Molecular markers for the reduced pyruvate level trait in onion

Abstract

The present invention relates to genetic markers for determining the presence or absence of one or more QTL conferring reduced pyruvate levels in onion plants or plant parts, the markers being selected from the group consisting of a marker linked to a QTL conferring reduced pyruvate located on chromosome 2, a marker linked to a QTL conferring reduced pyruvate located on chromosome 1, and a marker linked to a QTL conferring reduced pyruvate located on chromosome 7. The present invention further relates to the use of the markers of the present invention for determining the presence or absence of one or more QTL conferring reduced pyruvate levels in onion plants or plant parts. The present invention further relates to methods for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers of the present invention in said plants or plant parts. The present invention relates to the use of isolated nucleic acids and nucleotide sequences as provided herein for marker-assisted selection of onion plants or plant parts.

Description

[Technical Field]

[0001] FIELD OF THE INVENTION The present invention relates to the field of plant breeding. Genetic markers are provided for determining the presence or absence of one or more quantitative trait loci (QTL) conferring reduced pyruvate levels in onion (Allium cepa) plants or plant parts, the markers being selected from the group consisting of a marker linked to a QTL located on chromosome 2 that confers reduced pyruvate, a marker linked to a QTL located on chromosome 1 that confers reduced pyruvate, and a marker linked to a QTL located on chromosome 7 that confers reduced pyruvate. The present invention further relates to the use of the markers of the present invention for determining the presence or absence of one or more QTL conferring reduced pyruvate levels in onion plants or plant parts. The present invention further relates to methods for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers of the present invention in said plants or plant parts. The present invention relates to the use of isolated nucleic acids and nucleotide sequences as provided herein for marker-assisted selection of onion plants or plant parts. [Background technology]

[0002] background The onion plant is thought to have originated in Western or Central Asia. In Europe, onions have been known since the Bronze Age. The bulbs of the onion plant, or "onions," are used in many dishes and have a reputation for being very healthy. Plant breeding has focused on yield, appearance, harvestability, storability, flavor, and the content of several compounds that onions contain that have beneficial health effects. Some of these compounds are most effective when onions are eaten raw, and their concentration is often related to the solids content of the onion. Onions with a high solids content, which are mild and sweet enough to be consumed uncooked, deliver more of these health-promoting compounds from the diet.

[0003] The typical onion flavor or taste is pungency, which results from the conversion of the sulfur-containing flavor precursor alk(en)yl-L-cysteine ​​sulfoxide (ACSO) to thiosulfonate by the enzyme alliinase when onion cells are cut or injured. A by-product of this enzymatic process, pyruvate or pyruvic acid, is measured as an indicator of pungency (Schwimmer and Weston 1961, J. of Agric. Food Chem. 9: 301-4). The amount of pyruvate produced correlates directly with the pungency of the onion as determined by a taste panel (Schwimmer and Guadagni, 1962, J. Food Sc. 27:94-97).

[0004] Pungency is an important commercial trait because consumers prefer fresh onions that are sweeter and less pungent. Pungency masks the sweetness of the sugars present in the onion as water-soluble solids or carbohydrate portions. Pungency is strongly influenced by the presence or absence of sulfur in the soil or plant nutrients (Randle 1992, Euphytica 59: 151-156 and Randle and Bussard 1993, J. Amer. Soc. Hort. Sci. 118: 766-770), but also has a clear genetic component as shown by Lin (1995, J. Amer. Soc. Hort. Sci. 120: 119-122), Simon (1995, Euphytica 82: 1-8), Wall et al. (1996, Euphytica 87: 133-139), and Wall and Corgan (1999, Euphytica 106: 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 can increase significantly during storage. Thus, there is a demand for onions that are low in pungency at harvest, whereby their pungency does not increase significantly during storage. In particular, there is a demand for onions that have low pungency after at least about 2, 3, 4, 5, 6, 7, 8 or more months of storage. In particular, long-day onions can be stored, whereas short-day onions are generally consumed with little or no storage. In particular, there is a demand for long-day onions that have low pungency, whereby their pungency does not increase during storage and that remains constant or reduces (compared to harvest levels) during storage, i.e., is lower than harvest levels after at least about 2, 3, 4, 5, 6, 7, 8 or more months of storage. Thus, "reduced during storage" means that after a particular storage period (eg, after about 2, 3, 4, 5, 6, 7, 8 or more months of storage) the level is lower than at harvest.

[0006] Onion plants that produce onion bulbs with reduced pungency have been previously described. WO 2007011857 ​​A2 describes long-day onion plants with reduced pungency bulbs. WO 2009 / 092560 A1 describes long-day onion plants that can produce onion bulbs with a high content of soluble solids in combination with reduced pungency. EP 2992756 A1 describes onion plants with reduced alliinase gene expression, resulting in reduced amounts of pungency and tearing compounds produced when onion cells are destroyed. One common problem with reduced pungency onion varieties is that there can be reduced consistency with respect to pungency characteristics. One reason for this is that there is often a large genotype by environment interaction, which can be difficult to genetically fix by phenotypic selection. Further complicating this issue, onion breeding lines are often inbred to the F4 or F5 level until they "populate" and are maintained as a population rather than by individual lineages. This results in residual heterozygosity levels of up to 12.5%. Consequently, onion lines exhibit segregation at loci for traits of interest, including those controlling the pungency trait. In this regard, the development of reliable genetic markers to determine the presence of reduced pungency alleles has been unsuccessful. If molecular markers for the pungency trait were available in onion plants, it might be possible to increase the genetic stability of low-pungency lines by fixing these loci in breeding lines, resulting in more consistent pungency characteristics in the resulting onion varieties. Furthermore, the availability of reliable molecular markers would allow accelerated breeding of new low-pungency varieties, since a larger number of individual plants could be screened with molecular markers compared to the more labor-intensive phenotypic screening for pyruvate. Summary of the Invention

[0007] Summary of the Invention According to the present invention, there is provided a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, said markers being selected from the group consisting of a marker linked to a QTL conferring reduced pyruvate located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404; a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between marker isotig32772_1413 and marker isotig33099_885; and a marker linked to a QTL conferring reduced pyruvate located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218. The order of SNP markers identified for the present invention may be from Table 7 as provided herein below.

[0008] Further, the term "SEQ ID NO:1" as used herein refers to SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:15; SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:17. SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:21; SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:27; SEQ ID NO:29 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:33;An isolated nucleic acid is provided that comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:35 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:35; SEQ ID NO:37 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:37; SEQ ID NO:39 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:39; SEQ ID NO:41 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:41; SEQ ID NO:43 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:43; SEQ ID NO:45 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:45; SEQ ID NO:47 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:47; and SEQ ID NO:49 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:49, or a complementary nucleotide sequence thereof.

[0009] Also provided herein is the use of one or more of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 to 50 or fragments thereof, said fragments comprising nucleotide 51 or consisting of at least 15 nucleotides of said nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 to 50, or complementary sequences to one or more of said nucleotide sequences, for marker-assisted selection of onion plants or plant parts.

[0010] Also provided herein are SNP_01, which comprises a thymine at nucleotide 51 of SEQ ID NO: 1 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_02, which comprises an adenine at nucleotide 51 of SEQ ID NO: 3 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_03, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 5 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5; SNP_04, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 7 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7 on chromosome 2; SNP_04 comprising a thymine at nucleotide 51 of a sequence comprising at least 97%, at least 98%, or even at least 99% identity; SNP_05 comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 9; SNP_06 comprising an adenine at nucleotide 51 of SEQ ID NO: 11 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 11; SNP_07 comprising a cytosine at nucleotide 51 of SEQ ID NO: 13 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 13;SNP_08, on chromosome 1, comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09, on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_10, on chromosome 7, comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; SNP_11, on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO: 21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21. SNP_11 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23 on chromosome 2; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 comprising an adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27;SNP_15 on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO:29 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_18 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:35 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:35; SNP_18 comprising a thymine at nucleotide 51 of a sequence comprising at least 7%, at least 98%, or even at least 99% identity; SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 39; SNP_21 comprising a cytosine at nucleotide 51 of SEQ ID NO: 41 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 41;SNP_22 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 47 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47. and SNP_25 on chromosome 7 comprising a guanine at nucleotide 51 of SEQ ID NO:49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49. BRIEF DESCRIPTION OF THE SEQUENCE LISTING;

[0011] Sequence number 1 shows the pungency-reducing genotype of SNP_01. SEQ ID NO: 2 shows the high pungency genotype of SNP_01. Sequence number 3 shows the pungency-reducing genotype of SNP_02. SEQ ID NO: 4 shows the high pungency genotype of SNP_02. Sequence number 5 shows the pungency-reducing genotype of SNP_03. SEQ ID NO: 6 shows the high pungency genotype of SNP_03. Sequence number 7 shows the pungency-reducing genotype of SNP_04. Sequence number 8 shows the high pungency genotype of SNP_04. Sequence number 9 shows the pungency-reducing genotype of SNP_05. Sequence number 10 shows the high pungency genotype of SNP_05. Sequence number 11 shows the pungency-reducing genotype of SNP_06. Sequence number 12 shows the high pungency genotype of SNP_06. Sequence number 13 shows the pungency-reducing genotype of SNP_07. Sequence number 14 shows the high pungency genotype of SNP_07. Sequence number 15 shows the pungency-reducing genotype of SNP_08. Sequence number 16 shows the high pungency genotype of SNP_08. Sequence number 17 shows the pungency-reducing genotype of SNP_09. SEQ ID NO: 18 shows the high pungency genotype of SNP_09. Sequence number 19 shows the pungency-reducing genotype of SNP_10. SEQ ID NO: 20 shows the high pungency genotype of SNP_10. Sequence number 21 shows the pungency-reducing genotype of SNP_11. Sequence number 22 shows the high pungency genotype of SNP_11. Sequence number 23 shows the pungency-reducing genotype of SNP_12. SEQ ID NO: 24 shows the high pungency genotype of SNP_12. Sequence number 25 shows the pungency-reducing genotype of SNP_13. SEQ ID NO: 26 shows the high pungency genotype of SNP_13. SEQ ID NO: 27 shows the pungency-reducing genotype of SNP_14. SEQ ID NO: 28 shows the high pungency genotype of SNP_14. SEQ ID NO: 29 shows the pungency-reducing genotype of SNP_15. SEQ ID NO: 30 shows the high pungency genotype of SNP_15. SEQ ID NO: 31 shows the pungency-reducing genotype of SNP_16. SEQ ID NO: 32 shows the high pungency genotype of SNP_16. SEQ ID NO: 33 shows the pungency-reducing genotype of SNP_17. SEQ ID NO: 34 shows the high pungency genotype of SNP_17. SEQ ID NO: 35 shows the reduced pungency genotype of SNP_18. SEQ ID NO: 36 shows the high pungency genotype of SNP_18. SEQ ID NO: 37 shows the pungency-reducing genotype of SNP_19. SEQ ID NO: 38 shows the high pungency genotype of SNP_19. SEQ ID NO: 39 shows the pungency-reducing genotype of SNP_20. SEQ ID NO: 40 shows the high pungency genotype of SNP_20. SEQ ID NO: 41 shows the pungency-reducing genotype of SNP_21. SEQ ID NO: 42 shows the high pungency genotype of SNP_21. SEQ ID NO: 43 shows the pungency-reducing genotype of SNP_22. SEQ ID NO: 44 shows the high pungency genotype of SNP_22. SEQ ID NO: 45 shows the pungency-reducing genotype of SNP_23. SEQ ID NO: 46 shows the high pungency genotype of SNP_23. SEQ ID NO: 47 shows the pungency-reducing genotype of SNP_24. SEQ ID NO: 48 shows the high pungency genotype of SNP_24. SEQ ID NO: 49 shows the pungency-reducing genotype of SNP_25. SEQ ID NO: 50 shows the high pungency genotype of SNP_25. Sequence number 51 shows the pungency-reducing genotype of isotig30225_1454. SEQ ID NO: 52 shows the high pungency genotype of isotig30225_1454. Sequence number 53 shows the pungency-reducing genotype of isotig32865_1404. SEQ ID NO: 54 shows the high pungency genotype of isotig32865_1404. Sequence number 55 shows the pungency-reducing genotype of isotig32772_1413. Sequence number 56 shows the high pungency genotype of isotig32772_1413. Sequence number 57 shows the pungency-reducing genotype of isotig33099_885. Sequence number 58 shows the high pungency genotype of isotig33099_885. Sequence number 59 shows the pungency-reducing genotype of isotig28625_2789. SEQ ID NO: 60 shows the high pungency genotype of isotig28625_2789. Sequence number 61 shows the pungency-reducing genotype of isotig41937_218. Sequence number 62 shows the high pungency genotype of isotig41937_218. DETAILED DESCRIPTION OF THE INVENTION

[0012] Detailed Description of the Invention General definition The term "genome" refers to the genetic material of an organism. A genome is made up of DNA. A genome includes both genes and non-coding sequences of DNA.

