataa tgttcaggag ttaaaaccac agcaatgtca 60 tctatacatt ctgcgctgat cacttgtgag aagggcgtga a 101 <210> 28 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 28 cgtgaaagtg tggctaaaca ttttgcataa tgttcaggag ttaaaaccac ggcaatgtca 60 tctatacatt ctgcgctgat cacttgtgag aagggcgtga a 101 <210> 29 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 29 taagcttcat gaagctatat atatcacagt aaaacaggtt atttttatgg gcatggatta 60 ctttttaaat ttgtaagttg gttttgtctc ccttttggtt a 101 <210> 30 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 30 taagcttcat gaagctatat atatcacagt aaaacaggtt atttttatgg acatggatta 60 ctttttaaat ttgtaagttg gttttgtctc ccttttggtt a 101 <210> 31 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 31 acgtcggcgg gagctttctc ggtttgatac acgcctaaat agccggttgg atcgactctc 60 gcgtagatcg gaccgttgcc ttggattatt tgagttttgg c 101 <210> 32 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 32 acgtcggcgg gagctttctc ggtttgatac acgcctaaat agccggttgg gtcgactctc 60 gcgtagatcg gaccgttgcc ttggattatt tgagttttgg c 101 <210> 33 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 33 tatagtgtgg caaaggtgc attgcataga gcatttgatg agatagt agttgaaaga 60 aattgtggtc gagagagca gagagatcca atcaatatta a 101 <210> 34 <211> 101 <212> DNA <213> Allium cepa <400> 34 tatagtgtgg caaaggtgc attgcataga gcatttgatg agatagt tgttgaaaga 60 aattgtggtc gagagagca gagagatcca atcaatatta a 101 <210> 35 <211> 101 <212> DNA <213> Allium cepa <400> 35 tattatatt atagcagtg atgtcacatt cattaatttg tgcaccctca ttattatccc 60 tcgatgaaaa gtcaattatt tcgttagga tatccgtaga c 101 <210> 36 <211> 101 <212> DNA <213> Allium cepa <400> 36 tattatatatt atagcagtg atgtcacatt cattaatttg tgcaccctca atattatccc 60 tcgatgaaaa gtcaattatt tcgttagga tatccgtaga c 101 <210> 37 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 37 tgttgcattc cccattaccc aatatcactg tcacaactat gctccccaac tccttgctac 60 actgcaataa catcacatac aacttcactt ccccgaacaa c 101 <210> 38 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 38 tgttgcattc cccattaccc aatatcactg tcacaactat gctccccaac accttgctac 60 actgcaataa catcacatac aacttcactt ccccgaacaa c 101 <210> 39 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 39 cttcccctcg gtaaatattc tgttactatc gacaaatgtg gagactttgt gactgcaccc 60 ataaatagta caatatttgg atggcgaata cgtttcatta t 101 <210> 40 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 40 cttcccctcg gtaaatattc tgttactatc gacaaatgtg gagactttgt aactgcaccc 60 ataaatagta caatatttgg atggcgaata cgtttcatta t 101 <210> 41 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 41 tactgcccag tcactgcttg tggggatgga ttcttcgtct tcaagcgatg ctcgaattct 60 ctcaagatct ttctctgaag cttctttgaa attaatgtcc t 101 <210> 42 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 42 tactgcccag tcactgcttg tggggatgga ttcttcgtct tcaagcgatg ttcgaattct 60 ctcaagatct ttctctgaag cttctttgaa attaatgtcc t 101 <210> 43 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 43 gatacccaaa accctgatat gatcgactat ctcaaccaag aaaatgatta tactgaatca 60 tttatgaaag atactgaaaa attgcagcga aaattagtgg a 101 <210> 44 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 44 gatacccaaa accctgatat gatcgactat ctcaaccaag aaaatgatta cactgaatca 60 tttatgaaag atactgaaaa attgcagcga aaattagtgg a 101 <210> 45 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 45 ttatggtcga aagaagacct attgaacttt gtcatagcac ctccagtggg tatcttccca 60 cacagcttat tatagccgac gtcaaaatac accagtttga t 101 <210> 46 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 46 ttatggtcga aagaagacct attgaacttt gtcatagcac ctccagtggg catcttccca 60 cacagcttat tatagccgac gtcaaaatac accagtttga t 101 <210> 47 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 47 aaattggcta tggagaagat gaagattgat ttggcacaga aagataagat cctgtctgca 60 ttgctgagaa aatcaaaggc tgataatgaa gaaaagcata t 101 <210> 48 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 48 aaattggcta tggagaagat gaagattgat ttggcacaga aagataagat cctgtctgca 60 ttgctgagaa aatcaaaggc tgataatgaa gaaaagcata t 101 <210> 49 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 49 cattctgtca tggttatcag tcacatctaa tgatgcttta atactttccg gattcagaaa 60 tgacaaatgt gctccaccaa atgcttctac acatggttta c 101 <210> 50 <211> 101 <212> DNA <213> Onion (Allium cepa) <400> 50 cattctgtca tggttatcag tcacatctaa tgatgcttta atactttccg aattcagaaa 60 tgacaaatgt gctccaccaa atgcttctac acatggttta c 101 <210> 51 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 51 ctcgcttttg tctccggtca aatacttgaa cccatcatac aaaattcttt caaaaacgtc 60 cacttttatt tttccaacca acaccctttc agtactcttc tccaaaacag ataggaacaa 120 c 121 <210> 52 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 52 ctcgcttttg tctccggtca aatacttgaa cccatcatac aaaattcttt caaaaacgtc 60 aacttttatt tttccaacca acaccctttc agtactcttc tccaaaacag ataggaacaa 120 c 121 <210> 53 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (1)..(1) <223> n is a, c, g or t <400> 53 naatcgagcg gagttcgtcg gagtccatta ccgtctcttt ctttggctat ttaatatcgt 60 gtaatggagg ataaaagagg ataatgatgt aatattttat ggattggact atataaaaat 120 g 121 <210> 54 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (1)..(1) <223> n is a, c, g or t <400> 54 naatcgagcg gagttcgtcg gagtccatta ccgtctcttt ctttggctat ttaatatcgt 60 ttaatggagg ataaaagagg ataatgatgt aatattttat ggattggact atataaaaat 120 g 121 <210> 55 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 55 gaatcgcgaa cctttgaaat ggaggggaac accggtattg gagccgatac ccttctcgcc 60 ggtacaaatc gctctaaaat tctctgccgt tctgggaacg acgtcggcaa agagctcaat 120 g 121 <210> 56 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 56 gaatcgcgaa cctttgaaat ggaggggaac accggtattg gagccgatac ccttctcgcc 60 agtacaaatc gctctaaaat tctctgccgt tctgggaacg acgtcggcaa agagctcaat 120 g 121 <210> 57 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (48)..(48) <223> n is a, c, g or t <400> 57 agtgctcact gtattatcaa ttccggaagg ttttccatgg ataatctntt caccctcata 60 tgcccatttg tttatgagat caagttcctt ttcccctaaa ttcaaccacc cagattcttt 120 a 121 <210> 58 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (48)..(48) n is a, c, g or t <400> 58 agtgctcact gtattatcaa ttccggaagg ttttccatgg ataatctntt caccctcata 60 cgcccatttg tttatgagat caagttcctt ttcccctaaa ttcaaccacc cagattcttt 120 a 121 <210> 59 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 59 agttaaaagc acttccacgc ctaggccact atacatatag tccttctcct tcccgttcac 60 gtactccttg cgcctgtaaa aaggaagcac atccagcaca tcttcatttt ccttcagcca 120 c 121 <210> 60 <211> 121 <212> DNA <213> Onion (Allium cepa) <400> 60 agttaaaagc acttccacgc ctaggccact atacatatag tccttctcct tcccgttcac 60 atactccttg cgcctgtaaa aaggaagcac atccagcaca tcttcatttt ccttcagcca 120 c 121 <210> 61 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (1)..(1) <223> n is a, c, g or t <400> 61 nttaaagagg cctagcgcga gtagttggat cttcattgga ttctactttc atcatgaaaa 60 gatacccaat tatccacaag agcacatatg gaaaaggaat ccagcataaa catgccaata 120 g 121 <210> 62 <211> 121 <212> DNA <213> Onion (Allium cepa) <220> <221> misc_feature <222> (1)..(1) <223> n is a, c, g or t <400> 62 nttaaagagg cctagcgcga gtagttggat cttcattgga ttctactttc atcatgaaaa 60 tatacccaat tatccacaag agcacatatg gaaaaggaat ccagcataaa catgccaata 120 g 121

