Molecular markers for reduced pirubate level traits in onions

Abstract

This invention provides a method for identifying and / or selecting onion plants or plant parts. [Solution] The present invention relates to a genetic marker for determining the presence or absence of one or more QTLs that confer reduced pirubate levels in an onion plant or plant part, wherein the marker is selected from the group consisting of a marker located on chromosome 2 and linked to a reduced pirubate-contributing QTL, a marker located on chromosome 1 and linked to a reduced pirubate-contributing QTL, and a marker located on chromosome 7 and linked to a reduced pirubate-contributing QTL. Furthermore, the present invention relates to the use of the marker of the present invention for determining the presence or absence of one or more QTLs that confer reduced pirubate levels in an onion plant or plant part. The present invention further relates to a method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence of one or more markers of the present invention in the plant or plant part.

Description

Technical Field

[0001] Field of Invention The present invention relates to the field of plant breeding. There are provided genetic markers for determining the presence or absence of one or more quantitative trait loci (QTLs) that confer reduced pyruvate levels in onion (Allium cepa) plants or plant parts, said markers being markers linked to a reduced pyruvate-conferring QTL located on chromosome 2, markers linked to a reduced pyruvate-conferring QTL located on chromosome 1, and markers linked to a reduced pyruvate-conferring QTL located on chromosome 7, and being selected from the group consisting of. 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 QTLs that confer reduced pyruvate levels in onion plants or plant parts. The present invention further relates to a method 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 an isolated nucleic acid for marker-assisted selection of onion plants or plant parts, and to the use of nucleotide sequences as provided herein.

Background Art

[0002] background Onion plants are thought to originate in western or central Asia. In Europe, onions have been known since the Bronze Age. The bulbs of onion plants, i.e., "onions", are used in many dishes and are well-known for being very healthy. Plant breeding has focused on yield, appearance, harvestability, storage, flavor, and the content of several compounds in onions that have health-beneficial effects. Some of these compounds are most effective when onions are eaten raw, and their concentrations are often related to the solid content of the onions. Onions with a high solid content that are mild and sweet enough to be consumed without cooking deliver more health-promoting compounds from the diet.

[0003] The typical onion flavor or taste is the pungency produced by the conversion of the sulfur-containing flavor precursor, alcu(en)yl-L-cysteine-sulfoxide (ACSO), to a thiosulfonate by the enzyme alliinase when onion cells are cut or damaged. Pirvate, or pyruvate, a byproduct of this enzymatic process, is measured as an indicator of pungency (Schwimmer and Weston 1961, J. of Agric. Food Chem. 9: 301-4). The amount of pirubate produced is directly related to 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 less pungent and sweeter. Pungency masks the sweetness of sugars present in onions as water-soluble solids or carbohydrates. 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 it also has distinct genetic components, as shown by Lin (1995, J. Americ. 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 several 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. Therefore, there is a demand for onions that are less pungent at harvest and thus do not significantly increase in pungency during storage. In particular, there is a demand for less pungent onions after storage of at least approximately 2, 3, 4, 5, 6, 7, 8 months or longer. In particular, long-day onions can be stored, while short-day onions are generally consumed with little or no storage. In particular, there is a demand for long-day onions that are less pungent and thus do not increase in pungency during storage, but remain constant or decrease during storage (compared to the harvest level), i.e., lower than the harvest level after storage of at least approximately 2, 3, 4, 5, 6, 7, 8 months or longer. Therefore, "reduction during storage" means that the level after a specific storage period (e.g., after approximately 2, 3, 4, 5, 6, 7, or 8 months or longer) is lower than at harvest.

[0006] Onion plants that produce less pungent onion bulbs have been previously described. WO2007011857A2 describes a long-day onion plant containing less pungent bulbs. WO2009 / 092560A1 describes a long-day onion plant that can produce onion bulbs with low pungentness combined with a high content of soluble solids. EP2992756A1 describes an onion plant in which alliinase gene expression is reduced, resulting in reduced amounts of pungent and tear-inducing components produced when onion cells are destroyed. One common problem associated with less pungent onion varieties is that there may be a decrease in consistency regarding pungent characteristics. One reason for this is that there is often a large genotype due to environmental interactions, which can make genetic fixation by phenotypic selection difficult. This problem is further complicated by the fact that onion breeding lines are often inbred up to the F4 or F5 level until they "form a group," and are maintained as a population rather than as single-seed lines. This results in residual heterozygosity levels of up to 12.5%. Thus, segregation is observed in onion lines at the loci of the target trait, including the locus that controls pungency. In this regard, the development of reliable genetic markers to determine the presence of pungency-reducing alleles has not been successful. If molecular markers for pungency traits were available in onion plants, it would 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, if reliable molecular markers were available, a larger number of individual plants could be screened with molecular markers compared to the more laborious pyruvate phenotypic screening, enabling accelerated breeding of new low-pungency varieties. [Overview of the Initiative]

[0007] Summary of the Invention In the present invention, a method is provided for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs that confer reduced pirubate levels in an onion plant or plant part, wherein the markers are selected from the group consisting of a marker located between the markers isotig30225_1454 and isotig32865_1404 on chromosome 2 and linked to a reduced pirubate-contributing QTL; a marker located between the markers isotig32772_1413 and isotig33099_885 on chromosome 1 and linked to a reduced pirubate-contributing QTL; and a marker located between the markers isotig28625_2789 and isotig41937_218 on chromosome 7 and linked to a reduced pirubate-contributing QTL. The order of SNP markers specified in relation to the present invention may be from Table 7, as provided below in this specification.

[0008] Furthermore, this specification includes a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 1 or SEQ ID NO: 1; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 3 or SEQ ID NO: 3; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 5 or SEQ ID NO: 5; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 7 or SEQ ID NO: 7; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 9 or SEQ ID NO: 9; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 11 or SEQ ID NO: 11; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 13 or SEQ ID NO: 13; a fragment comprising at least 15 nucleotides, including nucleotide 51 of SEQ ID NO: 15 or SEQ ID NO: 15; and a fragment comprising nucleotide 51 of SEQ ID NO: 17 or SEQ ID NO: 17 The fragment consisting of at least 15 nucleotides; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 19 or SEQ ID NO: 19; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 21 or SEQ ID NO: 21; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 23 or SEQ ID NO: 23; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 25 or SEQ ID NO: 25; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 27 or SEQ ID NO: 27; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 29 or SEQ ID NO: 29; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 31 or SEQ ID NO: 31; the fragment consisting of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 33 or SEQ ID NO: 33;Isolated nucleic acids are provided comprising a nucleotide sequence selected from the group consisting of: a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 35 or SEQ ID NO: 35; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 37 or SEQ ID NO: 37; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 39 or SEQ ID NO: 39; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 41 or SEQ ID NO: 41; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 43 or SEQ ID NO: 43; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 45 or SEQ ID NO: 45; a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 47 or SEQ ID NO: 47; and a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 49 or SEQ ID NO: 49; or a fragment of at least 15 nucleotides containing nucleotide 51 of SEQ ID NO: 49; or a complementary nucleotide sequence thereof.

[0009] This specification also provides the use of one or more nucleotide sequences or fragments thereof (each fragment comprising nucleotide 51 of the nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50, or comprising at least 15 nucleotides) or one or more complementary sequences of the nucleotide sequences for the selection of onion plants or plant parts assisted by markers.

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

[0011] Sequence ID 1 indicates the spiciness reduction genotype of SNP_01. Sequence ID 2 indicates the high-spicy genotype of SNP_01. Sequence ID 3 indicates the spiciness reduction genotype of SNP_02. Sequence ID 4 indicates the high-spicy genotype of SNP_02. Sequence ID 5 indicates the spiciness reduction genotype of SNP_03. Sequence ID 6 indicates the high-spicy genotype of SNP_03. Sequence ID 7 indicates the spiciness reduction genotype of SNP_04. Sequence ID 8 indicates the high-spicy genotype of SNP_04. Sequence ID 9 indicates the spiciness reduction genotype of SNP_05. Sequence ID 10 indicates the high-spicy genotype of SNP_05. Sequence ID 11 indicates the spiciness reduction genotype of SNP_06. Sequence ID 12 indicates the high-spicy genotype of SNP_06. Sequence ID 13 indicates the spiciness reduction genotype of SNP_07. Sequence ID 14 indicates the high-spicy genotype of SNP_07. Sequence ID 15 indicates the spiciness-reducing genotype of SNP_08. Sequence ID 16 indicates the high-spicy genotype of SNP_08. Sequence ID 17 indicates the spiciness reduction genotype of SNP_09. Sequence ID 18 indicates the high-spicy genotype of SNP_09. Sequence ID 19 indicates the spiciness reduction genotype of SNP_10. Sequence ID 20 indicates the high-spicy genotype of SNP_10. Sequence ID 21 indicates the spiciness reduction genotype of SNP_11. Sequence ID 22 indicates the high-spicy genotype of SNP_11. Sequence ID 23 indicates the spiciness reduction genotype of SNP_12. Sequence ID 24 indicates the high-spicy genotype of SNP_12. Sequence ID 25 indicates the spiciness reduction genotype of SNP_13. Sequence ID 26 indicates the high-spicy genotype of SNP_13. Sequence ID 27 indicates the spiciness reduction genotype of SNP_14. Sequence ID 28 indicates the high-spicy genotype of SNP_14. Sequence ID 29 indicates the spiciness-reducing genotype of SNP_15. Sequence ID 30 indicates the high-spicy genotype of SNP_15. Sequence ID 31 indicates the spiciness reduction genotype of SNP_16. Sequence ID 32 indicates the high-spicy genotype of SNP_16. Sequence ID 33 indicates the spiciness reduction genotype of SNP_17. Sequence ID 34 indicates the high-spicy genotype of SNP_17. Sequence number 35 indicates the genotype for reducing pungency of SNP_18. Sequence number 36 indicates the high-pungency genotype of SNP_18. Sequence number 37 indicates the genotype for reducing pungency of SNP_19. Sequence number 38 indicates the high-pungency genotype of SNP_19. Sequence number 39 indicates the genotype for reducing pungency of SNP_20. Sequence number 40 indicates the high-pungency genotype of SNP_20. Sequence number 41 indicates the genotype for reducing pungency of SNP_21. Sequence number 42 indicates the high-pungency genotype of SNP_21. Sequence number 43 indicates the genotype for reducing pungency of SNP_22. Sequence number 44 indicates the high-pungency genotype of SNP_22. Sequence number 45 indicates the genotype for reducing pungency of SNP_23. Sequence number 46 indicates the high-pungency genotype of SNP_23. Sequence number 47 indicates the genotype for reducing pungency of SNP_24. Sequence number 48 indicates the high-pungency genotype of SNP_24. Sequence number 49 indicates the genotype for reducing pungency of SNP_25. Sequence number 50 indicates the high-pungency genotype of SNP_25. Sequence number 51 indicates the genotype for reducing pungency of isotig30225_1454. Sequence number 52 indicates the high-pungency genotype of isotig30225_1454. Sequence number 53 indicates the genotype for reducing pungency of isotig32865_1404. Sequence number 54 indicates the high-pungency genotype of isotig32865_1404. Sequence number 55 indicates the genotype for reducing pungency of isotig32772_1413. Sequence number 56 indicates the high-pungency genotype of isotig32772_1413. Sequence number 57 indicates the genotype for reducing pungency of isotig33099_885. Sequence ID 58 indicates the high-spicy genotype of isotig33099_885. Sequence ID 59 indicates the spiciness-reducing genotype of isotig28625_2789. Sequence ID 60 indicates the high-spicy genotype of isotig28625_2789. Sequence ID 61 indicates the spiciness-reducing genotype of isotig41937_218. Sequence ID 62 indicates the high-spicy genotype of isotig41937_218. [Modes for carrying out the invention]

[0012] Detailed description of the invention General definition The term "genome" refers to the genetic material of an organism. A genome consists of DNA. It includes both genes and non-coding sequences of DNA.