[0013] The term "genetic determinant" relates to the genetic information in a plant genome that gives rise to a particular trait in the plant. Thus, a genetic determinant comprises the genetic information (gene or locus or introgression) that confers a particular trait. Generally, a genetic determinant can comprise a single gene (or one quantitative trait locus (QTL)) or two or more genes.

[0014] A "phenotype" is the observable physical and / or physiological appearance of a plant that is the result of the interaction between the plant's genotype and its environment. Phenotype includes all observable morphological and physiological characteristics, and thus includes phenotypes such as pungency, PAD measurements, and soluble solids content of onion bulbs.

[0015] The term "trait" in the context of the present application refers to the phenotype of a plant. When a plant exhibits a trait of the present invention, its genome comprises at least one reduced pungency allele associated with the trait of the present invention, particularly when the reduced pungency allele is homozygous in the present invention. Thus, the plant has the genetic determinant of the present invention. References to a plant comprising a plant trait of the present invention are understood to refer to an onion plant comprising the reduced pungency trait as further described herein.

[0016] "Genotype" is the totality of a plant's inherited genetic information, influenced in part by environmental factors, which is expressed in the phenotype.

[0017] As used herein, an "onion plant" or "onion" is a plant or part thereof of the plant species Allium cepa L., such as (harvested) bulbs and seeds. The edible part of the plant, the "bulb," is harvested. Onion bulbs may be developing or mature. Mature bulbs are preferred herein, and these may be pre- or post-harvest bulbs.

[0018] "Long day" onion plants will initiate heading when there is at least about 14 or more consecutive hours of light (day length), e.g., at least about 14, 15, or 16 hours. This continuous light (hours per day) is preferably provided for 2, 4, 7, 14, 21, 25, or more days to initiate heading.

[0019] "Storage conditions" and "storage" include typical conditions used for storing onions (preferably fresh), such as darkness, low temperature (as used herein, low temperature means preferably below 12°C, e.g., about 3-12°C, 3-10°C, 5-10°C or about 3-5°C, preferably about 3, 4 or 5 degrees Celsius) and a relative humidity (RH) of about 60-80%, preferably about 70-80%, most preferably around 70%. Controlled ventilation is also preferred.

[0020] "Soluble solids" or "soluble solids content" (herein "SSC") is the percentage (%) of water-soluble compounds in an onion bulb as measured by refractometry according to the method 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).

[0021] "High SSC," as used herein, refers to an average SSC of a representative number of onion bulbs (e.g., at least 5, 6, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90 or more bulbs) of at least 7.0% or 7.5%, or even at least 8%, 9%, 10%, 11%, 12%, 15%, 20%, 25%, 30% or more. Thus, as used herein, 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.

[0022] "Pungency" is the typical hot taste of onions when onion bulb tissue is disrupted by crushing. Pungency is preferably determined by measuring the enzymatic generation of pyruvate according to the method of Schwimmer and Weston (1961, J. of Agric. Food Chemistry 9:301-304), which correlates strongly with flavor perception by taste panels (Schwimmer 1962, J. Food Sci. 27: 94-97; Wall and Corgan, 1992, Hort. Science 27: 1029-1030). Alternatively, pyruvate (also called pyruvate) can be measured using a colorimetric method such as that described in Anthon and Barrett (2003) Science of Food and Agriculture (83) 1210-1213. Pungency is expressed as μMol (also herein micromoles, μM, or μmol) pyruvate per gram of fresh bulb material (μMol / g FW), also referred to herein as "PAD measurement" (PAD from pyruvic acid generation) or "pyruvate measurement" or "pyruvate level."

[0023] The term "reduced pungency," as used herein, accordingly, refers to a pungency level that is reduced compared to the pungency level of a reference variety. Preferably, the reduced pungency level corresponds to a pungency level that is reduced to such an extent that the reduced pungency level corresponds to a low pungency level. "Low pungency," as used herein, refers to an average pungency of a representative number of (mature) onion bulbs (e.g., at least about 5, 8, 10, 15, 20, 30, 40, 50, 50, 60, 70, 80, 90 or more bulbs) of less than 5.5 μMol / g FW pyruvate, or even less than 5.0, 4.5, 4.0 μMol / g FW pyruvate, 3.8 or 3.75 μMol / g FW pyruvate or less, or 3.5, 3.0, 2.5, 2.3, 2.0, 1.8, 1.5, or 1.3 μMol / g FW pyruvate or less, as determined by PAD measurements. "High pungency" as used herein refers to an average pungency level of a representative number of (mature) onion bulbs that is higher than a low pungency level as defined herein, preferably greater than 5.5 μMol / g FW pyruvate, or even greater than 6.0, 6.5, or 7.0 μMol / g FW pyruvate. Pungency can be measured at harvest and / or after 2, 3, 4, 5, 6, 7, 8 or more months of storage.

[0024] A "narrow pungency range" refers to a narrow variation in pungency between individual bulbs from a single plant line, i.e., the difference between the pungency level of the hottest bulb (maximum) and the pungency level of the least pungent bulb (minimum) is preferably 5 μMol / g FW pyruvate or less, more preferably 4 μMol / g FW pyruvate or less, or 3.5 μMol / g FW pyruvate or less, more preferably 3.0, 2.5, 2.0, 1.5, or 1.0 μMol / g FW pyruvate or less. Preferably, the maximum pungency (of the hottest bulb produced by the plant) is 5 μMol / g FW pyruvate or less, preferably 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 or less. Preferably, the minimum pungency level (i.e., of the least pungent bulb produced by the plant) is no more than 3.0, 2.5 μMol / g FW pyruvate, more preferably no more than 2.0, 1.3, or 1.2 μMol / g FW pyruvate. Thus, a preferred range of pungency within a plant line is where all bulbs have a pungency between 0 (min) and 5 (max) μMol / g FW pyruvate, preferably 1 (min) and 5 (max) μMol / g FW pyruvate, more preferably 1 (min) and 4 (max) μMol / g FW pyruvate. Also, in one embodiment of the present invention, all bulbs have a pungency of 0 (min) to 5 (max) μMol / g FW pyruvate, preferably 1 (min) to 5 (max) μMol / g FW pyruvate, more preferably between 1 or 1.2 (min) and 4.9, 4.8, 4.7, or 4.5 (max) μMol / g FW pyruvate, more preferably between 1 (min) and 4 (max) μMol / g FW pyruvate. A narrow pungency range is an important quality characteristic for consumers. Pungency can be measured at harvest and / or, preferably, after a period of storage, e.g., at least about 2, 3, 4, 5, 6, 7, 8, or more months of storage.

[0025] "High pungency allele," as used herein, refers to an allele associated with the high pungency trait as further defined herein. In one embodiment, the high pungency allele is a wild-type allele.

[0026] "Reduced pungency allele," as used herein, refers to an allele associated with a reduced pungency trait as further defined herein. In one embodiment, the reduced pungency allele is a mutant allele.

[0027] "Wild-type plant," as used herein, refers to a plant of an onion species that produces bulbs having high pungency as defined herein. Such plants are suitable controls in phenotypic assays, for example, especially when the control plant has the same genetic background as the plant undergoing phenotypic testing (e.g., a low-pungency plant).

[0028] "Long-term storage," as used herein, refers to a storage length of at least 2, 3, 4, 5, 6, 7 months or more. Preferably, there is no significant increase in pungency and / or no significant decrease in SSC during storage, i.e., when comparing the average pungency and / or SSC levels at harvest (or shortly thereafter) to those after 2, 3, 4, 5, 6, 7 months or more of storage. "No significant increase in pungency," as used herein, refers to an increase in pungency measurements (i.e., pyruvate) of less than 10%, more preferably less than 5%, even more preferably less than 3%, 2%, or 1%, or more preferably no increase at all, after the storage period; in one embodiment, a decrease in pungency compared to measurements at harvest (or shortly thereafter). "No significant decrease in SSC," as used herein, refers to a decrease in SSC levels of less than 5%, 4%, 3%, or 2%, preferably less than 1% or 0.5%, or more preferably unchanged, after the storage period compared to SSC levels at harvest (or shortly thereafter). In one embodiment, the average SSC level after 2, 3, 4, 5, 6, 7 or more months of storage is at least about 80%, 85%, 87%, 88%, 89%, 90%, 95%, 98% of the level at harvest, more preferably at least about 100%, or 101%, 102%, 103%, 105% or more of the level at harvest.

[0029] Genetic determinants can be inherited in a recessive, intermediate, or dominant manner. Selection for phenotypic traits is easier when intermediate or dominant inheritance is involved, as the trait will be expressed in a larger proportion of the progeny. In general, genetic determinants can also comprise a combination of recessive and / or intermediate and / or dominant genes or QTLs.

[0030] Selection for genetic determinants (e.g., reduced pungency alleles) can be phenotypically (observable traits). Selection can also be achieved by using molecular genotyping methods, such as one or more molecular markers genetically linked to the reduced pungency allele, or preferably by molecular methods that use the gene or allele sequence itself to, for example, distinguish between the presence of the reduced pungency allele and the wild-type allele, or its product (e.g., mRNA or protein encoded by the allele). The use of molecular genotyping methods in breeding (e.g., "marker-assisted selection," when genetically linked markers are used, or other genotyping methods, such as SNP genotyping) requires smaller populations to screen (compared to phenotypic selection) and can be done at a very early stage. A further advantage of molecular genotyping methods is that homozygous plants or seeds that do not have any copies of the high pungency alleles as described herein can be easily distinguished from plants that have one or more copies of one or more of the high pungency alleles, even before the seed germinates or during early plant development, e.g., before onion bulb development.

[0031] "Plant line" or "breeding line" refers to a plant and its progeny. As used herein, the term "inbred line" refers to a plant line that has been repeatedly selfed and is nearly homozygous for every characteristic. Thus, "inbred line" or "parent line" refers to a plant that has undergone several generations (e.g., at least 4, 5, 6, 7 or more) of inbreeding to result in a plant line with high homogeneity.

[0032] The term "allele" refers to any of one or more alternative forms of a DNA sequence at a particular locus, all of which alleles relate to one trait or characteristic at a particular locus. In diploid cells of an organism, alleles of a given gene are located at specific locations, or loci, on chromosomes. One allele is present on each chromosome of a homologous chromosome pair. A diploid plant species can comprise many different alleles at a particular locus. These may be identical alleles of the gene (homozygous) or two different alleles (heterozygous).

[0033] The term "locus" refers to a particular location or locations on a chromosome where, for example, a gene or genetic marker is found. Thus, a reduced pungency locus as described herein is a location in the genome of an onion plant where a reduced pungency allele is found.

[0034] The term "linkage group," as used herein, is defined as a group of loci that are physically linked together on a single DNA molecule (chromosome) and that are transmitted together to progeny at a frequency higher than would be expected according to the law of independent inheritance. In the present invention, eight linkage groups have been identified. Preferably, each of these eight linkage groups, as used herein, corresponds to one of the eight chromosomes of the onion genome. Preferably, the term "linkage group 3," as used herein, corresponds to chromosome 3 (of onion). Preferably, the term "linkage group 4," as used herein, corresponds to chromosome 1 (of onion). Preferably, the term "linkage group 6," as used herein, corresponds to chromosome 7 (of onion).

[0035] The term "gene" refers to a (genomic) DNA sequence comprising a region transcribed into a messenger RNA molecule (mRNA) in a cell (transcribed region) and an operably linked regulatory region (e.g., promoter). Thus, a gene may comprise several operably linked sequences, such as a promoter, a 5' leader sequence comprising, for example, a sequence involved in the initiation of translation, a (protein) coding region (cDNA or genomic DNA), and a 3' untranslated sequence comprising, for example, a transcription termination site. Thus, different alleles of a gene are different alternative forms of that gene, and may differ, for example, in one or more nucleotides of the genomic DNA sequence (e.g., promoter sequence, exon sequence, intron sequence, etc.), in the mRNA and / or in the amino acid sequence of the encoded protein. A gene may be an endogenous gene (of the species of origin) or a chimeric gene (e.g., a transgene or cis-gene). A "promoter" of a gene sequence is defined as a region of DNA that initiates transcription of a particular gene. Promoters are located adjacent to, on the same strand as, and upstream of the DNA of the gene they transcribe. A promoter can be about 100 to 1000 base pairs in length, hi one aspect, a promoter is defined as the region about 1000 or more base pairs, e.g., about 1500 or 2000 base pairs upstream of the start codon (i.e., ATG) of the protein encoded by the gene.