Claims

1. A method for identifying and / or selecting onions ( Allium cepa A method for determining the presence or absence of one or more markers in an onion plant or plant part, the markers being adapted to determine the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, wherein the markers are markers linked to a QTL conferring reduced pyruvate levels between marker isotig32772_1413 and marker isotig33099_885 located on chromosome 1; wherein the QTLs are present in plants whose seeds are deposited with accession number PTA-9053, plants whose seeds are deposited with accession number PTA-9054, or plants whose seeds are deposited with accession number PTA-9055, and The markers linked to the QTL conferring reduced pyruvate located on chromosome 1 are selected from the following SNP markers: SNP_16, which is adenine at the 51st nucleotide of SEQ ID NO: 31; SNP_17, which is adenine at the 51st nucleotide of SEQ ID NO: 33; SNP_05, which is cytosine at nucleotide position 51 of SEQ ID NO: 9; SNP_07, which is cytosine at nucleotide position 51 of SEQ ID NO: 13; SNP_08, which is thymine at the 51st nucleotide of SEQ ID NO: 15; SNP_19, which is thymine at nucleotide position 51 of SEQ ID NO: 37; and SNP_20, which is guanine at the 51st nucleotide of SEQ ID NO:

39.

2. An isolated nucleic acid comprising a nucleotide sequence selected from: SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO:

39.

3. One or more nucleotide sequences selected from SEQ ID NO: 9, 13, 15 and SEQ ID NO: 31, 33, 37, 39 for use in marker-assisted selection of onion plants or plant parts having reduced pyruvate levels.

4. A marker for identifying onion plants that produce bulbs with reduced pyruvate levels, said marker comprising one or more SNPs selected from: SNP_05, which is cytosine at nucleotide position 51 of SEQ ID NO: 9; SNP_07, which is cytosine at nucleotide position 51 of SEQ ID NO: 13; SNP_08, which is thymine at the 51st nucleotide of SEQ ID NO: 15; SNP_16, which is adenine at the 51st nucleotide of SEQ ID NO: 31; SNP_17, which is adenine at the 51st nucleotide of SEQ ID NO: 33; SNP_19, which is thymine at nucleotide position 51 of SEQ ID NO: 37; and SNP_20, which is guanine at the 51st nucleotide of SEQ ID NO: 39.

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