[0013] The term "genetic determinant" refers to the genetic information in the plant genome that gives rise to specific traits in plants. Therefore, a genetic determinant consists of genetic information (genes, loci, or gene transfers) that confers a particular trait. Generally, a genetic determinant may consist of a single gene (or one quantitative trait locus (QTL)) or two or more genes.

[0014] "Phenotype" refers to the observable and / or physiological appearance of a plant as a result of the interaction between its genotype and its environment. Phenotype includes all observable morphological and physiological features, and therefore includes phenotypes such as the pungency of an onion bulb, PAD measurements, and soluble solids content.

[0015] In the context of this application, the term "trait" refers to the phenotype of a plant. When a plant exhibits the trait of the present invention, its genome comprises at least one pungency-reducing allele associated with the trait of the present invention, particularly when the pungency-reducing allele is isozyme in this invention. Thus, this plant has the genetic determinant of the present invention. When referring to a plant comprising the trait of the present invention, it is understood to mean an onion plant comprising the pungency-reducing trait, as further described herein.

[0016] A "genotype" is the totality of inherited genetic information in a plant, which is partially influenced by environmental factors and expressed in its phenotype.

[0017] As used herein, “onion plant” or “onion” refers to the plant body or part of the plant species Allium sepah L., such as the (harvested) bulb or seeds. The “bulb,” which is the edible part of this plant, is harvested. Onion bulbs may be developing or mature. In this specification, mature bulbs are preferred, and these are bulbs before or after harvest.

[0018] "Long-day" onion plants begin to form a head when the light (day length) is at least approximately 14 hours continuous, for example, at least approximately 14, 15, or 16 hours. To initiate head formation, this continuous light (hours per day) is preferably provided for 2, 4, 7, 14, 21, 25 days or more.

[0019] "Storage conditions" and "storage" include typical conditions used for storing (preferably raw) onions, such as darkness, low temperature (wherein used herein, low temperature preferably means 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 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" (hereinafter referred to as "SSC") is the percentage (%) of water-soluble compounds in onion bulbs, as measured by a refractometer according to the methods of Mann and Hoyle, 1945 (Proc. America. Soc. Hort. Sci. 46: 285-292) or Foskett and Peterson, 1949 (Proc. America. Soc. Hort. Sci. 55: 314-318).

[0021] "High SSC" as used herein refers to the average SSC of a representative number of onion bulbs (e.g., at least 5, 6, 10, 15, 20, 30, 40, 50, 50, 60, 70, 80, 90 or more bulbs) with at least 7.0% or 7.5%, or even more than 8%, 9%, 10%, 11%, 12%, 15%, 20%, 25%, 30%, or more. Thus, as used herein, average SSCs of 7.0–30%, 7.5–30%, or even more such as 7.0–20%, 8.0–20%, 7.0–15%, 8.0–15%, 7.0–10%, etc.

[0022] "Pungency" refers to the typical pungent taste of onions that occurs when the onion bulb tissue is broken down by crushing. Pungency is preferably determined by measuring the enzymatic development of pyruvate according to the method of Schwimmer and Weston (1961, J. of Agric. Food Chemistry 9:301-304), which correlates strongly with flavor perception by a taste panel (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 quantification method as described in Anthon and Barrett (2003) Science of Food and Agriculture (83) 1210-1213. Pungency is expressed as pirubate in μMol (also known as micromol, μM, or μmol) per gram of fresh bulb material (μMol / g FW). This is also referred to herein as the “PAD measurement” (PAD from pyruvate generation), “pirubate measurement,” or “pirubate level.”

[0023] The term "reduced pungency," as used herein, refers to a level of pungency that is correspondingly reduced compared to the pungency level of a reference variety. Preferably, the reduced pungency level corresponds to a level of pungency 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 the 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) that, as determined by PAD measurements, is less than 5.5 μMol / g FW piruvate, or even less than 5.0, 4.5, 4.0 μMol / g FW piruvate, 3.8 or 3.75 μMol / g FW piruvate, or 3.5, 3.0, 2.5, 2.3, 2.0, 1.8, 1.5, or 1.3 μMol / g FW piruvate. "High spiciness" as used herein refers to the average spiciness level of a representative number of (mature) onion bulbs that is higher than the low spiciness level as defined herein, preferably exceeding 5.5 μMol / g FW pirubate, or even exceeding 6.0, 6.5, or 7.0 μMol / g FW pirubate. Spiciness can be measured at harvest and / or after storage for 2, 3, 4, 5, 6, 7, or 8 months or longer.

[0024] "Narrow spiciness range" means that the variation in spiciness between individual bulbs obtained from multiple bulbs of a single plant lineage is narrow, that is, the difference between the spiciness level of the spiciest bulb (maximum value) and the spiciness level of the least spiciest bulb (minimum value) is preferably 5 μMol / g FW pirubate or less, more preferably 4 μMol / g FW pirubate or less or 3.5 μMol / g FW pirubate or less, more preferably 3.0, 2.5, 2.0, 1.5 or 1.0 μMol / g FW pirubate or less. Preferably, the maximum spiciness (of the spiciest bulb produced by the plant) is 5 μMol / g FW pirubate 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 pirubate or less. Preferably, the minimum spiciness level (i.e., of the least spicy bulb produced by the plant) is 3.0 or 2.5 μMol / g FW pirubate or less, more preferably 2.0, 1.3 or 1.2 μMol / g FW pirubate or less. Thus, the preferred range of spiciness within a plant line is when all bulbs have a spiciness level between 0 (minimum) and 5 (maximum) μMol / g FW pirubate, preferably between 1 (minimum) and 5 (maximum) μMol / g FW pirubate, and more preferably between 1 (minimum) and 4 (maximum) μMol / g FW pirubate. Furthermore, in one embodiment of the present invention, all bulbs have a pungency between 0 (minimum) and 5 (maximum) μMol / g FW pirubate, preferably 1 (minimum) and 5 (maximum) μMol / g FW pirubate, more preferably between 1 or 1.2 (minimum) and 4.9, 4.8, 4.7 or 4.5 (maximum) μMol / g FW pirubate, and more preferably between 1 (minimum) and 4 (maximum) μMol / g FW pirubate. A narrow pungency range is an important quality feature for consumers. Pungency can be measured at harvest and / or, preferably, after a certain storage period, for example, after storage for at least about 2, 3, 4, 5, 6, 7, or 8 months or longer.

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

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

[0027] "Wild-type plants" as used herein refer to onion species plants that produce bulbs with high spiciness as defined herein. Such plants are suitable controls in phenotypic testing, for example, especially when the control plants have the same genetic background as the plants being tested for phenotypic effects (e.g., low-spiciness plants).

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

[0029] Genetic determinants can be inherited in recessive, intermediate, or dominant manners. Selection of phenotypic traits is easier when intermediate or dominant inheritance is involved, as a larger proportion of the resulting offspring will exhibit that trait. In general, genetic determinants may also include combinations of recessive and / or intermediate and / or dominant genes or QTLs.

[0030] Selection of genetic determinants (e.g., spiciness-reducing alleles) can be performed phenotypicly (observable traits). Selection can also be performed by molecular genotyping methods, such as using one or more molecular markers genetically linked to the spiciness-reducing allele, or preferably by molecular methods that can identify the presence of, for example, the spiciness-reducing allele and the wild-type allele, or their products (e.g., mRNA or protein encoded by the allele), using the gene or the allele sequence itself. 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 a small population through screening (compared to phenotypic selection) and can be performed at a very early stage. A further advantage of molecular genotyping is that it allows for easy identification of isozygous plants or seeds lacking any copy of the hypertoxicity alleles described herein from plants having one or more copies of the hypertoxicity allele, and this can be done before seed germination or during early plant development, such as before onion bulbs develop.

[0031] "Plant lineage" or "breeding lineage" refers to a plant and its offspring. As used herein, the term "inbreeding lineage" refers to a plant lineage that has been repeatedly self-pollinated and is nearly isoconjugated in all characteristics. Thus, "inbreeding lineage" or "parent lineage" refers to a plant lineage that has undergone several generations of inbreeding (e.g., at least 4, 5, 6, 7 generations or more) to become a plant lineage with high homogeneity.

[0032] The term "allele" refers to any one or more selected forms of DNA sequences at a particular locus, all of which relate to a single trait or characteristic at that locus. In diploid cells of organisms, the alleles of a given gene are located at specific locations on the chromosome, or loci. There is one allele on each chromosome of a homologous chromosome pair. Diploid plant species can consist of many different alleles at a single particular locus. These may be identical alleles of a gene (isozygous) or two different alleles (heterozygous).

[0033] The term "locus" refers to a specific location on a chromosome where, for example, a gene or genetic marker is found. Therefore, a pungency reduction locus, as described herein, is a location in the genome of an onion plant where a pungency reduction 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 are transmitted together to offspring at a higher frequency than expected according to the law of independent inheritance. In this invention, eight linkage groups have been identified. Preferably, each of these eight linkage groups corresponds, as used herein, to one of the eight chromosomes of the onion genome. Preferably, the term "linkage group 3" corresponds, as used herein, to chromosome 3 (of the onion). Preferably, the term "linkage group 4" corresponds, as used herein, to chromosome 1 (of the onion). Preferably, the term "linkage group 6" corresponds, as used herein, to chromosome 7 (of the onion).

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

[0036] An "introduced gene" or "chimeric gene" refers to a gene locus that contains a DNA sequence, such as a recombinant gene, introduced into the plant genome through transformation, such as transformation mediated by Agrobacterium. Plants containing an introduced gene that is stably incorporated into the genome are called "transgenic plants."

[0037] "Genetic expression" refers to the process by which a suitable regulatory region, particularly a DNA region functionally linked to a promoter, can be translated into a biologically active protein or peptide (or active peptide fragment), or into an RNA that is itself active (e.g., post-transcriptional gene silencing or RNAi). The coding sequence may be sense-oriented 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 expression levels of a continuously distributed (quantitative) phenotype.