[0036] "Transgene" or "chimeric gene" refers to a genetic locus comprising a DNA sequence, such as a recombinant gene, that has been introduced into the genome of a plant by transformation, such as Agrobacterium-mediated transformation. A plant comprising a transgene stably integrated into its genome is called a "transgenic plant."

[0037] "Expression of a gene" refers to the process by which a DNA region operably linked to appropriate regulatory regions, particularly a promoter, is biologically active, i.e., is translated into a biologically active protein or peptide (or active peptide fragment), or is transcribed into RNA that is active itself (e.g., post-transcriptional gene silencing or RNAi). The coding sequence may be in the sense orientation and encodes a desired, biologically active protein or peptide, or an active peptide fragment.

[0038] A "quantitative trait locus," or "QTL," is a chromosomal locus that encodes one or more alleles that influence the degree of expression of a continuously distributed (quantitative) phenotype.

[0039] The "physical distance" between loci (e.g., between molecular markers and / or phenotypic markers) on the same chromosome is the actual physical distance expressed in bases or base pairs (bp), kilobases or kilobase pairs (kb), or megabases or megabase pairs (Mb).

[0040] The "genetic distance" between loci on the same chromosome (e.g., between molecular and / or phenotypic markers) is measured by the crossover frequency, or recombination frequency (RF), expressed in centimorgans (cM). 1 cM corresponds to a recombination frequency of 1%. If no recombination is observed, the RF is zero, and the loci are physically very close, or they are identical. The further apart two loci are, the higher the RF.

[0041] An "introgression fragment" or "introgression segment" or "introgression region" refers to a chromosome fragment (or chromosome portion or region) that has been introduced into another plant of the same or closely related species by crossing or conventional breeding techniques, e.g., backcrossing; i.e., the introgressed fragment is the result of a breeding method referred to by the verb "to introgress" (e.g., backcross). It is understood that the term "introgression fragment" never includes an entire chromosome, but only a portion of a chromosome. The gene transfer fragment may be large, for example, three-quarters or half of a chromosome, but is preferably smaller, for example, about 15 Mb or less, e.g., 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 (equivalent to 1,000,000 base pairs) or less, or about 0.5 Mb (equivalent to 500,000 base pairs) or less, for example, about 200,000 bp (equivalent to 200 kilobase pairs), about 100,000 bp (100 kb), about 50,000 bp (50 kb), or about 25,000 bp (25 kb).

[0042] The term "isogenic plant" refers to two plants that are genetically identical except for the pungency-reducing allele of the present invention. To study the effect of a pungency-reducing trait, a plant line (or variety) of interest can be crossed with a plant comprising a pungency-reducing allele, and progeny expressing the desired trait can be selected. In some cases, the progeny must be selfed one or more times so that the genetic determinants of the pungency-reducing trait can be determined in the plant phenotype. The progeny can then be backcrossed (at least twice, e.g., 3, 4, or preferably 5 or 6 times) with the plant line (or variety) of interest, selecting for progeny that have the same phenotype as the plant line (or variety) and express the genetic determinants of the pungency-reducing trait. The effect of pungency reduction can then be compared between the plant line (variety) of interest and its isogenic line that does not contain the genetic determinants of the pungency-reducing trait.

[0043] The terms "nucleic acid," "nucleic acid sequence," "nucleic acid molecule," or "polynucleotide" are used interchangeably and refer to DNA or RNA molecules in single- or double-stranded form, particularly DNA encoding a protein or protein fragment according to the invention. An "isolated nucleic acid" refers to a nucleic acid that is no longer in the natural environment from which it was isolated, for example, a nucleic acid in a bacterial host cell or in the nuclear or plastid genome of a plant.

[0044] The terms "protein," "peptide sequence," "amino acid sequence," or "polypeptide" are used interchangeably and refer to a molecule consisting of a chain of amino acids, regardless of its specific mode of action, size, tertiary structure, or origin. Thus, a "fragment" or "portion" of a protein is also referred to as a "protein." An "isolated protein" is used to refer to a protein that is not in its natural environment, for example, in vitro or in a recombinant bacterial or plant host cell.

[0045] An "active protein" or "functional protein" is a protein that has a protein activity that is measurable in vitro, e.g., by an in vitro activity assay, and / or in vivo, e.g., by a phenotype conferred by the protein. A "wild-type" protein is a fully functional protein as it exists in a wild-type plant. A "mutant protein," as used herein, is a protein comprising one or more mutations in the nucleic acid sequence encoding the protein, whereby the mutations result in (a mutant nucleic acid molecule encoding) a protein with altered activity, preferably a protein with reduced activity, and most preferably, an inactive protein.

[0046] A "functional derivative" of a protein as described herein is a fragment, mutant, analog, or chemical derivative of the protein that retains some of the activity or immunological cross-reactivity with antibodies specific for the mutant protein.

[0047] A fragment of a mutant protein refers to any subset of the molecule.

[0048] Variant peptides can be made by direct chemical synthesis, for example, using methods well known in the art.

[0049] An analog of a mutant protein refers to a non-naturally occurring protein substantially similar to the entire protein or a fragment thereof.

[0050] A "mutation" in a nucleic acid molecule is a change in one or more nucleotides compared to the wild-type sequence, for example by one or more nucleotide substitutions, deletions or insertions.

[0051] A "mutation" in an amino acid molecule constituting a protein is a change in one or more amino acids compared to the wild-type sequence, for example, by substitution, deletion, or insertion of one or more amino acids, and such a protein is also called a "mutant protein."

[0052] A "point mutation" is a substitution of a single nucleotide, or an insertion or deletion of a single nucleotide.

[0053] A "nonsense mutation" is a (point) mutation in a nucleic acid sequence encoding a protein in which a codon in the nucleic acid molecule is changed to a stop codon. This results in the presence of a premature stop codon in the mRNA, leading to the translation of a truncated protein. The truncated protein may exhibit reduced or no function.

[0054] A "missense or non-synonymous mutation" is a (point) mutation in a nucleic acid sequence encoding a protein in which a codon is changed to code for a different amino acid. The resulting protein may exhibit reduced or no function.

[0055] A "splice site mutation" is a mutation in a nucleic acid sequence encoding a protein that alters RNA splicing of a precursor mRNA, resulting in an mRNA with a different nucleotide sequence than the wild-type and a protein with a different amino acid sequence. The resulting protein may exhibit reduced or no function.

[0056] A "frameshift mutation" is a mutation in a nucleic acid sequence encoding a protein that alters the reading frame of the mRNA, resulting in a different amino acid sequence. The resulting protein may exhibit reduced or no function.

[0057] In the context of the present invention, a "deletion" is intended to mean that somewhere in a given nucleic acid sequence, at least one nucleotide is missing compared to the nucleic acid sequence of the corresponding wild-type sequence, or somewhere in a given amino acid sequence, at least one amino acid is missing compared to the amino acid sequence of the corresponding (wild-type) sequence.

[0058] "Truncation" means that at least one nucleotide is missing at either the 3'- or 5'-end of a nucleotide sequence compared to the nucleic acid sequence of the corresponding wild-type sequence, or at least one amino acid is missing at either the N- or C-terminus of a protein compared to the amino acid sequence of the corresponding wild-type protein, whereby in a 3'- or C-terminal truncation, at least the first nucleotide at the 5'-end or the first amino acid at the N-terminus, respectively, is still present, and in a 5'- or N-terminal truncation, at least the last nucleotide at the 3'-end or the last amino acid at the C-terminus, respectively, is still present. 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.

[0059] A "substitution" is intended to mean that at least one nucleotide of a nucleic acid sequence or one amino acid of a protein sequence differs due to an exchange of a nucleotide in the coding sequence of each protein compared to the corresponding wild-type nucleic acid sequence or the corresponding wild-type amino acid sequence, respectively.

[0060] An "insertion" is intended to mean that a nucleic acid sequence or the amino acid sequence of a protein comprises at least one additional nucleotide or amino acid compared to the corresponding wild-type nucleic acid sequence or the corresponding wild-type amino acid sequence, respectively.

[0061] In the context of the present invention, a "premature stop codon" means that a stop codon is present in the coding sequence (cds) closer to the start codon at the 5' end than the stop codon in the corresponding wild-type coding sequence.

[0062] A "mutation in a regulatory sequence" is, for example, a change in one or more nucleotides in a gene's promoter or enhancer compared to the wild-type sequence, e.g., by substitution, deletion, or insertion of one or more nucleotides, which results in, for example, reduced or no mRNA transcripts of the gene. Thus, a "promoter of a gene sequence" is defined as a DNA region that initiates transcription of a particular gene. Promoters are located on the same strand, upstream of the DNA, adjacent to the gene they transcribe. Promoters can be about 100 to 1000 base pairs in length. In one aspect, a promoter is defined as a region about 2000 or more base pairs upstream of the start codon (i.e., ATG) of the protein encoded by the gene; preferably, the promoter is about 1500 base pairs upstream of the start codon; more preferably, the promoter is about 1000 base pairs upstream of the start codon.

[0063] As used herein, the term "operably linked" refers to the linking of polynucleotide elements in a functional relationship.Nucleic acid is "operably linked" when it is placed in a functional relationship with another nucleic acid sequence.For example, a promoter, more specifically, a transcriptional regulatory sequence, is operably linked to a coding sequence when it affects the transcription of the coding sequence.Operatively linked means that the nucleic acid sequences that are linked are generally contiguous.

[0064] "Sequence identity" and "sequence similarity" can be determined by aligning two peptide or two nucleotide sequences using global or local alignment algorithms. Sequences can then be said to be "substantially identical" if they are optimally aligned, for example, by the programs GAP or BESTFIT or the Emboss program "Needle" (using default parameters, see below), and have at least a certain minimum sequence identity percentage (further defined below). These programs use the Needleman and Wunsch global alignment algorithm to align two sequences over their entire length, maximizing the number of matches and minimizing the number of gaps. Generally, default parameters are used, with a gap creation penalty of 10 and a gap extension penalty of 0.5 (for 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 scores can be determined using computer programs such as, for example, EMBOSS (available on the Internet at ebi.ac.uk at http: / / www.ebi.ac.uk under / Tools / psa / emboss_needle / ). Alternatively, sequence similarity or identity can be determined by searching databases such as FASTA, BLAST, etc., but hits must be retrieved and aligned pairwise to compare sequence identity.Two proteins or two protein domains, or two nucleic acid sequences have "substantial 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% (as determined by Emboss "needle" with default parameters, i.e., gap creation penalty = 0, gap extension penalty = 0.5, using the scoring matrix DNAFULL for nucleic acids and Blosum62 for proteins). Such sequences are also referred to herein as "variants," and include, for example, other variants of alleles resulting in the reduced pungency traits of the invention and proteins other than the specific nucleic acid and amino acid sequences disclosed herein, which may have the same effect on pungency as the plants of the invention.

[0065] The term "hybridization" as used herein generally refers to the hybridization of nucleic acids under appropriate stringency conditions (stringent hybridization conditions), which are readily apparent to those skilled in the art depending on the properties of the probe and target sequences. Hybridization and washing conditions are well known, and the conditions can be easily adjusted to the desired stringency by changing the incubation time, temperature, and / or 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 selection of conditions depends on the length of the hybridizing sequence, particularly the length of the probe sequence, the relative GC content of the nucleic acid, and the amount of mismatch to be tolerated. Low stringency conditions are preferred when partial hybridization between strands with low degrees of complementarity is desired. High stringency conditions are preferred when complete or near-complete complementarity is desired. Typical high stringency conditions include a hybridization solution containing 6x SSC, 0.01M EDTA, 1x Denhardt's solution, and 0.5% SOS. Hybridization is carried out at approximately 68°C for approximately 3-4 hours for cloned DNA fragments and approximately 12-16 hours for whole eukaryotic DNA. At lower stringency, the hybridization temperature is adjusted to a temperature above the melting point (T M ) is lowered by approximately 42°C. M is known to be a function of GC content and duplex length as well as the ionic strength of the solution.