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

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

[0041] A “transferred fragment,” “transferred segment,” or “transferred region” refers to a chromosomal fragment (or chromosome portion or region) introduced into another plant of the same or closely related species through crossbreeding or conventional breeding techniques, such as backcrossing; that is, a transferred fragment is the result of a breeding method referred to by the verb “transfer” (e.g., backcrossing). The term “transferred fragment” is understood to include only a portion of a chromosome, and never an entire 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, for example, about 10 Mb or less, about 9 Mb or less, about 8 Mb or less, about 7 Mb or less, about 6 Mb or less, about 5 Mb or less, about 4 Mb or less, about 3 Mb or less, about 2.5 Mb or 2 Mb or less, about 1 Mb (corresponding to 1,000,000 base pairs) or less, or about 0.5 Mb (corresponding to 500,000 base pairs) or less, for example, about 200,000 bp (corresponding to 200 kilobase pairs) or less, about 100,000 bp (100 kb) or less, about 50,000 bp (50 kb) or less, or about 25,000 bp (25 kb) or less.

[0042] The term "isogenic plants" refers to two plants that are genetically identical except for the spiciness-reducing allele of the present invention. To investigate the effect of the spiciness-reducing trait, the target plant line (or variety) can be crossed with a plant containing the spiciness-reducing allele and selected for offspring that express the desired trait. In some cases, the offspring may need to be self-pollinated at least once to determine the genetic determinants of the spiciness-reducing trait in the plant phenotype. Next, offspring that have the same phenotype as the target plant line (or variety) and express the genetic determinants of the spiciness-reducing trait can be selected and then backcrossed with the target plant line (or variety) (at least twice, for example, three, four, or preferably five or six times). Subsequently, the effect of spiciness reduction can be compared between the target plant line (or variety) and its isogenic line that does not contain the genetic determinants of the spiciness-reducing trait.

[0043] The terms “nucleic acid,” “nucleic acid sequence,” “nucleic acid molecule,” or “polynucleotide” are used interchangeably and refer to single-stranded or double-stranded DNA or RNA molecules, in particular DNA encoding proteins or protein fragments according to the present invention. “Isolated nucleic acid” refers to nucleic acids that are no longer in the natural environment in which they were isolated, for example, nucleic acids in bacterial host cells or in the nuclear genome or plastid genome of plants.

[0044] The terms "protein," "peptide sequence," "amino acid sequence," or "polypeptide" are used interchangeably and refer to molecules consisting of amino acid chains, regardless of their specific mode of action, size, tertiary structure, or origin. Therefore, a "fragment" or "part" of a protein is also called a "protein." "Isolated protein" is used to refer to a protein that does not exist in its natural environment, for example, in vitro or in recombinant bacteria or plant host cells.

[0045] An "active protein" or "functional protein" is a protein that has protein activity that can be measured in vitro, for example, by an in vitro activity assay, and / or in vivo, for example, by the phenotype conferred by the protein. A "wild-type" protein is a fully functional protein, such as those found in wild-type plants. A "mutant protein" is, as used herein, a protein comprising one or more mutations in the nucleic acid sequence encoding the protein, thereby resulting in a mutant nucleic acid molecule encoding a protein with altered activity, preferably a protein with reduced activity, most preferably an inactive protein.

[0046] As described herein, “functional derivatives” of proteins are protein fragments, variants, analogs, or chemical derivatives that retain some of the immunocross-reactivity with antibodies specific to the active or mutant protein.

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

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

[0049] A mutant protein analog refers to a non-native protein that is substantially similar to the whole protein or a fragment of it.

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

[0051] A "mutation" in the amino acid molecules that make up a protein is a change in one or more amino acids compared to the wild-type sequence, such as the substitution, deletion, or insertion of one or more amino acids. Such proteins are also called "mutant proteins."

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

[0053] A "nonsense mutation" is a (point) mutation in the nucleic acid sequence encoding a protein, in which a codon in the nucleic acid molecule is changed to a stop codon. As a result, an immature stop codon is present in the mRNA, leading to the translation of a truncated protein. A truncated protein may exhibit reduced or lost function.

[0054] A "missense or non-synonymous mutation" is a (point) mutation in a nucleic acid sequence that codes for a protein, in which a codon changes to code for a different amino acid. The resulting protein may exhibit reduced or lost function.

[0055] A "splice site mutation" is a mutation in the nucleic acid sequence encoding a protein that alters the RNA splicing of the precursor mRNA, resulting in mRNA with a different nucleotide sequence and a protein with a different amino acid sequence than the wild type. The resulting protein may exhibit reduced function or loss of function.

[0056] A "frameshift mutation" is a mutation in the nucleic acid sequence encoding a protein that alters the reading frame of mRNA, resulting in a different amino acid sequence. The resulting protein may exhibit reduced or lost function.

[0057] In relation to the present invention, “deletion” means that at least one nucleotide is missing somewhere in a given nucleic acid sequence compared to the corresponding wild-type sequence, or that at least one amino acid is missing somewhere in a given amino acid sequence compared to the corresponding (wild-type) sequence.

[0058] "Terminal cleavage" means that at least one nucleotide is lost at either the 3' or 5' end of a nucleotide sequence compared to the corresponding wild-type sequence, or at least one amino acid is lost at either the N-terminus or C-terminus of a protein compared to the corresponding wild-type protein sequence. It should be understood that in a 3' or C-terminus cleavage, at least the first nucleotide at the 5' end or the first amino acid at the N-terminus, respectively, remains present, and in a 5' or N-terminus cleavage, at least the last nucleotide at the 3' end or the last amino acid at the C-terminus, respectively, remains present. The 5' end is determined by the ATG codon used as the start codon in the translation of the corresponding wild-type sequence.

[0059] "Substitution" means that, compared to the corresponding wild-type nucleic acid sequence or the corresponding wild-type amino acid sequence, at least one nucleotide in the nucleic acid sequence or one amino acid in the protein sequence is different due to the exchange of nucleotides in the coding sequence of each protein.

[0060] "Insertion" means that the nucleic acid sequence or amino acid sequence of a protein contains 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.

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

[0062] A “mutation in a regulatory sequence” is, for example, a change in one or more nucleotides compared to the wild-type sequence in the promoter or enhancer of a gene, such as a substitution, deletion or insertion of one or more nucleotides, which results in, for example, a decrease or no production of the gene’s mRNA transcript. Thus, a “promoter of a gene sequence” is defined as the DNA region that initiates transcription of a particular gene. Promoters are located upstream of their DNA on the same strand, in close proximity to the gene they transcribe. Promoters can be about 100 to 1000 base pairs long. In one aspect, a promoter is defined as a region about 2000 base pairs or more upstream of the start codon (i.e., ATG) of the protein encoded by the gene, preferably a region about 1500 base pairs upstream of the start codon, and more preferably a region about 1000 base pairs upstream of the start codon.

[0063] As used herein, the term “functionally linked” refers to the linking of polynucleotide elements in a functional relationship. A nucleic acid is “functionally linked” when it is positioned in a functional relationship with another nucleic acid sequence. For example, a promoter, or more precisely, a transcriptional regulatory sequence, is functionally linked to a coding sequence if it affects the transcription of that sequence. Functionally linked generally means that the linked nucleic acid sequences are contiguous.

[0064] Sequence identity and sequence similarity can be determined by the alignment of two peptide or nucleotide sequences using a global or local alignment algorithm. Sequences can then be considered "substantially identical" if they are optimally aligned by, for example, the GAP or BESTFIT or Emboss program "Needle" (using default parameters, see below) and possess 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 across 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 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 and BLAST, 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 their percentage sequence identity is at least 95%, 96%, 97%, 98%, 98.3%, 98.7%, 99.0%, or 99.3%, or more preferably 99.7% (determined using 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 "mutants," and it is possible to identify, for example, other mutants of alleles that produce the spiciness-reducing trait of the present invention and proteins other than the specific nucleic acid and amino acid sequences disclosed herein, which have the same effect on spiciness as the plants of the present invention.

[0065] The term "hybridization," as used herein, generally refers to the hybridization of nucleic acids under appropriate stringency conditions (stringent hybridization conditions), as will be readily apparent to those skilled in the art, given the nature of the probe and target sequences. Hybridization and washing conditions are well known, and adjustments to the conditions according to the desired stringency are readily achieved by changing the incubation time, temperature, and / or the ionic strength of the solution. See, for example, Sambrook, J. et al., Molecular Cloning: A Laboratory Manual, 2nd edition, Cold Spring Harbor Press, Cold Spring Harbor, New York, 1989. The selection of conditions depends on the length of the sequences to be hybridized, particularly the length of the probe sequence, the relative GC content of the nucleic acids, and the amount of acceptable mismatch. Low stringency conditions are preferred when partial hybridization between strands with a low degree of complementarity is desired. High stringency conditions are preferred when complete or near-complete complementarity is desired. Typical high-stringency conditions involve a hybridization solution containing 6×SSC, 0.01M EDTA, 1×Denhart solution, and 0.5% SOS. Hybridization is performed at approximately 68°C for about 3-4 hours for cloned DNA fragments and about 12-16 hours for whole eukaryotic DNA. For lower stringency conditions, the hybridization temperature is lowered to the melting point (T) of the double helix. M Lower the temperature by approximately 42°C. M It is known that this is a function of GC content, double chain length, and ionic strength of the solution.

[0066] As used herein, the phrase “hybridizes” a DNA or RNA molecule means that the hybridizing molecule, e.g., oligonucleotide, polynucleotide, or any nucleotide sequence (sense or antisense orientation), recognizes a sequence of another nucleic acid molecule that is approximately the same size and has sufficient sequence similarity to it to perform hybridization under appropriate conditions, and hybridizes with it. For example, a 100-nucleotide molecule derived from the 3' coding or non-coding region of a gene will recognize and hybridize with a 100-nucleotide portion of any other plant gene, provided that there is at least about 70% sequence similarity between the nucleotide sequence or two sequences within the 3' coding or non-coding region of that gene. The size of the corresponding portion should be understood to allow some mismatch for hybridization, such that the corresponding portion may be shorter or longer than the molecule it hybridizes with, for example, 20-30% longer or shorter, preferably about 12-15% longer or shorter.

[0067] As used herein, the phrases “a sequence having at least 95% sequence identity,” “a sequence having at least 95% amino acid sequence identity,” or “a sequence having at least 95% nucleotide sequence identity” mean a sequence having 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 an indicated reference sequence. Sequence identity can be determined according to the methods described herein.

[0068] A “fragment” of a gene sequence or DNA sequence refers to any subset of that molecule, for example, a shorter polynucleotide or oligonucleotide. In one aspect, a fragment comprises mutations as defined by the present invention.

[0069] A “mutant” of a gene or DNA refers to a molecule substantially similar to the whole gene or a fragment thereof, for example, a nucleotide substitution mutant 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 mutant comprises a spiciness-reducing allele as defined by the present invention.

[0070] As used herein, the term “plant” includes a complete plant or any part or derivative thereof, such as plant organs (e.g., harvested or unharvested flowers, leaves, bulbs, etc.), plant cells, plant protoplasts, plant cells or tissue cultures capable of redifferentiating a complete plant, plant cells with or without the ability to redifferentiate, plant callus, plant cell masses, and intact plant cells within a plant, or plant parts, such as embryos, pollen, ovules, ovaries (e.g., harvested tissue or organs), flowers, leaves, seeds, bulbs, clonal plants, roots, stems, cotyledons, hypocotyls, root tips, etc. It also includes any developmental stage, such as seedling, immature, and mature. Preferably, a plant part or derivative comprises a gene or locus as defined by the present invention.

[0071] "Plant lineage" or "breeding lineage" refers to a plant and its offspring.

[0072] A “plant variety” or “cultivar” is a group of plants within the same lowest known plant taxonomy, which can be defined based on the expression of a characteristic resulting from a particular genotype or combination of genotypes (regardless of whether the conditions for granting plant breeders’ rights are met), which can be distinguished from any other group of plants by the expression of at least one of those characteristics, and which can be considered an entity because it is reproducible without any alteration. Therefore, the term “plant variety” cannot be used to describe a group of plants that, even if they are of the same kind, are all characterized by the presence of a single locus or gene (or a set of phenotypic characteristics from this single locus or gene), but may otherwise differ significantly from one another with respect to other loci or genes. "F1, F2, etc." refers to successive related generations following a cross between two parent plants or parent lines. Plants grown from seeds produced by the cross of two plants or lines are called the F1 generation. Self-pollination of F1 plants yields F2 generations, etc. An "F1 hybrid" plant (or F1 seed or hybrid) is a generation obtained by crossing two inbreeding parent lines. Therefore, "self-pollination" refers to the self-pollination of a plant, that is, the fusion of gametes from the same plant.

[0073] Backcrossing refers to a breeding method in which a (single) trait, such as the ability to induce a reduction in spiciness, can be transferred from one genetic background (generally called a "donor," which is a lower-level genetic background) to another genetic background (generally called a "recurrent parent," which is a higher-level genetic background). The progeny of a cross (for example, F1 plants obtained by crossing a first plant of a certain plant species containing the spiciness-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 spiciness-reducing allele of the present invention); or F2 or F3 plants obtained by self-pollinating the F1) are "backcrossed" with the parent plant of the second plant species. After repeated backcrossing, the trait of the donor genetic background, for example, the spiciness-reducing allele that confers the spiciness-reducing trait of the present invention, is incorporated into the recurrent genetic background. In this context, the terms “genetic conversion,” “converted plant,” or “single-locus conversion” refer to a plant produced by a backcross in which, in addition to one or more genes introduced from the donor parent, substantially all of the desired morphological and / or physiological characteristics of the recurrent parent are restored. Plants grown from seeds produced by backcrossing F1 plants with a second parent plant line are called the “BC1 generation.” Plants from the BC1 population can be self-pollinated to obtain the BC1F2 generation, or they can be back-pollinated again with the cultivated parent plant line to obtain the BC2 generation. The “M1 population” is a group of mutagenic seeds / plants of a particular plant line. “M2, M3, M4, etc.” refer to successive generations obtained after self-pollinated the first mutagenic seed / plant (M1).

[0074] The terms “cultivated plant” or “cultivar” refer to a given species of plant that is cultivated by humans and possesses good agricultural characteristics, such as a variety, breeding line, or cultivar of the said species. So-called heirloom varieties or cultivars, i.e., open-pollinated varieties or cultivars that were commonly cultivated in the early stages of human history and are often adapted to specific geographical areas, are included herein as cultivated plants in one aspect of the present invention. The term “cultivated plant” does not include wild plants. “Wild plants” include, for example, wild accessions.

[0075] The term "food" refers to any substance consumed to nourish the body. Food is typically of plant or animal origin and contains essential nutrients such as carbohydrates, fats, proteins, vitamins, or minerals. Living organisms ingest these substances, and their cells absorb them to produce energy, sustain life, or stimulate growth. The term "food" includes substances consumed to nourish the bodies of both humans and animals.

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

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

[0078] In this specification and in the claims, the verb “contains” and its conjugations are used in their non-restrictive sense, meaning that the items following the word are included, but not that items not specifically mentioned are excluded. Furthermore, references to elements with the indefinite article “a” or “an” do not exclude the possibility of two or more elements being present unless the context clearly requires the presence of only one or two of those elements. Thus, the indefinite article “a” or “an” usually means “at least one.” Furthermore, when “sequence” is referred to herein, it is generally understood to refer to an actual material molecule having a specific sequence of subunits (e.g., amino acids or nucleic acids).

[0079] Markers and their use The present invention provides markers for identifying onion plants that produce bulbs having reduced pirubate levels, the markers being selected from the group consisting of: a marker located between markers isotig30225_1454 and isotig32865_1404 on chromosome 2 and linked to a reduced pirubate-contributing QTL; a marker located between markers isotig32772_1413 and isotig33099_885 on chromosome 1 and linked to a reduced pirubate-contributing QTL; and a marker located between markers isotig28625_2789 and isotig41937_218 on chromosome 7 and linked to a reduced pirubate-contributing QTL. The markers of the present invention are particularly useful for determining the presence or absence of one or more QTLs that confer reduced pirubate levels in onion plants or plant parts, as described in WO2009 / 092560A1. Therefore, in one embodiment, the present invention provides a suitable marker for determining the presence of one or more QTLs that confer a reduced pirubate level in an onion plant or plant part, wherein the one or more QTLs conferring a reduced pirubate level are plants whose seeds are deposited under accession number PTA-9053, plants whose seeds are deposited under accession number PTA-9054, or plants whose seeds are deposited under accession number PTA-9055.Therefore, in one embodiment, the present invention provides a suitable marker for determining the presence of one or more QTLs conferring a reduced pirubate level in an onion plant or plant portion obtained by crossing a plant whose seeds were deposited as accession number PTA-9053, a plant whose seeds were deposited as accession number PTA-9054, or a plant whose seeds were deposited as accession number PTA-9055 with another onion plant, and this marker is the chromosome 2 marker isotig30225_1454 The group is selected from the following: a marker located between marker isotig32865_1404 and linked to a QTL that reduces pirubate; a marker located between marker isotig32772_1413 and marker isotig33099_885 on chromosome 1 and linked to a QTL that reduces pirubate; and a marker located between marker isotig28625_2789 and marker isotig41937_218 on chromosome 7 and linked to a QTL that reduces pirubate.

[0080] The publicly available gene markers isotig30225_1454 and isotig32865_1404, located at map B9885×B8667 on chromosome 2, are well known in the art and are described in detail by Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci.,145(1), 67-72. The publicly available gene markers isotig32772_1413 and isotig33099_885, located at map Char×B5351 on chromosome 1, are well known in the art and are described in detail by Havey (2000) J. Amer. Soc. Hort. Sci.,145(2), 110-119. The publicly available gene markers isotig28625_2789 and isotig41937_218, located at map B9885×B8667 on chromosome 7, are well known in the art and are described in detail by Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72. All publicly available gene markers referenced herein are described in further detail by Duangjit et al. (2013) Theor Appl Genet 126, 2093-2101. The nucleotide sequences of these publicly available gene markers are further listed in Table 5.

[0081] Preferably, the present invention relates to SNP_01, in which nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1, or containing thymine; SNP_02, in which nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 3, or containing adenine; SNP_03, in which nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 5, or containing cytosine; and SNP_03, in which nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 7, or at least 95% (more preferably at least 96%, at least SNP_04 comprising thymine in nucleotide 51 of a sequence having at least 97%, at least 98%, or even more than 99% identity; SNP_05 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 9 on chromosome 1; SNP_06 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 11 on chromosome 1; SNP_07 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 12 on chromosome 1 or at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 13 on chromosome 1;SNP_08 on chromosome 1, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 17; SNP_10 on chromosome 7, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19; SNP_08 on chromosome 2, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%) identity with nucleotide 51 of SEQ ID NO: 21 SNP_11 comprising adenine in nucleotide 51 of a sequence having at least 98% or even more than 99% identity; SNP_12 of chromosome 2 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 23; SNP_13 of chromosome 2 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 25; SNP_14 of chromosome 2 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27;SNP_15 of chromosome 2, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 29; SNP_16 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 35; SNP_18 comprising thymine in nucleotide 51 of a sequence having 7%, at least 98%, or even more than at least 99% identity; SNP_19 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 37 on chromosome 1; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 39 on chromosome 1; SNP_21 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 41 on chromosome 1;SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 43 or sequence number 43 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_23 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 45 or sequence number 45 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 47 or sequence number 47 having at least 95 The present invention provides a marker for identifying onion plants that produce bulbs with reduced pirubate levels, comprising one or more SNPs selected from the group consisting of: SNP_24 having cytosine in nucleotide 51 of a sequence having % (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_25 having guanine in nucleotide 51 of chromosome 7, either in nucleotide 51 of sequence number 49 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with sequence number 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) and can be used to distinguish and / or identify an individual from another. In one embodiment, a reduced pirubate-granting QTL is located between SNP_11, which is located at nucleotide 51 of SEQ ID NO: 21 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 21, and SNP_04, which is located at nucleotide 51 of SEQ ID NO: 7 on chromosome 2 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 7. Experts can easily identify one or more suitable genetic markers linked to a reduction pirubate-donating QTL 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) using conventional methods. In one embodiment, the reduction pirubate-donating QTL is located on chromosome 1 between SNP_16, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 31, and SNP_20, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 39.An expert can easily identify one or more suitable genetic markers linked to a reduction pirubate-donating QTL 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) using conventional methods. In one embodiment, the reduction pirubate-donating QTL is located between SNP_22, located at nucleotide 51 of SEQ ID NO: 43 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 43, and the distal end of chromosome 7, including SNP_10, located at nucleotide 51 of SEQ ID NO: 19 on chromosome 7 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 19. Experts can readily identify, using conventional methods, one or more suitable genetic markers linked to a reduced pirubate-conferring QTL located at a locus of chromosome 7 as defined herein (i.e., between marker isotig28625_2789 and marker isotig41937_218 and / or at the distal end of chromosome 7 containing SNP_22 and SNP_10 as further defined herein). As used herein, “linked markers” specifically means “markers that are genetically linked.”

[0083] Therefore, the present invention provides a marker for determining the presence or absence of one or more QTLs that confer a reduced pirubate level in an onion plant or plant part, the marker being a marker linked to a reduced pirubate-contributing QTL located between SNP_11 located at nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 21 and SNP_04 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 5 of SEQ ID NO: 7, and SNP_04 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 5 of SEQ ID NO: 31 The group consists of a marker linked to a reduced pirubate-conducting QTL located between SNP_16 located at 1 and nucleotide 51 of SEQ ID NO: 39 or SNP_20 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 39, and a marker linked to a reduced pirubate-conducting QTL located between the distal end of chromosome 7, including SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 43 and SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 19.