[0066] As used herein, the phrase "hybridizes" to a DNA or RNA molecule means that the hybridizing molecule, e.g., an oligonucleotide, polynucleotide, or any nucleotide sequence (sense or antisense orientation), recognizes and hybridizes to the sequence of another nucleic acid molecule that is approximately the same size and has sufficient sequence similarity to it to achieve hybridization under appropriate conditions. For example, a 100-nucleotide molecule derived from the 3' coding or non-coding region of a gene will recognize and hybridize to the nucleotide sequence within the 3' coding or non-coding region of that gene or to an approximately 100-nucleotide portion of any other plant gene, so long as there is about 70% or more sequence similarity between the two sequences. It should be understood that the size of the corresponding portion allows for some mismatch in hybridization, so that the corresponding portion can be shorter or longer than the molecule to which it hybridizes, e.g., 20-30% longer or shorter, preferably about 12-15% or less longer or shorter.

[0067] As used herein, the phrase "a sequence comprising at least 95% sequence identity" or "a sequence comprising at least 95% amino acid sequence identity" or "a sequence comprising at least 95% nucleotide sequence identity" refers to a sequence that has at least 95%, for example, at least 96%, 97%, 98%, 98.3%, 98.7%, 99.0%, or 99.3%, or more preferably 99.7%, sequence identity when compared to the reference sequence indicated. Sequence identity can be determined according to the methods described herein.

[0068] A "fragment" of a gene or DNA sequence refers to any subset of that molecule, e.g., a shorter polynucleotide or oligonucleotide. In one aspect, the fragment comprises a mutation as defined by the present invention.

[0069] A "variant" of a gene or DNA refers to a molecule substantially similar to the entire gene or a fragment thereof, e.g., a nucleotide substitution variant having one or more substituted nucleotides, but retaining the ability to hybridize with a particular gene or to encode an mRNA transcript that hybridizes with native DNA. Preferably, the variant comprises a reduced pungency allele as defined by the present invention.

[0070] As used herein, the term "plant" includes an intact plant or any part or derivative thereof, such as a plant organ (e.g., harvested or unharvested flower, leaf, bulb, etc.), plant cell, plant protoplast, plant cell or tissue culture from which an intact plant can be regenerated, plant cell with or without regeneration potential, plant callus, plant cell mass, and intact plant cells within a plant, or plant parts, such as embryos, pollen, ovules, ovaries (e.g., harvested tissues or organs), flowers, leaves, seeds, bulbs, clonally propagated plants, roots, stems, cotyledons, hypocotyls, root tips, etc. Also included are any developmental stages, such as seedlings, immature, and mature. Preferably, the plant part or derivative comprises a gene or locus as defined by the present invention.

[0071] "Plant line" or "breeding line" refers to a plant and its progeny.

[0072] A "plant variety" or "cultivar" is a group of plants within the same lowest known botanical taxon that can be defined based on the expression of characteristics resulting from a particular genotype or combination of genotypes (whether or not the conditions for granting plant breeders' rights are met), that can be distinguished from any other group of plants by the expression of at least one of those characteristics, and that can be considered an entity because it is reproducible without any change. Thus, the term "plant variety" cannot be used to describe a group of plants, even if they are of the same species, that are all characterized by the presence of one genetic locus or gene (or a set of phenotypic characteristics due to this single genetic locus or gene) but may otherwise differ significantly from each other with respect to other genetic loci or genes. "F1, F2, etc." refer to successive related generations following a cross between two parent plants or parent lines. Plants grown from seeds produced by crossing two plants or lines are called the F1 generation. Selfing an F1 plant results in an F2 generation, etc. An "F1 hybrid" plant (or F1 seed or hybrid) is the generation resulting from crossing two inbred parent lines. Thus, "selfing" refers to the self-pollination of a plant, i.e., the combination of gametes from the same plant.

[0073] "Backcrossing" refers to a breeding method in which a (single) trait, such as the ability to induce reduced pungency, can be transferred from one genetic background (commonly, but not necessarily, referred to as the "donor," which is a lower genetic background) to another genetic background (commonly, but not necessarily, referred to as the "recurrent parent," which is a higher genetic background). The progeny of the cross (e.g., an F1 plant obtained by crossing a first plant of a plant species comprising a pungency-reducing allele of the present invention with a second plant of the same plant species or a different plant species that can be crossed with the first plant species, where the second plant species does not contain the pungency-reducing allele of the present invention; or an F2 or F3 plant obtained by selfing the F1) is "backcrossed" with a parent plant of the second plant species. After repeated backcrossing, the trait of the donor genetic background, e.g., the pungency-reducing allele conferring the pungency-reducing trait of the present invention, is incorporated into the recurrent genetic background. In this context, the term "gene conversion" or "converted plant" or "single locus conversion" refers to a plant produced by backcrossing in which substantially all of the desired morphological and / or physiological characteristics of the recurrent parent are restored in addition to one or more genes introduced from the donor parent. Plants grown from seeds produced by backcrossing an F1 plant with a second parent plant line are called the "BC1 generation." Plants from the BC1 population can be selfed to obtain the BC1F2 generation or backcrossed again with the cultivated parent plant line to obtain the BC2 generation. An "M1 population" is multiple mutagenized seeds / plants of a particular plant line. "M2, M3, M4, etc." refer to successive generations obtained after selfing of the first mutagenized seed / plant (M1).

[0074] The term "cultivated plant" or "cultivar" refers to a plant of a given species, e.g., a variety, breeding line, or cultivar of said species, that has been cultivated by humans and has favorable agronomic characteristics. So-called heirloom varieties or cultivars, i.e., open-pollinated varieties or cultivars that were commonly grown early in human history and often adapted to specific geographic regions, are included herein as cultivated plants in one aspect of the present invention. The term "cultivated plant" does not include wild plants. "Wild plants" includes, for example, wild accessions.

[0075] The term "food" is any substance consumed to provide nutrition to the body. Food is usually 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 the organism's cells to produce energy, sustain life, or stimulate growth. The term food includes substances consumed to provide nutrition to both human and animal bodies.

[0076] Throughout this specification, "average" and "mean" are used interchangeably and refer to the arithmetic mean.

[0077] A comparison between different plant lines is understood to include growing a plurality of plants of a line (variety) (e.g., at least 5 plants per line, preferably at least 10 plants) under the same conditions as plants of one or more control plant lines (preferably wild-type plants), and determining differences, preferably statistically significant differences, between the plant lines when grown under the same environmental conditions. Preferably, the plants are of the same line or variety.

[0078] In this specification and claims, the verb "comprises" and its conjugations are used in their open-ended sense, meaning that the items that follow the word are included, but items not specifically recited are not excluded. Furthermore, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one element is present, unless the context clearly requires that one and only one of those elements be present. Thus, the indefinite article "a" or "an" typically means "at least one." Furthermore, when referring to a "sequence" herein, it is generally understood to refer to an actual physical molecule having a specific sequence of subunits (e.g., amino acids or nucleic acids).

[0079] Markers and their uses The present invention provides markers for identifying onion plants that produce bulbs with reduced pyruvate levels, the markers being selected from the group consisting of a marker linked to a QTL conferring reduced pyruvate located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404, a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between marker isotig32772_1413 and marker isotig33099_885, and a marker linked to a QTL conferring reduced pyruvate located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218. The markers of the present invention are particularly useful 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. Thus, in one embodiment, the present invention provides markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in an onion plant or plant part, wherein the one or more QTLs conferring reduced pyruvate levels are from the plant whose seeds are deposited under accession number PTA-9053, the plant whose seeds are deposited under accession number PTA9054 or the plant whose seeds are deposited under accession number PTA-9055.Thus, in one embodiment, the present invention provides a marker suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in an onion plant or plant part obtained by crossing the plant whose seeds have been deposited under accession number PTA-9053, the plant whose seeds have been deposited under accession number PTA9054 or the plant whose seeds have been deposited under accession number PTA-9055 with another onion plant, the marker being marker isotig30225_1454 on chromosome 2. and marker isotig32865_1404 on chromosome 1; a marker linked to a QTL conferring reduced pyruvate located between marker isotig32772_1413 and marker isotig33099_885 on chromosome 1; and a marker linked to a QTL conferring reduced pyruvate located between marker isotig28625_2789 and marker isotig41937_218 on chromosome 7.

[0080] The publicly available genetic markers isotig30225_1454 and isotig32865_1404, which map to chromosome 2 at map B9885×B8667, are known in the art and are described in 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, which map to chromosome 1 at map Char×B5351, are known in the art and are described in detail in Havey (2000) J. Amer. Soc. Hort. Sci., 145(2), 110-119. The publicly available genetic markers isotig28625_2789 and isotig41937_218, which map to chromosome 7 at map B9885×B8667, are known in the art and are described in more detail in Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72. All publicly available genetic markers referenced herein are described in more detail in Duangjit et al. (2013) Theor Appl Genet 126, 2093-2101. The nucleotide sequences of these publicly available genetic markers are further set forth in Table 5.

[0081] Preferably, the present invention provides SNP_01, which comprises a thymine at nucleotide 51 of SEQ ID NO: 1 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_02, which comprises an adenine at nucleotide 51 of SEQ ID NO: 3 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_03, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 5 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5; SNP_04, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 7 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7 on chromosome 2. SNP_04 comprising a thymine at nucleotide 51 of a sequence comprising at least 97%, at least 98%, or even at least 99% identity; SNP_05 comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 9; SNP_06 comprising an adenine at nucleotide 51 of SEQ ID NO: 11 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 11; SNP_07 comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 13;SNP_08, on chromosome 1, comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09, on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_10, on chromosome 7, comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; SNP_11, on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO: 21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21. SNP_11 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23 on chromosome 2; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 comprising an adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27;SNP_15 on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO:29 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_18 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:35 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:35; SNP_18 comprising a thymine at nucleotide 51 of a sequence comprising at least 7%, at least 98%, or even at least 99% identity; SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 39; SNP_21 comprising a cytosine at nucleotide 51 of SEQ ID NO: 41 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 41;SNP_22 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 47 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47. and SNP_25 on chromosome 7 comprising a guanine at nucleotide 51 of SEQ ID NO:49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49.

[0082] A "marker," or "genetic marker," is a DNA fragment of known chromosomal location that is polymorphic among individuals (e.g., individual plants forming part of a plant population) that can be used to distinguish and / or identify individuals from others. In one embodiment, the reduced pyruvate-conferring QTL is located between SNP_11, located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO:21, and SNP_04, located at nucleotide 51 of SEQ ID NO:7 on chromosome 2 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO:7. A skilled person can readily identify, using conventional methods, one or more suitable genetic markers linked to a reduced pyruvate-conferring QTL such as is located at a locus defined herein on chromosome 2 (i.e., between isotig30225_1454 and marker isotig32865_1404 and / or between SNP_11 and SNP_4, as further defined herein). In one embodiment, the reduced pyruvate-conferring QTL is located on chromosome 1 between SNP_16, located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31, and SNP_20, located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:39.A skilled artisan can readily identify, using conventional methods, one or more suitable genetic markers linked to a reduced pyruvate-conferring QTL such as those located 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 reduced pyruvate-conferring QTL is located between SNP_22, located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:43, and the distal end of chromosome 7 which comprises SNP_10, located at nucleotide 51 of SEQ ID NO:19 on chromosome 7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:19. A skilled artisan can readily identify, using conventional methods, one or more suitable genetic markers that are linked to a reduced pyruvate-conferring QTL such as is located at a locus defined herein on chromosome 7 (i.e., between marker isotig28625_2789 and marker isotig41937_218 and / or at the distal end of chromosome 7 comprising SNP_22 and SNP_10 as further defined herein). As used herein, the reference to "linked markers" specifically means "markers that are genetically linked."

[0083] Thus, 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, said markers being linked to a reduced pyruvate-conferring QTL located on chromosome 2 between SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 and SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7; a marker on chromosome 1 linked to a reduced pyruvate-conferring QTL located between SNP_11 located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; and a marker linked to a reduced pyruvate-conferring QTL located on chromosome 7 between SNP_16 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39 and SNP_20 located at nucleotide 51 of SEQ ID NO: 43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43, and the distal end of chromosome 7 comprising SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19.