[0084] Despite the presence of residual heterozygosity in the initially obtained low-pungency onion lines, the inventors successfully identified three significant QTLs that confer reduced pirubate levels in bulbs produced by onion plants. Various technical difficulties had to be overcome before the QTLs according to the present invention could be identified. The construction of multiple mapping populations required careful planning, and the parent plants of the populations were cultivated for almost six years before the material was available for QTL analysis. Since the mechanism of low pirubate in low-pirubate donors was unknown, several crosses were performed. These results indicated that the low-pirubate trait is a complex trait controlled by at least three loci, and no overlapping QTs were detected in the two populations; therefore, it was necessary to construct and analyze multiple mapping populations to identify the three QTLs in the present invention. QTL validation, in this case as well, required an unconventional approach due to the long generation time of onions. Apart from attempts related to actual mapping and validation, these efforts to develop genome-wide molecular markers required considerable effort to enable genetic mapping and the development of low-piruvate donor lines by phenotypic selection (which requires decades of directional breeding). One reduced-piruvate-granting QTL was identified on linkage group 3 located between SNP_11, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 21, and SNP_04, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 7.Further reduction pirubate-conferring QTLs were identified on linkage group 4 between SNP_16 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 31, and SNP_20 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 39. Further reduction pirubate-contributing QTLs were identified on linkage group 6 between the distal ends of linkage group 6, which includes SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 43, and SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19.

[0085] 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. Therefore, the term "linkage group 3" corresponds to the term "chromosome 2" when used herein. Therefore, the term "linkage group 4" corresponds to the term "chromosome 1" when used herein. Therefore, the term "linkage group 6" corresponds to the term "chromosome 7" when used herein.Therefore, the present invention provides a marker for determining the presence or absence of one or more QTLs that confer a reduced pirubate level in an onion plant or plant part, the marker being a marker linked to a reduced pirubate-contributing QTL located between SNP_11 located at nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 21 and SNP_04 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 5 of SEQ ID NO: 7, and SNP_04 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 5 of SEQ ID NO: 31 A marker linked to a reduced pirubate-conducting QTL located between SNP_16 located at 1 and nucleotide 51 of SEQ ID NO: 39 or SNP_20 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 51; and a marker linked to a reduced pirubate-conducting QTL located between the distal ends of chromosome 7, including SNP_22 located at nucleotide 51 of SEQ ID NO: 43 or SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 43 and SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 19.

[0086] Preferably, the present invention provides a marker for determining the presence or absence of one or more QTLs that confer a reduced pirubate level in an onion plant or plant part, the marker being a marker linked to a reduced pirubate-contributing QTL located between SNP_01 located at nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1 and SNP_04 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (at least 98%, or at least 99%) identity with nucleotide 51 of SEQ ID NO: 7 and SNP_16 located at nucleotide 51 of a sequence of chromosome 1 having at least 95% (at least 98%, or at least 99%) identity with nucleotide 51 of SEQ ID NO: 31 and nucleotide 51 of SEQ ID NO: 39 A marker linked to a reduced pirubate-contributing QTL located at SNP_20, which is located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 39; and a marker linked to a reduced pirubate-contributing QTL located at the distal end of chromosome 7, which includes SNP_22, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 43, and SNP_10, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 19. Thus, the present invention provides a marker for determining the presence or absence of one or more QTLs that confer a reduced pirubate level in an onion plant or plant part.Such markers, as referred to herein as “molecular markers,” may be any measurable indicator genetically linked to the trait of interest, and therefore, with respect to the present invention, to the spiciness reduction allele. Particularly preferred with respect to the present invention are, but are not limited to, restriction fragment length polymorphism (RFLP) markers, cleavage-amplified polymorphism (CPAS) markers, microsatellite markers (short tandem repeat (STR) or simple repeat (SSR)), restriction fragment length polymorphism (RFLP) markers, random-amplified polymorphic DNA (RAPD) markers, amplified fragment length polymorphism (AFLP) markers, and DNA-based markers including single nucleotide polymorphism (SNP) markers. Preferably, the markers according to the present invention are SNP markers.

[0087] In relation to the present invention, different specific SNP markers linked to reduced pirubate-granting QTLs located on chromosome 2 have also been identified. Markers linked to such SNP reduced pirubate-granting QTLs located on chromosome 2 include: SNP_11 located at nucleotide 51 of SEQ ID NO: 21 or in a sequence having at least 95% (at least 98% or at least 99%) identity with SEQ ID NO: 21; SNP_12 located at nucleotide 51 of SEQ ID NO: 23 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 23; SNP_13 located at nucleotide 51 of SEQ ID NO: 25 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 25; and SNP_13 located at nucleotide 51 of SEQ ID NO: 27 or in a sequence having at least 95% (more preferably at least 99%) identity with SEQ ID NO: 27. SNP_14 located at nucleotide 51 of a sequence containing at least 6%, at least 97%, at least 98%, or even more than 99% identity; SNP_01 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1; SNP_02 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 3; SNP_3 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 5;SNP_04 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 7; and SNP_15 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 29. Therefore, a suitable example of an SNP marker for determining the presence or absence of a reduced pirate-conferring QTL located between SNP_11, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 21, and SNP_04, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 21, or at least 95% (more preferably at least 96%) identity with nucleotide 51 of SEQ ID NO: 21; SNP_11 located at nucleotide 51 of a sequence containing at least 97%, at least 98%, or even more than 99% identity; SNP_12 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 23; SNP_13 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 25; SNP_14 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27; SNP_14 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1 or sequence number SNP_01 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SNP 1; SNP_02 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 3; SNP_3 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 5; SNP_04 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 7;and SNP_15 located at nucleotide 51 of sequence SEQ ID NO: 29 or sequence SNP_15 located at nucleotide 51 of sequence SEQ ID NO: 29, which has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 29. Preferably, the markers linked to a specific SNP reduction pirate-granting QTL located on chromosome 2 are: SNP_11 at nucleotide 51 of SEQ ID NO: 21 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 21; SNP_12 located at nucleotide 51 of a sequence containing 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 a sequence containing 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; and SNP_13 at nucleotide 51 of SEQ ID NO: 27 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 27. SNP_14 located at nucleotide 51 of a sequence having identity (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%); SNP_01 located at nucleotide 51 of a sequence having identity (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) of nucleotide 51 of SEQ ID NO: 1; SNP_02 located at nucleotide 51 of a sequence having identity (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) of nucleotide 51 of SEQ ID NO: 3; SNP_3 located at nucleotide 51 of a sequence having identity (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) of nucleotide 51 of SEQ ID NO: 5;and selected from the group consisting of nucleotide 51 of SEQ ID NO: 7 or SNP_04 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 7. Therefore, a specific example of a suitable SNP marker for determining the presence or absence of a reduced pirubate-conferring QTL located on chromosome 2 between marker isotig30225_1454 and marker isotig32865_1404 (preferably between SNP_11 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 21 and SNP_04 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 7) is SNP_11 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 2 SNP_12 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence 3 or sequence number 23; SNP_13 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 25; SNP_14 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 27; SNP_01 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 1 or sequence number 1;SNP_02 located at nucleotide 51 of sequence SEQ ID NO: 3 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 3; SNP_3 located at nucleotide 51 of sequence SEQ ID NO: 5 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 5; and SNP_04 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 7. Therefore, markers linked to SNP-reducing pirubate-contributing QTLs located on chromosome 2 may be useful for determining the presence of QTLs that confer reduced pirubate levels, where SNP_11 comprises an adenine sequence in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 21; SNP_12 comprises a cytosine sequence in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 23; SNP_13 comprises at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 25 SNP_14 comprises thymine in nucleotide 51 of a sequence having at least 99% identity with SEQ ID NO: 27 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 27; SNP_01 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 1 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 1; SNP_02 comprises adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 3 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 3;SNP_03 comprises cytosine in nucleotide 51 of sequence SEQ ID NO: 5 or in sequence SEQ ID NO: 5, which has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 5; SNP_04 comprises thymine in nucleotide 51 of sequence SEQ ID NO: 7 or in sequence SEQ ID NO: 7, which has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 7; and SNP_15 comprises guanine in nucleotide 51 of sequence SEQ ID NO: 29 or in sequence SEQ ID NO: 29, which has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 29. Therefore, preferably, SNP markers linked to a QTL conferring reduced pirubate levels located on chromosome 2 may be useful in determining the presence of a QTL conferring reduced pirubate levels, wherein SNP_11 contains adenine in nucleotide 51 of SEQ ID NO: 21 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 21; SNP_12 contains adenine in nucleotide 51 of SEQ ID NO: 23 or in nucleotide 51 of SEQ ID NO: 23 having at least 95% (more preferably at least 96%) identity with SEQ ID NO: 23; The nucleotide 51 of the sequence contains cytosine, having at least 97%, at least 98%, or even more than 99% identity; SNP_13 contains cytosine in the nucleotide 51 of SEQ ID NO: 25 or in the nucleotide 51 of the sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 25 Containing thymine; SNP_14 contains adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27; SNP_01 contains thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1; and nucleotide 51 of SEQ ID NO: 3 or at least 95% (more preferably at least 96%, at least 99%) identity with nucleotide 51 of SEQ ID NO: 3. SNP_02 comprises adenine in nucleotide 51 of a sequence having 7%, at least 98%, or even more than 99% identity; SNP_03 comprises cytosine in nucleotide 51 of sequence SEQ ID NO: 5 or of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence SEQ ID NO: 5; and SNP_04 comprises thymine in nucleotide 51 of sequence SEQ ID NO: 7 or of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence SEQ ID NO: 7.