[0084] Despite residual heterozygosity in the initially obtained low-pungency onion lines, the present inventors successfully identified three significant QTLs that confer reduced pyruvate levels in the bulbs produced by onion plants. Various technical difficulties had to be overcome before the QTLs of the present invention could be identified. Construction of multiple mapping populations required careful planning, and the parent plants of a population were cultivated for approximately six years before material was available for QTL analysis. Because the mechanism of low pyruvate in the low-pyruvate donor was unknown, several crosses were performed. These results indicated that the low-pyruvate trait is a complex trait under the control of at least three loci. Since no overlapping QTLs were detected in the two populations, it was necessary to construct and analyze multiple mapping populations to identify the three QTLs of the present invention. Validation of the QTLs again required an unconventional approach due to the long generation time of onions. These efforts to develop genome-wide molecular markers, apart from the efforts involved in actual mapping and validation, required extensive effort to enable genetic mapping and the development of low-pyruvate donor lines through phenotypic selection, which required decades of directed breeding. One reduced-pyruvate-conferring QTL was identified on linkage group 3, located between SNP_11, located at nucleotide 51 of SEQ ID NO:21 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO:21, and SNP_04, located at nucleotide 51 of SEQ ID NO:7 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO:7.A further reduced pyruvate-conferring QTL was identified on linkage group 4 between SNP_16 located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31 and SNP_20 located at nucleotide 51 of SEQ ID NO:39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:39. A still further reduced pyruvate-conferring QTL was identified on linkage group 6 between SNP_22 located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:43 and the distal end of linkage group 6 comprising SNP_10 located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:19.

[0085] It was found that linkage group 3 corresponds to onion chromosome 2, linkage group 4 corresponds to onion chromosome 1, and linkage group 6 corresponds to onion chromosome 7. Thus, the term "linkage group 3," as used herein, corresponds to the term "chromosome 2." Thus, the term "linkage group 4," as used herein, corresponds to the term "chromosome 1." Thus, the term "linkage group 6," as used herein, corresponds to the term "chromosome 7."Thus, 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, said markers being linked to a reduced pyruvate-conferring QTL located on chromosome 2 between SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 and SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7; a marker on chromosome 1 linked to a reduced pyruvate-conferring QTL located between SNP_11 located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; markers linked to a reduced pyruvate-conferring QTL located on chromosome 1 between SNP_16 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 51; and markers linked to a reduced pyruvate-conferring QTL located on chromosome 7 between SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43 and the distal end of the chromosome comprising SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19.

[0086] Preferably, 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, said markers being a marker linked to a reduced pyruvate-conferring QTL located on chromosome 2 between SNP_01 located at nucleotide 51 of SEQ ID NO: 1 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1 and SNP_04 located at nucleotide 51 of SEQ ID NO: 7 or at nucleotide 51 of a sequence comprising at least 95% (at least 98% or at least 99%) identity to SEQ ID NO: 7; a marker linked to a reduced pyruvate-conferring QTL located on chromosome 1 between SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising at least 95% (at least 98% or at least 99%) identity to SEQ ID NO: 31 and SNP_17 located at nucleotide 51 of SEQ ID NO: 39; and a marker linked to a QTL conferring reduced pyruvate located on chromosome 7 at the distal end of chromosome 7 comprising SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43 and SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19. Thus, the present invention provides markers for determining the presence or absence of one or more QTL conferring reduced pyruvate levels in an onion plant or plant part.Such markers, referred to herein as "molecular markers," may be any measurable indicator that is genetically linked to a trait of interest, and thus, in the context of the present invention, to a reduced pungency allele. Particularly preferred in the context of the present invention are DNA-based markers, including, but not limited to, restriction fragment length polymorphism (RFLP) markers, cleaved amplified polymorphic sequence (CPAS) markers, microsatellite markers (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 present invention are SNP markers.

[0087] In the context of the present invention, different specific SNP markers linked to a reduced pyruvate-conferring QTL located on chromosome 2 have also been identified. Markers linked to such SNP-reduced pyruvate-conferring QTL located on chromosome 2 include SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (at least 98% or at least 99%) identity to SEQ ID NO:21; SNP_12 located at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 located at nucleotide 51 of SEQ ID NO:25 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 located at nucleotide 51 of SEQ ID NO:27 or at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_14 located at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_01 located at nucleotide 51 of SEQ ID NO: 1 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_02 located at nucleotide 51 of SEQ ID NO: 3 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_3 located at nucleotide 51 of SEQ ID NO: 5 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5;SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7; and SNP_15 located at nucleotide 51 of SEQ ID NO:29 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29. Thus, an example of a SNP marker suitable for determining the presence or absence of a reduced pyruvate-conferring QTL located on chromosome 2 between SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 and SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7 is SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21. SNP_11 located at nucleotide 51 of a sequence comprising 5% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity; SNP_12 located at nucleotide 51 of SEQ ID NO:23 or at a sequence comprising 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 a sequence comprising 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 a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_01 located at nucleotide 51 of SEQ ID NO:1 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:1; SNP_02 located at nucleotide 51 of SEQ ID NO:3 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:3; SNP_3 located at nucleotide 51 of SEQ ID NO: 5 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5; SNP_04 located at nucleotide 51 of SEQ ID NO: 7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7; and SNP_15 located at nucleotide 51 of SEQ ID NO: 29 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 29. Preferably, markers linked to specific SNP-reduced pyruvate-conferring QTLs located on chromosome 2 are SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21; SNP_12 located at nucleotide 51 of SEQ ID NO:23 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23;SNP_13 located at nucleotide 51 of SEQ ID NO:25 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 located at nucleotide 51 of SEQ ID NO:27 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_15 located at nucleotide 51 of SEQ ID NO:1 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:1; SNP_01 located at nucleotide 51 of a sequence comprising at least 97%, at least 98% or even at least 99% identity; SNP_02 located at nucleotide 51 of SEQ ID NO: 3 or at a sequence comprising at least 95% identity (more preferably at least 96%, at least 97%, at least 98% or even at least 99% identity to SEQ ID NO: 3); SNP_3 located at nucleotide 51 of SEQ ID NO: 5 or at a sequence comprising at least 95% identity (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) to SEQ ID NO: 5;and SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7. Thus, a specific example of a SNP marker suitable for determining the presence or absence of a reduced pyruvate-conferring QTL located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404 (preferably between SNP_11 located at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 and SNP_04 located at nucleotide 51 of SEQ ID NO:7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7) is SNP_11 located at nucleotide 51 of SEQ ID NO:23 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_12 located at nucleotide 51 of SEQ ID NO:23 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 located at nucleotide 51 of SEQ ID NO:25 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 located at nucleotide 51 of SEQ ID NO:27 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27;SNP_01 located at nucleotide 51 of SEQ ID NO: 1 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_02 located at nucleotide 51 of SEQ ID NO: 3 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_3 located at nucleotide 51 of SEQ ID NO: 5 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5; and SNP_04 located at nucleotide 51 of SEQ ID NO: 7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7. Thus, markers linked to SNPs located on chromosome 2 that confer reduced pyruvate QTL may be useful for determining the presence of QTLs that confer reduced pyruvate levels, where SNP_11 comprises an adenine sequence at nucleotide 51 of SEQ ID NO: 21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21; SNP_12 comprises a cytosine at nucleotide 51 of SEQ ID NO: 23 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 23; SNP_13 comprises an adenine sequence at nucleotide 51 of SEQ ID NO: 25 or at nucleotide 51 of SEQ ID NO: 26; SNP_14 comprises an adenine at nucleotide 51 of SEQ ID NO:27 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_01 comprises a thymine at nucleotide 51 of SEQ ID NO:1 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:1; SNP_02 comprises an adenine at nucleotide 51 of SEQ ID NO:1 SNP_03 comprises an adenine at nucleotide 51 of SEQ ID NO:3 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:3; SNP_03 comprises a cytosine at nucleotide 51 of SEQ ID NO:5 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:5; SNP_04 comprises a thymine at nucleotide 51 of SEQ ID NO:7 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7;and SNP_15 comprises a guanine at nucleotide 51 of SEQ ID NO:29 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29. Thus, preferably, SNP markers linked to reduced pyruvate-conferring QTL located on chromosome 2 may be useful for determining the presence of QTL conferring reduced pyruvate levels, with SNP_11 comprising an adenine at nucleotide 51 of SEQ ID NO:21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; and SNP_13 comprising a cytosine at nucleotide 51 of SEQ ID NO:25 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25. SNP_14 comprises an adenine at nucleotide 51 of SEQ ID NO:27 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_01 comprises a thymine at nucleotide 51 of SEQ ID NO:1 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:1; SNP_02 comprises an adenine at nucleotide 51 of SEQ ID NO:3 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:3;SNP_03 comprises a cytosine at nucleotide 51 of SEQ ID NO:5 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:5; and SNP_04 comprises a thymine at nucleotide 51 of SEQ ID NO:7 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7.

[0088] In the context of the present invention, different specific SNP markers have also been identified that are linked to a reduced pyruvate-conferring QTL located on chromosome 1. Markers linked to such SNP-reduced pyruvate-conferring QTL located on chromosome 1 include SNP_16 located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 located at nucleotide 51 of SEQ ID NO:33 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_05 located at nucleotide 51 of SEQ ID NO:9 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:9; SNP_06 located at nucleotide 51 of a sequence comprising at least 96%, at least 97%, at least 98% or even at least 99% identity; SNP_7 located at nucleotide 51 of SEQ ID NO: 12 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 15 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 35 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 37 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 37; SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39; and SNP_21 located at nucleotide 51 of SEQ ID NO: 41 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 51. Thus, between marker isotig32772_1413 and marker isotig33099_885 on chromosome 1 (preferably SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising 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_16 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising 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), Specific examples of SNP markers suitable for determining the presence or absence of reduced pyruvate-conferring QTLs located between SEQ ID NO: 31 and SNP_20 are SNP_16, located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; SNP_17, located at nucleotide 51 of SEQ ID NO: 33 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 33;SNP_05 located at nucleotide 51 of SEQ ID NO:9 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:9; SNP_06 located at nucleotide 51 of SEQ ID NO:11 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:11; SNP_7 located at nucleotide 51 of SEQ ID NO:12 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:13; SNP_8 located at nucleotide 51 of SEQ ID NO:15 or at least 95% (more preferably, at least 96%, at least 97% SNP_08 located at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 35; SNP_18 located at nucleotide 51 of SEQ ID NO: 35 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 35; SNP_19 located at nucleotide 51 of SEQ ID NO: 37 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 37; SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39;and SNP_21 located at nucleotide 51 of SEQ ID NO:41 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:41. Preferably, the SNP markers linked to the reduced pyruvate-conferring QTL located on chromosome 1 are: SNP_16 located at nucleotide 51 of SEQ ID NO:31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 located at nucleotide 51 of SEQ ID NO:33 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_05 located at nucleotide 51 of SEQ ID NO:9 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:9; Preferably, SNP_06 located at nucleotide 51 of a sequence comprising at least 96%, at least 97%, at least 98% or even at least 99% identity; SNP_7 located at nucleotide 51 of SEQ ID NO: 12 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 15 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 35 or at a sequence comprising 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 nucleotide 51 of SEQ ID NO: 37 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 37; SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39; and SNP_21 located at nucleotide 51 of SEQ ID NO: 41 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 41. Thus, a reduced pyruvate-conferring QT gene is located on chromosome 1 between SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31 and SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39. Specific examples of SNP markers suitable for determining the presence or absence of L are SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; SNP_17 located at nucleotide 51 of SEQ ID NO: 33 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 33;SNP_05 located at nucleotide 51 of SEQ ID NO:9 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:9; SNP_06 located at nucleotide 51 of SEQ ID NO:11 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:11; SNP_07 located at nucleotide 51 of SEQ ID NO:12 or at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:13. Preferably, SNP_7 located at nucleotide 51 of a sequence comprising at least 96%, at least 97%, at least 98% or even at least 99% identity; SNP_08 located at nucleotide 51 of SEQ ID NO: 15 or at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09 located at nucleotide 51 of SEQ ID NO: 35 or at least 95% (more preferably, at least 96%, at least 97%, at least 98% or; SNP_18 located at nucleotide 51 of SEQ ID NO:37 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:37; SNP_19 located at nucleotide 51 of SEQ ID NO:37 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:37; and SNP_20 located at nucleotide 51 of SEQ ID NO:39 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:39. Thus, SNP markers linked to reduced pyruvate-conferring QTLs located on chromosome 1 may be useful for determining the presence of QTLs conferring reduced pyruvate levels, such as SNP_16 comprising an adenine at nucleotide 51 of SEQ ID NO: 31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; SNP_17 comprising an adenine at nucleotide 51 of SEQ ID NO: 33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 33; SNP_05 comprising an adenine at nucleotide 51 of SEQ ID NO: 9 SNP_06 comprises a cytosine at nucleotide 51 of SEQ ID NO: 11 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 11; SNP_07 comprises a cytosine at nucleotide 51 of SEQ ID NO: 12 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 13;SNP_08 comprises a thymine at nucleotide 51 of SEQ ID NO: 15 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_18 comprises a thymine at nucleotide 51 of SEQ ID NO: 35 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 35; SNP_19 comprises a thymine at nucleotide 51 of SEQ ID NO: 37 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 37. SNP_20 comprises a thymine at nucleotide 51 of SEQ ID NO:39 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:39; SNP_21 comprises a cytosine at nucleotide 51 of SEQ ID NO:41 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:41. Thus, preferably, SNP markers linked to reduced pyruvate-conferring QTLs located on chromosome 1 may be useful for determining the presence of QTLs conferring reduced pyruvate levels, wherein SNP_16 comprises an adenine at nucleotide 51 of SEQ ID NO: 31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; SNP_17 comprises an adenine at nucleotide 51 of SEQ ID NO: 33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 33;SNP_05 comprises a cytosine at nucleotide 51 of SEQ ID NO:9 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:9; SNP_06 comprises an adenine at nucleotide 51 of SEQ ID NO:11 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:11; SNP_07 comprises a cytosine at nucleotide 51 of SEQ ID NO:12 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:13; SNP_08 comprises a cytosine at nucleotide 51 of SEQ ID NO:15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:15. SNP_18 comprises a thymine at nucleotide 51 of SEQ ID NO:35 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:35; SNP_19 comprises a thymine at nucleotide 51 of SEQ ID NO:37 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:37; and SNP_20 comprises a guanine at nucleotide 51 of SEQ ID NO:39 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:39;

[0089] In the context of the present invention, different specific SNP markers linked to a reduced pyruvate-conferring QTL located on chromosome 7 have also been identified. SNP markers linked to such reduced pyruvate-conferring QTL located on chromosome 7 include SNP_22, located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:43; SNP_23, located at nucleotide 51 of SEQ ID NO:45 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:45; SNP_24, located at nucleotide 51 of SEQ ID NO:47 or at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:47; Preferably, SNP_24 located at nucleotide 51 of a sequence comprising at least 96%, at least 97%, at least 98% or even at least 99% identity; SNP_25 located at nucleotide 51 of SEQ ID NO:49 or at a sequence comprising 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 located at nucleotide 51 of SEQ ID NO:17 or at a sequence comprising 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 located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:19. Thus, a specific example of a SNP marker suitable for determining the presence or absence of a reduced pyruvate-conferring QTL located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218 (preferably between SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43 and the distal end of chromosome 7 comprising SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19) is SNP_22 located at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:45; SNP_23 located at nucleotide 51 of SEQ ID NO:45 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:45; SNP_24 located at nucleotide 51 of SEQ ID NO:47 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:47; SNP_25 located at nucleotide 51 of SEQ ID NO:49 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49;SNP_09 located at nucleotide 51 of SEQ ID NO: 17 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; and SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19. Thus, SNP markers linked to reduced pyruvate-conferring QTLs located on chromosome 7 may be useful for determining the presence of QTLs conferring reduced pyruvate levels, with SNP_22 comprising a thymine at nucleotide 51 of SEQ ID NO:43 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:43; SNP_23 comprising a thymine at nucleotide 51 of SEQ ID NO:45 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:45; SNP_24 comprising a thymine at nucleotide 51 of SEQ ID NO:47 SNP_25 comprises a cytosine at nucleotide 51 of SEQ ID NO:49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49; SNP_25 comprises a guanine at nucleotide 51 of SEQ ID NO:49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49; SNP_09 comprises a thymine at nucleotide 51 of SEQ ID NO:17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:17;and SNP_10 comprises a guanine at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19;

[0090] The marker according to the invention is preferably linked to a QTL conferring reduced pyruvate, located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404 (preferably between SNP_11 located at nucleotide 51 of SEQ ID NO: 21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21 and SNP_04 located at nucleotide 51 of SEQ ID NO: 7 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7). a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between marker isotig32772_1413 and marker isotig33099_885 (preferably between SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31 and SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39);and markers linked to a QTL conferring reduced pyruvate located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218 (preferably between SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43 and the distal end of chromosome 7 comprising SNP_10 located at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19), which are therefore particularly useful for determining the presence or absence of one or more QTL conferring reduced pyruvate levels in onion plants or plant parts;

[0091] Thus, the present invention provides SNP_01, which comprises a thymine at nucleotide 51 of SEQ ID NO: 1 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; SNP_02, which comprises an adenine at nucleotide 51 of SEQ ID NO: 3 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_03, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 5 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5; SNP_04, which comprises a cytosine at nucleotide 51 of SEQ ID NO: 7 on chromosome 2 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7 on chromosome 2; SNP_04 comprising a thymine at nucleotide 51 of a sequence comprising at least 97%, at least 98%, or even at least 99% identity; SNP_05 comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 9; SNP_06 comprising an adenine at nucleotide 51 of SEQ ID NO: 11 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 11; SNP_07 comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 13;SNP_08 on chromosome 1, comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09 on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_10 on chromosome 7, comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; SNP_11 on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO: 21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21; SNP_11 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23 on chromosome 2; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 comprising an adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27;SNP_15 on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO:29 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_18 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:35 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:35; SNP_18 comprising a thymine at nucleotide 51 of a sequence comprising at least 7%, at least 98%, or even at least 99% identity; SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 39; SNP_21 comprising a cytosine at nucleotide 51 of SEQ ID NO: 41 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 41;SNP_22 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 47 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47. and SNP_25 on chromosome 7 comprising a guanine at nucleotide 51 of SEQ ID NO:49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:49.

[0092] Methods for identifying and / or selecting plants or plant parts The present invention provides a method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence, in said plant or plant part, of one or more markers as described herein. Thus, the present invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence in said plant or plant part of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, said markers being selected from the group consisting of: a marker linked to a QTL conferring reduced pyruvate, located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404; a marker linked to a QTL conferring reduced pyruvate, located on chromosome 1 between marker isotig32772_1413 and marker isotig33099_885; and a marker linked to a QTL conferring reduced pyruvate, located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218.

[0093] The method for identifying and / or selecting onion plants or plant parts of the present invention is particularly useful 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. Thus, 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, in said plant or plant part, of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, wherein the one or more QTLs conferring reduced pyruvate levels are present in the plant whose seeds have been deposited under accession number PTA-9053, the plant whose seeds have been deposited under accession number PTA9054 or the plant whose seeds have been deposited under accession number PTA-9055. Thus, in one embodiment, the present invention provides a method for identifying and / or selecting an onion plant or plant part, the method comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in said plant or plant part, which onion plant or plant part is obtainable by crossing the plant whose seeds are deposited under accession number PTA-9053, the plant whose seeds are deposited under accession number PTA-9054 or the plant whose seeds are deposited under accession number PTA-9055 with another onion plant. wherein the markers are selected from the group consisting of a marker linked to a QTL conferring reduced pyruvate located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404; a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between marker isotig32772_1413 and marker isotig33099_885; and a marker linked to a QTL conferring reduced pyruvate located on chromosome 7 between marker isotig28625_2789 and marker isotig41937_218.

[0094] Preferably, the present invention provides a method for identifying and / or selecting onion plants or plant parts, comprising determining the presence or absence in said plant or plant part of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in onion plants or plant parts, said markers being SNP_11 located on chromosome 2 at nucleotide 51 of SEQ ID NO:21 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 and SNP_11 located on chromosome 2 at nucleotide 51 of SEQ ID NO:7 or at a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7. a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between SNP_04 located at nucleotide 51 of SEQ ID NO: 31 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; a marker linked to a QTL conferring reduced pyruvate located on chromosome 1 between SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31 and SNP_20 located at nucleotide 51 of SEQ ID NO: 39 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39;and a marker linked to a reduced pyruvate-conferring QTL located on chromosome 7 between SNP_22 located at nucleotide 51 of SEQ ID NO:43 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:43 and the distal end of chromosome 7 comprising SNP_10 located at nucleotide 51 of SEQ ID NO:19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:19;

[0095] Preferably, the method comprises screening at the DNA, RNA (or cDNA) or protein level using known methods to detect the presence or absence of one or more QTLs that confer reduced pyruvate levels in an onion plant or plants as described herein. Many methods exist for detecting the presence or absence of reduced pungency alleles of the present invention.

[0096] For example, there may be a single nucleotide polymorphism (SNP) between the wild-type allele and the reduced-pungency allele, and an SNP genotyping assay can be used to detect whether a plant, plant part, or cell contains one or more wild-type (high-pungency) or reduced-pungency nucleotides in its genome. For example, one or more SNPs can be easily detected using a KASP assay, for example, by selecting 50 base pairs upstream and 50 base pairs downstream of the SNP and designing two allele-specific forward primers and one allele-specific reverse primer; for details of the KASP assay, see, for example, Allen et al. (2011) Plant Biotechnology J 9, 1086-1099, especially pp. 1097-1098.

[0097] Equivalently, other genotyping assays can be used, such as TaqMan SNP genotyping assays, high sensitivity melting (HRM) assays, SNP genotyping arrays (e.g., Fluidigm, Illumina, etc.), or DNA sequencing.

[0098] Molecular markers can also be used to aid in the identification of plants (or plant parts or nucleic acids derived therefrom) containing a reduced-pungency allele. For example, one or more suitable molecular markers can be developed that are closely genetically linked (and preferably also physically linked) to the reduced-pungency allele. Most preferably, the causative genetic mutation is used as the molecular marker used to identify plants (or plant parts or nucleic acids derived therefrom) containing a reduced-pungency allele. Suitable molecular markers can be developed by crossing an onion plant having the reduced-pungency trait with a wild-type plant and developing a segregating population (e.g., an F2 or backcross population) from the cross. This segregating population can then be phenotyped for a reduced pungency phenotype and genotyped, for example, using molecular markers such as SNPs (single nucleotide polymorphisms), AFLPs (amplified fragment length polymorphisms; see, e.g., EP 534858), or others, and software analysis can identify molecular markers that cosegregate with the reduced pungency trait in the segregating population, and as further described herein, the order and genetic distance (centimorgan distance, cM) between a reduced pyruvate-conferring QTL located on chromosome 2, a reduced pyruvate-conferring QTL located on chromosome 1, and a reduced pyruvate-conferring QTL located on chromosome 7 can be determined. Molecular markers that are closely linked to one of the reduced pyruvate-conferring QTLs described herein, for example, within a distance of 5 cM, can then be used to detect and / or select plants or plant parts that comprise or carry (e.g., in an introgression fragment) a reduced pungency allele. Such closely linked molecular markers can replace (or be used in addition to) phenotypic selection in breeding programs, i.e., marker-assisted selection (MAS). 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 of the QTLs that confer reduced pyruvate levels in onion plants or plant parts as described herein.

[0099] As described herein, different specific SNP markers linked to different reduced pyruvate-conferring QTLs have been identified, with one reduced pyruvate-conferring QTL located on chromosome 2, one reduced pyruvate-conferring QTL located on chromosome 1, and one reduced pyruvate-conferring QTL located on chromosome 7. Thus, the method of the invention for identifying and / or selecting an onion plant or plant part comprises identifying onion plants or plant parts on said plant or plant part SNP_01 comprising a thymine at nucleotide 51 of SEQ ID NO: 1 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1 on chromosome 2; SNP_02 comprising an adenine at nucleotide 51 of SEQ ID NO: 3 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3 on chromosome 2; SNP_03 comprising an adenine at nucleotide 51 of SEQ ID NO: 5 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5 on chromosome 2. SNP_03 comprising a cytosine at nucleotide 51 of the sequence; SNP_04 comprising a thymine at nucleotide 51 of SEQ ID NO: 7 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 7; SNP_05 comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 9; SNP_06 comprising an adenine at nucleotide 51 of SEQ ID NO: 11 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 11;SNP_07, on chromosome 1, comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 13; SNP_08, on chromosome 1, comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09, on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_09, on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 19 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; SNP_10 comprising a guanine at nucleotide 51 of SEQ ID NO:21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 on chromosome 2; SNP_11 comprising an adenine at nucleotide 51 of SEQ ID NO:21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21 on chromosome 2; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23 on chromosome 2; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25 on chromosome 2;SNP_14, which comprises an adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27; SNP_15, which comprises a guanine at nucleotide 51 of SEQ ID NO:29 on chromosome 2 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16, which comprises an adenine at nucleotide 51 of SEQ ID NO:31 on chromosome 1 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17, which comprises an adenine at nucleotide 51 of SEQ ID NO:33 on chromosome 1 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33 on chromosome 1 SNP_17 comprising an adenine at nucleotide 51 of a sequence comprising at least 7%, at least 98%, or even at least 99% identity; SNP_18 comprising a thymine at nucleotide 51 of SEQ ID NO: 35 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 35; SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 39;SNP_21 on chromosome 1 comprising a cytosine at nucleotide 51 of SEQ ID NO: 41 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 41; SNP_22 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 47 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47. SNP_24 comprising a cytosine at nucleotide 51 of SEQ ID NO: 49 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 49 on chromosome 7; SNP_25 comprising a guanine at nucleotide 51 of SEQ ID NO: 49 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 49 on chromosome 2; isotig30225_1454 comprising a cytosine at nucleotide 61 of SEQ ID NO: 51 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 51 on chromosome 2; isotig32865_1404 comprising a guanine at nucleotide 61 of SEQ ID NO: 53 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 53 on chromosome 2;isotig32772_1413 of chromosome 1, comprising a guanine at nucleotide 61 of SEQ ID NO: 55 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 55; isotig33099_885 of chromosome 1, comprising a thymine at nucleotide 61 of SEQ ID NO: 57 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 57; and isotig41937_218 of chromosome 7, comprising a guanine at nucleotide 61 of SEQ ID NO: 61 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 61;