[0088] With regard to the present invention, different specific SNP markers linked to reduction pirubate-donating QTLs located on chromosome 1 have also been identified. Markers linked to such SNP reduction pirubate-donating QTLs located on chromosome 1 include: SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 31; SNP_17 located at nucleotide 51 of SEQ ID NO: 33 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 33; SNP_05 located at nucleotide 51 of SEQ ID NO: 9 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 9; and SNP_05 located at nucleotide 51 of SEQ ID NO: 11 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with SEQ ID NO: 11. SNP_06 located at nucleotide 51 of a sequence containing at least 96%, at least 97%, at least 98%, or even at least 99% identity; SNP_7 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 12 or SEQ ID NO: 13; SNP_08 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 15 or SEQ ID NO: 15; SNP_18 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 35 or SEQ ID NO: 35;Selected from the group consisting of: SNP_19 located at nucleotide 51 of sequence SEQ ID NO: 37 or sequence SEQ ID NO: 37 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_20 located at nucleotide 51 of sequence SEQ ID NO: 39 or sequence SEQ ID NO: 39 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; and SNP_21 located at nucleotide 51 of sequence SEQ ID NO: 41 or sequence SEQ ID NO: 51 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity. Therefore, between the marker isotig32772_1413 and the marker isotig33099_885 of chromosome 1 (preferably, SNP_16 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 31 and SNP_16 located at nucleotide 51 of SEQ ID NO: 39 or SEQ ID NO: 39, and at least 95% (more preferably at least 96%) identity with nucleotide 51 of SEQ ID NO: 39; Specific examples of SNP markers suitable for determining the presence or absence of a reduction pirubate-conferring QTL located between SNP_20 located at nucleotide 51 of a sequence containing at least 97%, at least 98%, or even at least 99% identity are: SNP_16 located at nucleotide 51 of SEQ ID NO: 31 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 31; SNP_17 located at nucleotide 51 of SEQ ID NO: 33 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 33; SNP_05 located at nucleotide 51 of SEQ ID NO: 9 or in a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 9; sequence number SNP_06 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence 11; SNP_7 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence 12 or sequence 13; SNP_08 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence 15; SNP_18 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence 35;SNP_19 is located at nucleotide 51 of sequence SEQ ID NO: 37 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 37; SNP_20 is located at nucleotide 51 of sequence SEQ ID NO: 39 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 39; and SNP_21 is located at nucleotide 51 of sequence SEQ ID NO: 41 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 41. Preferably, SNP markers located on chromosome 1 and linked to a reduced pirubate-contributing QTL include: SNP_16 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31; SNP_17 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; and SNP_17 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 9. Preferably, SNP_05 located at nucleotide 51 of a sequence having at least 96%, at least 97%, at least 98%, or even at least 99% identity; SNP_06 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 11; SNP_7 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with 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 with nucleotide 51 of SEQ ID NO: 13;SNP_08 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_18 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 35; SNP_19 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 37; SNP_20 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 39;The group consists of and selected from the group comprising nucleotide 51 of sequence number 41 or SNP_21 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence number 41. Therefore, a specific example of a suitable SNP marker for determining the presence or absence of a reduced pirate-conferring QTL located between SNP_16, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31, and SNP_20, located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 39, is a SNP marker having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31. SNP_16 located at nucleotide 51 of a sequence comprising: SNP_17 located at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; SNP_05 located at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 9; SNP_06 located at nucleotide 51 of a sequence comprising at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 11;SNP_7 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 12 or SEQ ID NO: 13; SNP_08 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15 or SEQ ID NO: 15; SNP_08 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 35 or SEQ ID NO: 35 SNP_18 is located at nucleotide 51 of a sequence having at least 98% or even more than 99% identity; SNP_19 is located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 37; and SNP_20 is located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 39. Therefore, SNP markers located on chromosome 1 and linked to QTLs that confer reduced pirubate levels may be useful in determining the presence of QTLs that confer reduced pirubate levels, such that SNP_16 contains adenine in nucleotide 51 of SEQ ID NO: 31 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 31; SNP_17 contains adenine in nucleotide 51 of SEQ ID NO: 33 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 33; SNP_05 contains adenine in nucleotide 51 of SEQ ID NO: 9 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%) identity with SEQ ID NO: 9; SNP_06 comprises cytosine in nucleotide 51 of a sequence having at least 97%, at least 98%, or even more than 99% identity with SEQ ID NO: 11 or adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 11; SNP_07 comprises at least 95% (or Preferably, the nucleotide 51 of the sequence contains cytosine, having at least 96%, at least 97%, at least 98%, or even more than 99% identity; SNP_08 contains thymine, having at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 15; SNP_18 contains thymine, having at least 95% (more preferably, at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 35 or sequence number SNP_19 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SNP 35; SNP_20 comprises guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SNP 37; and SNP_21 comprises cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SNP 41.Therefore, preferably, an SNP marker located on chromosome 1 and linked to a QTL conferring reduced pirubate levels may be useful for determining the presence of a QTL conferring reduced pirubate levels, wherein SNP_16 contains adenine at nucleotide 51 of SEQ ID NO: 31 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 31; SNP_17 comprises adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; SNP_05 comprises cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 9; SNP_06 comprises adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 11; SNP_07 comprises at least 95% (more preferably at least 96%, at least 96%, at least 99%) identity with nucleotide 51 of SEQ ID NO: 12 or at least 95% (more preferably at least 96%) identity with nucleotide 51 of SEQ ID NO: 13 SNP_08 comprises cytosine in nucleotide 51 of a sequence having at least 97%, at least 98%, or even more than 99% identity with SEQ ID NO: 15 or 15; nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 15; SNP_18 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 35; SNP_19 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 37;Furthermore, SNP_20 contains guanine in nucleotide 51 of SEQ ID NO: 39 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 39.

[0089] With regard to the present invention, different specific SNP markers linked to reduction pirubate-conducting QTLs located on chromosome 7 have also been identified. These SNP markers linked to reduction pirubate-conducting QTLs located on chromosome 7 include: SNP_22 located at nucleotide 51 of sequence SEQ ID NO: 43 or sequence SEQ ID NO: 43 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity; SNP_23 located at nucleotide 51 of sequence SEQ ID NO: 45 or sequence SEQ ID NO: 45 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity; and SNP_23 located at nucleotide 51 of sequence SEQ ID NO: 47 or sequence SEQ ID NO: 47 having at least 95% (more preferably) identity; SNP_24 located at nucleotide 51 of a sequence containing at least 96%, at least 97%, at least 98%, or even at least 99% identity; SNP_25 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with sequence number 49; SNP_09 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with sequence number 17;The group consists of and selected from the group comprising nucleotide 51 of SEQ ID NO: 19 or SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 19. Therefore, a specific example of a suitable SNP marker for determining the presence or absence of a reduced pirate-conferring QTL located between the marker isotig28625_2789 and the marker isotig41937_218 on chromosome 7 (preferably between the distal end of chromosome 7, including SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 43, or SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 19) is a suitable SNP marker for determining the presence or absence of a reduced pirate-conferring QTL located at nucleotide 51 of SEQ ID NO: 43, or at least 95% (more preferably at least 96%, at least 97%) identity with43, or at least 97% SNP_22 located at nucleotide 51 of a sequence containing at least 98% (more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 45 or SNP_23 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 45; SNP_24 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 47 or SNP_25 located at nucleotide 51 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 49 or SNP_25 located at nucleotide 51 of a sequence containing 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 is located at nucleotide 51 of sequence SEQ ID NO: 17 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 17; and SNP_10 is located at nucleotide 51 of sequence SEQ ID NO: 19 or at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 19. Therefore, SNP markers located on chromosome 7 and linked to a QTL that confers reduced pirubate levels may be useful in determining the presence of a QTL that confers reduced pirubate levels, with SNP_22 comprising thymine in nucleotide 51 of SEQ ID NO: 43 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 43; SNP_23 comprising thymine in nucleotide 51 of SEQ ID NO: 45 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 45; and SNP_24 comprising nucleotide 51 of SEQ ID NO: 47 SNP_25 comprises cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 49 or SNP_09 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 49; SNP_09 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 17;Furthermore, SNP_10 contains guanine in nucleotide 51 of SEQ ID NO: 19 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 19.

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

[0091] Therefore, the present invention relates to SNP_01, which comprises thymine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 1; SNP_02, which comprises adenine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 3; SNP_03, which comprises cytosine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 5; and nucleotide 51 of chromosome 2 having at least 95% (more preferably at least 96%, at least 96%, at least 99%) identity with nucleotide 51 of SEQ ID NO: 7. SNP_04 comprising thymine in nucleotide 51 of a sequence having 97%, at least 98%, or even more than at least 99% identity; SNP_05 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 9 on chromosome 1; SNP_06 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 11 on chromosome 1; SNP_07 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 12 on chromosome 1 or with SEQ ID NO: 13 on chromosome 1 on chromosome 1 on chromosome 1 on nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 12 on chromosome 1 or with nucleotide 51 of SEQ ID NO: 13 on chromosome 1.SNP_08 on chromosome 1, containing thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, containing thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 17; SNP_10 on chromosome 7, containing guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19; SNP_08 on chromosome 2, containing thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, containing thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%) identity with nucleotide 51 of SEQ ID NO: 19; SNP_10 on chromosome 7, containing guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%) identity with nucleotide 51 of SEQ ID NO: 21 SNP_11 comprising adenine in nucleotide 51 of a sequence having at least 98% or even more than 99% identity; SNP_12 of chromosome 2 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 23; SNP_13 of chromosome 2 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 25; SNP_14 of chromosome 2 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27;SNP_15 of chromosome 2, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 29; SNP_16 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 35; SNP_18 comprising thymine in nucleotide 51 of a sequence having 7%, at least 98%, or even more than at least 99% identity; SNP_19 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 37 on chromosome 1; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 39 on chromosome 1; SNP_21 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 41 on chromosome 1;SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 43 or sequence number 43 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_23 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 45 or sequence number 45 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of sequence number 47 or sequence number 47 having at least 95 The present invention provides a marker for identifying onion plants that produce bulbs with reduced pirubate levels, comprising one or more SNPs selected from the group consisting of: SNP_24 having cytosine in nucleotide 51 of a sequence having % (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; and SNP_25 having guanine in nucleotide 51 of chromosome 7, either in nucleotide 51 of sequence number 49 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with sequence number 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 of one or more markers as described herein in the plant or plant part. Accordingly, the present invention provides a method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs that confer a reduced pirubate level in the onion plant or plant part, the markers being selected from the group consisting of: a marker located between marker isotig30225_1454 and marker isotig32865_1404 on chromosome 2 and linked to a reduced pirubate-contributing QTL; a marker located between marker isotig32772_1413 and marker isotig33099_885 on chromosome 1 and linked to a reduced pirubate-contributing QTL; and a marker located between marker isotig28625_2789 and marker isotig41937_218 on chromosome 7 and linked to a reduced pirubate-contributing QTL.

[0093] The present invention provides a method for identifying and / or selecting onion plants or plant parts, which is particularly useful for determining the presence or absence of one or more QTLs that confer a reduced pirubate level in onion plants or plant parts, as described in WO2009 / 092560A1. Thus, in one embodiment, the present invention provides a method for identifying and / or selecting onion plants or plant parts, which comprises determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs that confer a reduced pirubate level in onion plants or plant parts, wherein the one or more QTLs conferring a reduced pirubate level are present in plants whose seeds are deposited under accession number PTA-9053, plants whose seeds are deposited under accession number PTA-9054, or plants whose seeds are deposited under accession number PTA-9055. Therefore, in one embodiment, the present invention is 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 that confer a reduced pirubate level in an onion plant or plant part obtained by crossing a plant whose seeds are deposited as accession number PTA-9053, a plant whose seeds are deposited as accession number PTA-9054, or a plant whose seeds are deposited as accession number PTA-9055 with another onion plant. The markers provided are selected from the group consisting of: a marker located between the markers isotig30225_1454 and isotig32865_1404 on chromosome 2, linked to a reduction pirubate-conducting QTL; a marker located between the markers isotig32772_1413 and isotig33099_885 on chromosome 1, linked to a reduction pirubate-conducting QTL; and a marker located between the markers isotig28625_2789 and isotig41937_218 on chromosome 7, linked to a reduction pirubate-conducting QTL.

[0094] Preferably, the present invention provides a method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs conferring a reduced pirubate level in the onion plant or plant part, wherein the markers are SNP_11 located at nucleotide 51 of a sequence of chromosome 2, having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 21 or SEQ ID NO: 21 and at least 95% (more preferably at least 96%, at least 97%, at least 98%) identity with nucleotide 51 of SEQ ID NO: 7 or SEQ ID NO: 7 A marker linked to a reduced pirubate-conducting QTL located between SNP_04 located at nucleotide 51 of a sequence containing at least 99% identity; a marker linked to a reduced pirubate-conducting QTL located between SNP_16 located at nucleotide 51 of sequence SEQ ID NO: 31 or sequence SEQ ID NO: 31 containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity and SNP_20 located at nucleotide 51 of sequence SEQ ID NO: 39 or sequence SEQ ID NO: 39 containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity;The markers are selected from the group consisting of SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 43, and SNP_10 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19, and markers linked to a reduced pirubate-contributing QTL located between the distal ends of chromosome 7, including SNP_22 located at nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19.

[0095] Preferably, this method involves 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 a reduced pirubate level in onion plants or plants as described herein. Many methods exist for detecting the presence or absence of the pungent alleles of the present invention.

[0096] For example, a single nucleotide polymorphism (SNP) may exist between the wild-type allele and the spiciness-reducing allele, and SNP genotyping assays can be used to detect whether a plant, plant part, or cell contains one or more wild-type (high-spiciness) nucleotides or spiciness-reducing nucleotides within its genome. For example, one or more SNPs can be readily detected using a KASP assay, where, for example, 50 base pairs upstream and 50 base pairs downstream of the SNP can be selected to design two allele-specific forward primers and one allele-specific reverse primer; for the KASP assay method, 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. For example, TaqMan SNP genotyping assays, high-sensitivity thawing (HRM) assays, SNP genotyping arrays (e.g., Fluidigm, Illumina, etc.), or DNA sequencing can be used.

[0098] Molecular markers can also be used to aid in the identification of plants (or plant parts or nucleic acids derived therefrom) that contain the pungent allele. For example, one or more suitable molecular markers that are genetically closely linked (and preferably also physically linked) to the pungent allele can be developed. Most preferably, the causative gene mutation is used as a molecular marker for identifying plants (or plant parts or nucleic acids derived therefrom) that contain the pungent allele. Suitable molecular markers can be developed by crossing onion plants with the pungent trait with wild-type plants and developing segregated populations (e.g., F2 or backcross populations) from the cross. Next, the phenotype of the spiciness reduction phenotype in this segregation can be analyzed, and the genotype can be analyzed using molecular markers such as SNPs (single nucleotide polymorphisms), AFLPs (amplification fragment length polymorphisms; see, e.g., EP534858), or others. Software analysis can also be used to identify molecular markers that segregate within the segregation along with the spiciness reduction trait, and, as further described herein, reduce-pirubate-donating QTLs located on chromosome 2, reduce-pirubate-donating QTLs located on chromosome 1, and reduce-pirubate-donating QTLs located on chromosome 7, along with their order and genetic distance (centimorgan distance, cM). Next, molecular markers closely linked to one of the reduce-pirubate-donating QTLs described herein, for example, markers within a distance of 5 cM, can be used to detect and / or select plants or plant parts that contain or retain the spiciness reduction allele (e.g., in a gene transfer fragment). 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, adjacent markers are used in MAS, i.e., one marker on either side of one or more QTLs that confer the reduced pirubate levels described herein in an onion plant or plant part.

[0099] As described herein, different specific SNP markers linked to different reduction pirubate-conducting QTLs have been identified, some located on chromosome 2, some on chromosome 1, and some on chromosome 7. Therefore, the present invention's method for identifying and / or selecting an onion plant or plant part comprises, in the plant or plant part, SNP_01 comprising thymine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 1; SNP_02 comprising adenine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 3; and a compound comprising at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 5. SNP_03 having cytosine in nucleotide 51 of a sequence; SNP_04 on chromosome 2 having thymine in nucleotide 51 of a sequence that has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 7; SNP_05 on chromosome 1 having cytosine in nucleotide 51 of a sequence that has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 9; SNP_06 on chromosome 1 having adenine in nucleotide 51 of a sequence that has at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 11;SNP_07 of chromosome 1, comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 12 or SEQ ID NO: 13; SNP_08 of chromosome 1, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15 or SEQ ID NO: 15; SNP_09 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 17 or SEQ ID NO: 17; SNP_09 of chromosome 7, comprising thymine in nucleotide 51 of SEQ ID NO: 19 or SEQ ID NO: 19 SNP_10 comprising guanine in nucleotide 51 of a sequence having at least 98% or even more than 99% identity with SEQ ID NO: 21; SNP_11 of chromosome 2 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 21; SNP_12 of chromosome 2 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 23; SNP_13 of chromosome 2 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 25;SNP_14 of chromosome 2, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 27; SNP_15 of chromosome 2, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 29; SNP_16 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 31; SNP_16 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 33; SNP_17 comprising adenine in nucleotide 51 of a sequence having 7%, at least 98%, or even more than at least 99% identity; SNP_18 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 35 on chromosome 1; SNP_19 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 37 on chromosome 1; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 39 on chromosome 1;SNP_21 of chromosome 1, comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 41; SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 43; SNP_23 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 45; SNP_23 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence number 47 SNP_24 comprising cytosine in nucleotide 51 of a sequence containing at least 99% identity with SEQ ID NO: 49 or SNP_25 comprising guanine in nucleotide 51 of a sequence containing 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 on chromosome 7; isotig30225_1454 comprising cytosine in nucleotide 61 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 51 on chromosome 2; isotig32865_1404 comprising guanine in nucleotide 61 of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 53 on chromosome 2;isotig32772_1413, is a sequence of chromosome 1 containing guanine in nucleotide 61 of sequence number 55 or sequence number 55 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; isotig33099_885, is a sequence of chromosome 1 containing thymine in nucleotide 61 of sequence number 57 or sequence number 57 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; and a sequence of chromosome 7 containing guanine in nucleotide 61 of sequence number 59 or sequence number 59. This may involve determining the presence or absence of one or more markers (e.g., at least two, three, four, or four) selected from the group consisting of isotig28625_2789, which contains guanine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 61 of chromosome 7, or isotig41937_218, which contains guanine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 61.

[0100] The present invention's method for identifying and / or selecting an onion plant or plant part preferably comprises, in the plant or plant part, SNP_01 comprising thymine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 1; SNP_02 comprising adenine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 3; SNP_03 comprising cytosine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 5; and SNP_03 comprising cytosine in nucleotide 51 of a sequence of chromosome 2 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 7. SNP_04 comprising thymine in nucleotide 51 of a sequence having 5% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_05 comprising cytosine in nucleotide 51 of sequence SEQ ID NO: 9 of chromosome 1; SNP_05 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 9; SNP_05 comprising cytosine in nucleotide 51 of sequence SEQ ID NO: 11 of chromosome 1 SNP_06 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with 1 or SEQ ID NO: 11; SNP_07 comprising cytosine in nucleotide 51 of a sequence of chromosome 1 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 12 or SEQ ID NO: 13;SNP_08 on chromosome 1, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 17; SNP_10 on chromosome 7, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19; SNP_08 on chromosome 2, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15; SNP_09 on chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%) identity with nucleotide 51 of SEQ ID NO: 21 SNP_11 comprising adenine in nucleotide 51 of a sequence having at least 98% or even more than 99% identity; SNP_12 of chromosome 2 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 23; SNP_13 of chromosome 2 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 25; SNP_14 of chromosome 2 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27;SNP_15 of chromosome 2, comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 29; SNP_16 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 31; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 33; SNP_17 of chromosome 1, comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 35; SNP_18 comprising thymine in nucleotide 51 of a sequence having 7%, at least 98%, or even more than at least 99% identity; SNP_19 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 37 on chromosome 1; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 39 on chromosome 1; SNP_21 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than at least 99%) identity with nucleotide 51 of SEQ ID NO: 41 on chromosome 1;SNP_22 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 43; SNP_23 of chromosome 7, comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 45; SNP_24 of chromosome 7, comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 47; SNP_24 of chromosome 7, comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 49; SNP_25, comprising guanine in nucleotide 51 of a sequence having at least 99% identity; isotig30225_1454, comprising cytosine in nucleotide 61 of sequence number 51 of chromosome 2, or having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with sequence number 51; nucleotide 61 of sequence number 53 of chromosome 2, or having at least 95% (more preferably) identity with sequence number 53 isotig32865_1404, wherein nucleotide 61 of a sequence containing at least 96%, at least 97%, at least 98%, or even more than 99% identity contains guanine; isotig32772_1413, wherein nucleotide 61 of chromosome 1 contains guanine, or of a sequence containing at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence number 55;isotig33099_885; This may involve determining the presence or absence of one or more markers (e.g., at least two, three, four, or four) selected from the group consisting of isotig28625_2789, which contains guanine at nucleotide 61 of sequence 61 of chromosome 7, or isotig41937_218, which contains guanine at nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence 61.

[0101] Preferably, the markers used in the method according to the present invention are fragment length polymorphism (RFLP) markers, cleavage-amplified polymorphism sequence (CPAS) markers, microsatellite markers, restriction enzyme 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 the reduced pirubate-granting QTL located on chromosome 2, used in the method according to the present invention, are: SNP_11 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 21; SNP_12 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 23; SNP_13 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 25; and SNP_13 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 27. SNP_14 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity; SNP_01 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 1 or SEQ ID NO: 01; SNP_02 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 3 or SEQ ID NO: 3; SNP_03 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with nucleotide 51 of SEQ ID NO: 5 or SEQ ID NO: 5;SNP_04 comprising thymine in nucleotide 51 of sequence SEQ ID NO: 7 or sequence SEQ ID NO: 7 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence SEQ ID NO: 7; SNP_15 comprising guanine in nucleotide 51 of sequence SEQ ID NO: 29 or sequence SEQ ID NO: 29 having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of sequence SEQ ID NO: 5 An SNP marker selected from the group consisting of isotig30225_1454, which contains cytosine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with 1; and isotig32865_1404, which contains guanine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 53.

[0103] Preferably, the markers linked to the reduced pirubate-granting QTL located on chromosome 1, used in the method according to the present invention, are: SNP_16 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 31; SNP_17 comprising adenine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 33; SNP_05 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 9; and SNP_05 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 11. SNP_06 comprising adenine in nucleotide 51 of a sequence having % (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity; SNP_07 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 12 or SEQ ID NO: 13; SNP_08 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 15 or SEQ ID NO: 15; SNP_18 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 35 or SEQ ID NO: 35;SNP_19 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 37; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 39; SNP_20 comprising guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 41 The SNP marker is selected from the group consisting of: SNP_21, which contains cytosine in nucleotide 51 of a sequence having identity with SEQ ID NO: 55; isotig32772_1413, which contains guanine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 55; and isotig33099_885, which contains thymine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with SEQ ID NO: 57.