[0100] The method of the invention for identifying and / or selecting onion plants or plant parts preferably comprises identifying onion plants or plant parts on said plants or plant parts SNP_01 comprising a thymine at nucleotide 51 of SEQ ID NO: 1 or of a sequence comprising 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 on chromosome 2; SNP_02 comprising an adenine at nucleotide 51 of SEQ ID NO: 3 or of a sequence comprising 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 on chromosome 2; SNP_03 comprising a cytosine at nucleotide 51 of SEQ ID NO: 5 or of a sequence comprising 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 on chromosome 2; SNP_04 comprising a cytosine at nucleotide 51 of SEQ ID NO: 7 or of a sequence comprising 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 on chromosome 2. SNP_04, comprising a thymine at nucleotide 51 of a sequence comprising at least 5% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity; SNP_05, comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 of chromosome 1 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 9; SNP_06, comprising a cytosine at nucleotide 51 of SEQ ID NO: 11 of chromosome 1 SNP_06, comprising an adenine at nucleotide 51 of SEQ ID NO: 1 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 11; SNP_07, comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 13, on chromosome 1;SNP_08, on chromosome 1, comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_09, on chromosome 7, comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_10, on chromosome 7, comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; SNP_11, on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO: 21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 21. SNP_11 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23 on chromosome 2; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 comprising an adenine at nucleotide 51 of SEQ ID NO:27 on chromosome 2 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27;SNP_15 on chromosome 2, comprising a guanine at nucleotide 51 of SEQ ID NO:29 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:31; SNP_17 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:33; SNP_18 on chromosome 1, comprising an adenine at nucleotide 51 of SEQ ID NO:35 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:35; SNP_18 comprising a thymine at nucleotide 51 of a sequence comprising at least 7%, at least 98%, or even at least 99% identity; SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 39; SNP_21 comprising a cytosine at nucleotide 51 of SEQ ID NO: 41 on chromosome 1 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even at least 99%) identity to SEQ ID NO: 41;SNP_22 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 on chromosome 7 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 on chromosome 7 comprising a cytosine at nucleotide 51 of SEQ ID NO: 47 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47; SNP_25 on chromosome 7 comprising a cytosine at nucleotide 51 of SEQ ID NO: 49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 49. SNP_25 on chromosome 2, comprising a guanine at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 51; isotig30225_1454 on chromosome 2, comprising a cytosine at nucleotide 61 of SEQ ID NO: 53 on chromosome 2, or a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 53; or isotig32865_1404, which comprises a guanine at nucleotide 61 of a sequence comprising at least 96%, at least 97%, at least 98% or even at least 99% identity; isotig32772_1413 of chromosome 1, which comprises a guanine at nucleotide 61 of SEQ ID NO: 55 or of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 55;isotig33099_885, comprising a thymine at nucleotide 61 of SEQ ID NO: 57 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 57, from chromosome 1; isotig33099_885, comprising a thymine at nucleotide 61 of SEQ ID NO: 59 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 59, from chromosome 7 and isotig41937_218 of chromosome 7, comprising a guanine at nucleotide 61 of SEQ ID NO: 61 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 61;

[0101] Preferably, the markers used in the method according to the invention are fragment length polymorphism (RFLP) markers, cleaved amplified polymorphic sequence (CPAS) markers, microsatellite markers, restriction fragment length polymorphism (RFLP) markers, random amplified polymorphic DNA (RAPD) markers, amplified fragment length polymorphism (AFLP) markers or single nucleotide polymorphism (SNP) markers, preferably SNP markers.

[0102] Preferably, the markers linked to a QTL located on chromosome 2 used in the method according to the invention are SNP_11 comprising an adenine at nucleotide 51 of SEQ ID NO:21 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:21; SNP_12 comprising a cytosine at nucleotide 51 of SEQ ID NO:23 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 of SEQ ID NO:25 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:25; SNP_14 comprising a thymine at nucleotide 51 of SEQ ID NO:27 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:27. SNP_14 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity; SNP_01 comprising a thymine at nucleotide 51 of SEQ ID NO: 1 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 01; SNP_02 comprising an adenine at nucleotide 51 of SEQ ID NO: 3 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 3; SNP_03 comprising a cytosine at nucleotide 51 of SEQ ID NO: 5 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5;SNP_04 comprising a thymine at nucleotide 51 of SEQ ID NO:7 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:7; SNP_15 comprising a guanine at nucleotide 51 of SEQ ID NO:29 or at a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO:29; SNP_16 comprising a guanine at nucleotide 61 of SEQ ID NO:51 or at nucleotide 61 of SEQ ID NO:5 isotig30225_1454 comprising a cytosine at nucleotide 61 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 1; and isotig32865_1404 comprising a guanine at nucleotide 61 of SEQ ID NO: 53 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 53;

[0103] Preferably, the markers linked to the reduced pyruvate-conferring QTL located on chromosome 1 used in the method according to the invention are SNP_16 comprising an adenine at nucleotide 51 of SEQ ID NO: 31 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 31; SNP_17 comprising an adenine at nucleotide 51 of SEQ ID NO: 33 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 33; SNP_05 comprising a cytosine at nucleotide 51 of SEQ ID NO: 9 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 9; SNP_06 comprising an adenine at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to nucleotide 51 of SEQ ID NO: 12 or to SEQ ID NO: 13; SNP_07 comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 or to a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 13; SNP_08 comprising a thymine at nucleotide 51 of SEQ ID NO: 15 or to a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 15; SNP_18 comprising a thymine at nucleotide 51 of SEQ ID NO: 35 or to a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 35;SNP_19 comprising a thymine at nucleotide 51 of SEQ ID NO: 37 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 37; SNP_20 comprising a guanine at nucleotide 51 of SEQ ID NO: 39 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 39; SNP_31 comprising a guanine at nucleotide 51 of SEQ ID NO: 41 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 41. isotig32772_1413 comprising a guanine at nucleotide 61 of SEQ ID NO: 55 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 55; and isotig33099_885 comprising a thymine at nucleotide 61 of SEQ ID NO: 57 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 57;

[0104] Preferably, the markers linked to the reduced pyruvate-conferring QTL located on chromosome 7 used in the method according to the invention are SNP_22 comprising a thymine at nucleotide 51 of SEQ ID NO: 43 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 43; SNP_23 comprising a thymine at nucleotide 51 of SEQ ID NO: 45 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 45; SNP_24 comprising a cytosine at nucleotide 51 of SEQ ID NO: 47 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 47; SNP_25 comprising a cytosine at nucleotide 51 of SEQ ID NO: 49 or of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 49; SNP_25 comprising a guanine at nucleotide 51 of SEQ ID NO: 17 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; SNP_09 comprising a thymine at nucleotide 51 of SEQ ID NO: 17 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 17; and SNP_10 comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19; isotig28625_2789 comprising a guanine at nucleotide 61 of SEQ ID NO: 59 or a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 59;and isotig41937_218 comprising a guanine at nucleotide 61 of SEQ ID NO: 61 or of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 61;

[0105] Preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts comprises determining the presence or absence of two or more markers in said plant or plant part. Thus, the method according to the invention for identifying and / or selecting onion plants or plant parts may comprise determining the presence or absence in said plant or plant part 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 and at least one (e.g. at least two, three, four or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 1. The method according to the invention for identifying and / or selecting onion plants or plant parts may also comprise determining the presence or absence in said plant or plant part 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 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. The method according to the invention for identifying and / or selecting onion plants or plant parts may also comprise determining the presence or absence in said plant or plant part of at least one (e.g. at least two, three, four or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 1 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.Even more preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts also comprises determining the presence or absence in said plant or plant part 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, at least one (e.g. at least two, three, four or four) marker linked to a QTL conferring reduced pyruvate located on chromosome 1 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.

[0106] Preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts comprises determining the presence or absence in said plant or plant part of markers linked to at least one QTL conferring reduced pyruvate located on chromosome 2, markers linked to at least one QTL conferring reduced pyruvate located on chromosome 1 and markers linked to at least one QTL conferring reduced pyruvate located on chromosome 7.

[0107] Preferably, the method according to the invention for identifying and / or selecting onion plants or plant parts comprises determining the presence or absence in said plant or plant part of one or more (e.g. two or three) peak markers, preferably one or more (e.g. two or three) peak markers as set out in Table 2. As used herein, the term "peak marker" refers to a marker that has been found to be as accurate as possible, preferably with a false positive and / or false negative rate of 0%.

[0108] Thus, a marker linked to a QTL conferring reduced pyruvate located on chromosome 2 is preferably SNP_03, comprising a cytosine at nucleotide 51 of SEQ ID NO: 5 or at nucleotide 51 of a sequence comprising at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5. A marker linked to a QTL conferring reduced pyruvate located on chromosome 1 is preferably SNP_07, comprising a cytosine at nucleotide 51 of SEQ ID NO: 12 or at least 95% (more preferably, at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 13. The marker linked to the reduced pyruvate-conferring QTL located on chromosome 7 is preferably SNP_10 comprising a guanine at nucleotide 51 of SEQ ID NO: 19 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 19.

[0109] Thus, the method according to the invention for identifying and / or selecting onion plants or plant parts preferably comprises the step of: identifying onion plants or plant parts by locating in said plants or plant parts at least one (e.g. at least two, three, four or four) markers linked to a QTL conferring reduced pyruvate located on chromosome 2 (this marker on chromosome 2 is SNP_03 comprising a cytosine at nucleotide 51 of SEQ ID NO: 5 or at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5); at least one (e.g. at least two, three, four or four) markers linked to a QTL conferring reduced pyruvate located on chromosome 1 (this marker on chromosome 1 is SNP_03 comprising a cytosine at nucleotide 51 of SEQ ID NO: 5 or at least 95% (more preferably at least 96%, at least 97%, at least 98% or even at least 99%) identity to SEQ ID NO: 5); and determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduced pyruvate-conferring QTL located on chromosome 7 (the marker on chromosome 7 is SNP_10, which is SNP_10, which is SNP_19, which ...

[0110] Nucleic acids and their uses The present invention further relates to SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:15; SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:17. SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:21; SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:27; SEQ ID NO:29 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:29; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:33;An isolated nucleic acid is provided which comprises a nucleotide sequence selected from the group consisting of SEQ ID NO:35 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:35; SEQ ID NO:37 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:37; SEQ ID NO:39 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:39; SEQ ID NO:41 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:41; SEQ ID NO:43 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:43; SEQ ID NO:45 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:45; SEQ ID NO:47 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:47; and SEQ ID NO:49 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:49, or a complementary nucleotide sequence thereof. The present invention preferably provides SEQ ID NO:1 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:1; SEQ ID NO:3 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:3; SEQ ID NO:5 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:5; SEQ ID NO:7 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:7; SEQ ID NO:9 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:9; SEQ ID NO:11 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:11; SEQ ID NO:13 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:13; SEQ ID NO:15 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:15;SEQ ID NO:17 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:17; SEQ ID NO:19 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:19; SEQ ID NO:21 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:21; SEQ ID NO:23 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:23; SEQ ID NO:25 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:25; SEQ ID NO:27 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:27; SEQ ID NO:31 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:31; SEQ ID NO:33 or a fragment thereof consisting of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO:33; SEQ ID NO:3 or a complementary nucleotide sequence thereof; or an isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 35 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 35; SEQ ID NO: 37 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 37; SEQ ID NO: 39 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 39; SEQ ID NO: 43 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 43; SEQ ID NO: 45 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 45; SEQ ID NO: 47 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 47; and SEQ ID NO: 49 or a fragment thereof of at least 15 nucleotides comprising nucleotide 51 of SEQ ID NO: 49; or a complementary nucleotide sequence thereof.

[0111] Thus, an isolated nucleic acid as provided herein comprises at least 15 nucleotides comprising nucleotide 51 of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1-50. Additionally, an isolated nucleic acid as provided herein comprises a complementary sequence of the isolated nucleic acid comprising at least 15 nucleotides comprising nucleotide 51 of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1-50. This means that an isolated nucleic acid as provided herein comprises a fragment of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1-50 of at least 15 contiguous nucleotides, said fragment further comprising nucleotide 51 of said nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-50 or their complementary nucleotide sequence. Preferably, the isolated nucleic acid of the present invention comprises more than 15 nucleotides comprising nucleotide 51 of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 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, 90, 95 or 100 nucleotides comprising nucleotide 51 of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1-50, or their complementary nucleotide sequences.

[0112] The nucleic acids according to the invention are particularly useful for use in or the development of methods for identifying and / or selecting onion plants or plant parts, and also for methods for producing onion plants comprising crossing a first onion plant with a second onion plant and selecting from the progeny of said cross on the basis of the presence or absence of one or more markers of the invention. Thus, the present invention provides the use of one or more of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 to 50, preferably SEQ ID NOs: 1 to 50, or fragments thereof, for marker-assisted selection of onion plants or plant parts, said fragments consisting of at least 15 nucleotides comprising nucleotide 51 of said nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50 or one or more complementary sequences of said nucleotide sequences. Furthermore, the present invention provides the use of one or more nucleotide sequences selected from the group consisting of SEQ ID NOs: 51 to 62, preferably SEQ ID NOs: 51 to 62, or fragments thereof, wherein said fragments consist of at least 15 nucleotides comprising nucleotide 61 of said nucleotide sequences selected from the group consisting of SEQ ID NOs: 51 to 62 or one or more complementary sequences of said nucleotide sequences, for marker-assisted selection of onion plants or plant parts.Preferably, the nucleotide sequence used in the present invention is, for example, more than 15 nucleotides comprising any one nucleotide 51 of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50, each of which comprises more than 15 nucleotides comprising any one nucleotide 61 of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 51 to 62, for example, any one nucleotide 61 of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 51 to 62, or a complementary sequence of said nucleotide sequence. 51 of any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1-50, comprising 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 as described herein.

[0113] Seed deposit A representative sample of seeds comprising a QTL conferring reduced pyruvate levels as described herein was deposited with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209, USA) on March 13, 2008, by Nunhems BV in accordance with the Budapest Treaty under Expert Solutions (EPC 2000 Rule 32(1)). The seeds were given the following deposit numbers: PTA-9053 (seeds of line I37853B as further described in WO2009 / 092560A1), PTA-9054 (seeds of line I37554A as further described in WO2009 / 092560A1) and PTA-9055 (seeds of line I37554B as further described in WO2009 / 092560A1).

[0114] The applicant requests that samples of the biological material and any material derived therefrom be made available only to designated experts in accordance with Rule 32(1) EPC or the relevant legislation or treaties of any country with similar rules or legislation until the mention of the grant of the patent, or for a period of 20 years from the filing date if the application is refused, withdrawn or deemed to be withdrawn.

[0115] During the pendency of this application, access to the deposit will be made available to any person determined by the Commissioner of Patents to be entitled thereto upon request. Pursuant to 37 C.FR § 1.808(b), all restrictions imposed by the depositor on the availability to the public of the deposited material will be irrevocably removed upon the granting of a patent. The deposit will be maintained for 30 years, or for 5 years from the latest request, or for the enforceable life of the patent, whichever is longer, and will be replaced if it becomes unviable during that period. Applicant does not waive any rights granted under this application or this patent under the Plant Variety Protection Act (7 U.S.C. 2321 et seq.). [Example]

[0116] Example 1 QTL mapping A single low-pungency (reduced pungency) line, I37720B, derived from a cross between I37554B and material in the I37554B pedigree, was crossed with two pungency inbred lines, I37977B ("Population 1") and I37545-7 ("Population 2"). The resulting F1 hybrid was self-pollinated to produce two segregating populations of F2 plants. A total of 331 F2 plants were grown in Population 1, and a total of 236 plants were grown in Population 2 under field conditions in Brooks, OR. Leaf tissue was collected from each F2 plant for DNA extraction. Bulbs were harvested and stored for 4 months, after which pyruvate levels were measured.

[0117] A panel of 283 KASP markers was applied to DNA extracted from each F2 individual. Monomorphic markers were discarded, and genetic linkage maps were calculated independently for each population using the mapping function in the Kosambi package in JoinMap software. The resulting maps were used in conjunction with pyruvate measurements to identify quantitative trait loci (QTLs) using the interval mapping method in the MapQTL software package. A threshold LoD score for significant association between loci and pyruvate concentration was set using a genome-wide permutation test with 200 iterations of 1,000 permutations and a cumulative count of at least 0.95 for each population.

[0118] In population 1, two significant QTLs above 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 in the integrated genetic linkage map, and additional flanking markers were added to the F2 population map. The number of additional markers added is detailed in Table 1. Information on the peak marker and flanking markers for each significant QTL is shown in Table 2.

[0119] After integrating additional markers, the peak marker for the QTL on linkage group 3 (chromosome 2) explained 5.6% of the variation in pyruvate values, the peak marker for the QTL on linkage group 4 (chromosome 1) explained 45.6% of the variation, and the peak marker for the QTL on linkage group 6 (chromosome 7) explained 6.5% of the variation in pyruvate values.

[0120] [Table 1]

[0121] [Table 2]

[0122] [Table 3]

[0123] Furthermore, the QTL of the present invention was located on public genetic maps of onion. All public markers referenced herein are detailed in Duangjit et al. (2013) Theor Appl Genet 126, 2093-2101. The referenced "B9885 × B8667" map is detailed in Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72, and the referenced "Char × B5351" map is detailed in Havey (2000) J. Amer. Soc. Hort. Sci., 145(2), 110-119. The QTL of the present invention was located on these public maps by integrating internal datasets with public marker information, and the low-pungency line I37720B was genotyped with the public markers to determine alleles linked to the pyruvate-reducing locus. Publicly available markers that further define the locus of the QTL of the present invention are set forth in Table 4, provided herein below.

[0124] [Table 4]

[0125] [Table 5]

[0126] Therefore, it can be concluded that the QTL conferring reduced pyruvate, located on chromosome 2, is located between public marker isotig30225_1454 (SEQ ID NO: 51) and public marker isotig32865_1404 (SEQ ID NO: 53), which corresponds to an interval of 19.4 cM. The QTL conferring reduced pyruvate, located on chromosome 1, is located between public marker isotig32772_1413 (SEQ ID NO: 55) and public marker isotig33099_885 (SEQ ID NO: 57), which corresponds to an interval of 14.5 cM. The QTL conferring reduced pyruvate is located on chromosome 7, between public marker isotig28625_2789 (SEQ ID NO: 59) and public marker isotig41937_218 (SEQ ID NO: 61), which corresponds to an interval of 11.2 cM.

[0127] Additionally, previously detailed markers were placed on the individual published maps, and because we did not have access to segregants for these maps to calculate precise genetic distances, they were placed at intervals based on the published maps.

[0128] [Table 6]

[0129] Example 2 QTL marker validation To confirm the usefulness of the identified markers for predicting pyruvate levels, we genotyped a panel of lines across a range of pyruvate values: five bulbs from each line were genotyped, and pyruvate concentrations were assigned based on the average of the bulbs from that line.

[0130] Pyruvate measurements were performed on bulbs after 4 months of storage. 5-10 mm thick slices were prepared from the equator of onion bulbs (25-50 g). These slices were divided into quarters, mixed with deionized water (1:10 dilution), and homogenized in an immersion blender until no clumps remained (approximately 45 seconds). One mL of onion juice was centrifuged for 5 minutes at 16,000 x g at room temperature. The supernatant was used for pyruvate measurements, which were performed using the method of Anthon and Barrett (2003) with slight modifications. Six 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 minutes and then mixed with 50 mL of 1.5 N sodium hydroxide (NaOH). After the mixture was cooled to room temperature, the absorbance was read at 515 nm. Pyruvate analysis was performed in triplicate for each sample. A calibration curve was constructed using 0.4, 0.8, and 1.2 mM pyruvate standard solutions. Results are reported in μmol pyruvate per gram of tissue fresh weight (μmol / g).

[0131] The results of this validation confirmed that the reduced pungency haplotype (referred to as the "B" allele) was enriched in the reduced pungency lines, and that lines with lower mean pyruvate values ​​and less variability in pyruvate levels had a lower abundance of the high pyruvate ("A") allele (Table 7). For all reduced pungency materials, soluble solids content (SSC), as measured by Brix, was greater than 7% and was not correlated with pyruvate level (R 2 =0.2 negative slope).

[0132] The linkage groups, as described herein above, were mapped to known markers to determine which chromosome number each linkage group corresponds to. Thus, linkage group 3 was found to correspond to onion chromosome 2, linkage group 4 to onion chromosome 1, and linkage group 6 to onion chromosome 7.

[0133] [Table 7] JPEG0007801218000008.jpg246156

[0134] JPEG0007801218000009.jpg209149

Claims

1. 1. A method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence, in said plant or plant part, of one or more markers suitable for determining the presence of one or more QTLs conferring reduced pyruvate levels in the onion plant or plant part, said markers comprising: a marker linked to a QTL conferring reduced pyruvate located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404; the QTL is present in the plant whose seeds are deposited under accession number PTA-9053, the plant whose seeds are deposited under accession number PTA-9054, or the plant whose seeds are deposited under accession number PTA-9055; and A marker linked to the QTL conferring reduced pyruvate located on chromosome 2 is SNP_11 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:21; SNP_12 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:23; SNP_13 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:25; SNP_14 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:27; SNP_01 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:1; SNP_02 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:3; SNP_03 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:5; SNP_04 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:7; and SNP_15 comprising a guanine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:29 The method of claim 1, wherein the SNP marker is selected from the group consisting of:

2. determining the presence or absence in said plant or plant part of at least one marker linked to a QTL located on chromosome 2 conferring reduced pyruvate, at least one marker linked to a QTL located on chromosome 1 conferring reduced pyruvate, and at least one marker linked to a QTL located on chromosome 7 conferring reduced pyruvate; the marker linked to the QTL for conferring reduced pyruvate located on chromosome 1 is a marker between marker isotig32772_1413 and marker isotig33099_885; and the marker linked to the QTL for conferring reduced pyruvate located on chromosome 7 is a marker between marker isotig28625_2789 and marker isotig41937_218; the QTL is present in the plant whose seeds are deposited under accession number PTA-9053, the plant whose seeds are deposited under accession number PTA-9054, or the plant whose seeds are deposited under accession number PTA-9055; A marker linked to the QTL conferring reduced pyruvate located on chromosome 1 is SNP_16 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:31; SNP_17 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:33; SNP_05 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:9; SNP_06 comprising an adenine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO: 11; SNP_07 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO: 13; SNP_08 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO: 15; SNP_18 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:35; SNP_19 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:37; SNP_20 comprising a guanine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:39; SNP_21 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:41; isotig32772_1413 comprising a guanine at nucleotide 61 in the nucleotide sequence set forth in SEQ ID NO: 55; and isotig33099_885 comprising a thymine at nucleotide 61 in the nucleotide sequence set forth in SEQ ID NO: 57; and Markers linked to the QTL conferring reduced pyruvate located on chromosome 7 are: SNP_22 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:43; SNP_23 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:45; SNP_24 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:47; SNP_25 comprising a guanine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:49; SNP_09 comprising a thymine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO: 17; and SNP_10 comprising a guanine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO: 19; The method of claim 1, wherein the SNP marker is selected from the group consisting of:

3. 3. The method of claim 2, wherein the marker on chromosome 2 is SNP_03 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:5; the marker on chromosome 1 is SNP_07 comprising a cytosine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:13; and the marker on chromosome 7 is SNP_10 comprising a guanine at nucleotide 51 in the nucleotide sequence set forth in SEQ ID NO:

19.

4. 1. Use of one or more of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 to 8 and 21 to 30, or fragments thereof, or a complementary sequence to one or more of said nucleotide sequences, for marker-assisted selection of onion plants or plant parts having reduced pyruvate levels, comprising: The fragment consists of at least 15 nucleotides, including nucleotide 51 of the nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-8 and 21-30.

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