[0104] Preferably, the markers linked to the reduced pirubate-granting QTL located on chromosome 7, used in the method according to the present invention, are: SNP_22 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 43; SNP_23 comprising thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 45; SNP_24 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 47; and SNP_24 comprising cytosine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more preferably at least 99%) identity with nucleotide 51 of SEQ ID NO: 49. SNP_25 comprises guanine in nucleotide 51 of a sequence having at least 96%, at least 97%, at least 98%, or even more than 99% identity; SNP_09 comprises thymine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 17; and SNP_10 comprises guanine in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 51 of SEQ ID NO: 19; and isotig28625_2789 comprises guanine in nucleotide 61 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with nucleotide 61 of SEQ ID NO: 59;The SNP marker is selected from the group consisting of isotig41937_218, which contains guanine in nucleotide 61 of sequence number 61 or in a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even more than 99%) identity with sequence number 61.

[0105] Preferably, a method according to the present invention for identifying and / or selecting an onion plant or plant part comprises determining the presence or absence of two or more markers in the plant or plant part. Thus, a method according to the present invention for identifying and / or selecting an onion plant or plant part may comprise determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 2 and at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 1 in the plant or plant part. A method according to the present invention for identifying and / or selecting an onion plant or plant part may also comprise determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 2 and at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 7 in the plant or plant part. A method according to the present invention for identifying and / or selecting an onion plant or plant part may also include determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 1 and at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 7 in the plant or plant part.More preferably, a method according to the present invention for identifying and / or selecting an onion plant or plant part also includes determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 2, at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 1, and at least one (e.g., at least two, three, four, or four) markers linked to a reduction pirubate-granting QTL located on chromosome 7.

[0106] Preferably, the method according to the present invention for identifying and / or selecting an onion plant or plant part comprises determining the presence or absence of a marker linked to at least one reduction pirubate-granting QTL located on chromosome 2, a marker linked to at least one reduction pirubate-granting QTL located on chromosome 1, and a marker linked to at least one reduction pirubate-granting QTL located on chromosome 7 in the plant or plant part.

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

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

[0109] Therefore, the method according to the present invention for identifying and / or selecting an onion plant or plant part preferably comprises, in the plant or plant part, at least one (e.g., at least two, three, four or four) markers linked to a reduced pirubate-granting QTL located on chromosome 2 (the marker on chromosome 2 is an SNP_03 having cytosine in nucleotide 51 of sequence SEQ ID NO: 5 or in nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with SEQ ID NO: 5); and at least one (e.g., at least two, three, four or four) markers linked to a reduced pirubate-granting QTL located on chromosome 1 (the marker on chromosome 1 is The method includes determining the presence or absence of at least one (e.g., at least two, three, four, or four) markers linked to a reduced pirubate-granting QTL located on chromosome 7 (this marker on chromosome 7 is at least one (e.g., at least two, three, four, or four) markers, at least one (e.g., at least two, three, four, or four) markers linked to the nucleotide 51 of sequence number 19 or at least one (e.g., at least two, three, four, or four) nucleotide 51 of a sequence having at least 95% (more preferably at least 96%, at least 97%, at least 98%, or even at least 99%) identity with sequence number 19).

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

[0111] Therefore, an isolated nucleic acid as provided herein comprises at least 15 nucleotides, each comprising nucleotide 51 of any one nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50. Furthermore, an isolated nucleic acid as provided herein comprises a complementary sequence of the isolated nucleic acid comprising at least 15 nucleotides, each comprising nucleotide 51 of any one nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50. This means that an isolated nucleic acid as provided herein comprises a fragment of at least 15 consecutive nucleotides, each comprising nucleotide 51 of any nucleotide sequence or a complementary nucleotide sequence thereof, selected from the group consisting of SEQ ID NOs: 1 to 50. Preferably, the isolated nucleic acid of the present invention comprises more than 15 nucleotides, each comprising one nucleotide 51 from any nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 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, each comprising one nucleotide 51 from any nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50, or any complementary nucleotide sequence thereof.

[0112] The nucleic acids according to the present invention are particularly useful for use in or development in methods for identifying and / or selecting onion plants or plant parts, and for methods for producing onion plants comprising crossing a first onion plant with a second onion plant and selecting onion plants from the offspring of the cross based on the presence or absence of one or more markers of the present invention. Accordingly, the present invention provides the use of one or more 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 the selection of onion plants or plant parts assisted by markers, wherein the fragments consist of at least 15 nucleotides comprising nucleotide 51 of the nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50 or one or more complementary sequences of the nucleotide sequence. 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, for marker-assisted selection of onion plants or plant parts, wherein the fragments consist of at least 15 nucleotides comprising nucleotide 61 of the nucleotide sequence selected from the group consisting of SEQ ID NOs. 51 to 62, or one or more complementary sequences of the nucleotide sequence.Preferably, the nucleotide sequence used in the present invention contains, for example, more than 15 nucleotides, each containing one nucleotide 61 from any of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 51 to 62, each containing one nucleotide 51 from any of the nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 to 50, for example, a nucleotide sequence selected from the group consisting of SEQ ID NOs: 51 to 62, or one nucleotide 61 from a complementary sequence of the nucleotide sequence. This may be any one of the nucleotide sequences described herein, 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, which include nucleotide 51 of any one nucleotide sequence selected from the group consisting of SEQ ID NOs: 1 to 50.

[0113] Seed deposit Representative samples of seeds containing QTLs that impart reduced pirubate levels as described herein were deposited by Nunhems BV on March 13, 2008, in accordance with the Budapest Convention and under the Expert Solution (EPC 2000 Rule 32(1)), with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209, USA). The seeds were assigned the following deposit numbers: PTA-9053 (seeds of the I37853B lineage as further described in WO2009 / 092560A1), PTA-9054 (seeds of the I37554A lineage as further described in WO2009 / 092560A1), and PTA-9055 (seeds of the I37554B lineage as further described in WO2009 / 092560A1).

[0114] The applicant requires that samples of the biological material and any material derived therefrom be made available only to designated experts, in accordance with the relevant laws or treaties of each country with EPC Rule 32(1) or similar rules or regulations, until the patent is granted, or for 20 years from the filing date if the patent is rejected, withdrawn, or deemed withdrawn.

[0115] During the pendency of this application, access to the deposited material will be granted to any person whom the Director of the United States Patent and Trademark Office determines to have such rights at the time of the claim. In accordance with 37C.FR §1.808(b), any restrictions imposed by the depositor regarding the public availability of the deposited material will be irrevocably removed upon grant of the patent. The deposited material will be maintained for 30 years, or 5 years from the most recent claim, or for the enforceable term of the patent, whichever is longer, and will be replaced if it becomes unsustainable during that period. The applicant does not waive any rights granted under this patent or under the Plant Variety Protection Act (7 USC 2321 or later). [Examples]

[0116] Example 1 QTL map creation A single low-pungency (reduced-pungency) line, I37720B, obtained from a cross between l37554B and material from the I37554B line, was crossed with two asymmetric pungency lines, I37977B ("Population 1") and I37545-7 ("Population 2"). The resulting F1 hybrids were self-pollinated to produce two separate populations of F2 plants. A total of 331 F2 plants were cultivated in Population 1, and a total of 236 plants were cultivated in Population 2 under field conditions at Brooks, OR. Leaf tissue was collected from each F2 plant for DNA extraction. Bulbs were harvested, stored for 4 months, and then the pirubate levels were measured.

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

[0118] In population 1, two significant QTLs exceeding the calculated LOD threshold were detected: one on linkage group 3 (chromosome 2) and one on linkage group 6 (chromosome 7). Population 2 contained a single significant QTL on linkage group 4 (chromosome 1). Peak markers for these three QTLs were confirmed in the combined linkage map, and additional proximity markers were added to the F2 population map. The number of additional markers added is detailed in Table 1. Information on peak and proximity markers for each significant QTL is shown in Table 2.

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

[0120] [Table 1]

[0121] [Table 2]

[0122] [Table 3]

[0123] Furthermore, the QTLs of the present invention were placed on the publicly available genetic maps of onion. All publicly available markers referenced herein are described in detail in Duangjit et al. (2013) Theor Appl Genet 126, 2093-2101. The referenced “B9885×B8667” map is described in detail in Munaiz and Havey (2020) J. Amer. Soc. Hort. Sci., 145(1), 67-72, and the referenced “Char×B5351” map is described in detail in Havey (2000) J. Amer. Soc. Hort. Sci., 145(2), 110-119. The QTLs of the present invention were placed on these publicly available maps by integrating internal datasets with publicly available marker information, and genotyping of the low-pungency strain I37720B with the publicly available markers was performed to determine the alleles linked to the piruvate reduction locus. Publicly available markers that further define the QTL locus of the present invention are listed in Table 4, provided below in this specification.

[0124] [Table 4]

[0125] [Table 5]

[0126] Therefore, it can be concluded that the reduced pirubate-contributing QTL located on chromosome 2 is situated between the publicly available markers isotig30225_1454 (sequence number 51) and isotig32865_1404 (sequence number 53), which correspond to an interval of 19.4 cM. The reduced pirubate-contributing QTL located on chromosome 1 is situated between the publicly available markers isotig32772_1413 (sequence number 55) and isotig33099_885 (sequence number 57), which correspond to an interval of 14.5 cM. The reduced pirubate-contributing QTL on chromosome 7 is situated between the publicly available markers isotig28625_2789 (sequence number 59) and isotig41937_218 (sequence number 61), which correspond to an interval of 11.2 cM.

[0127] Furthermore, the previously detailed markers were also placed on individual public maps. Since the inventors did not access isolated individuals to calculate precise gene distances for these maps, they placed them at intervals based on the public maps.

[0128] [Table 6]

[0129] Example 2 QTL marker validation To confirm that the identified markers are useful for predicting pirubate levels, the inventors performed genotyping of a strain panel with a certain range of pirubate values. Genotyping was performed on five bulbs of each strain, and the pirubate concentration was assigned based on the average of the bulbs of that strain.

[0130] Pilvate levels were measured in onion bulbs after 4 months of storage. Sections 5-10 mm thick were prepared from the equator of onion bulbs (25-50 g). These sections were divided into four parts, mixed with deionized water (1:10 dilution), and homogenized in an immersion blender until no lumps remained (approximately 45 seconds). 1 mL of onion juice was centrifuged for 5 minutes (16,000 x g, room temperature). The supernatant was used for pilvate measurement, which was performed using the Anthon and Barrett method (2003) with some modifications. In a 96-well microplate, 6 mL of onion juice was mixed with 50 mL of 0.025% dinitrophenylhydrazine (DNPH) reagent. This mixture was incubated at 37°C for 15 minutes, and then 50 mL of 1.5 N sodium hydroxide (NaOH) was added. After cooling this mixture to room temperature, the absorbance was read at 515 nm. Pilvate analysis was performed in three replicates for each sample. Calibration curves were prepared using 0.4, 0.8, and 1.2 mM pirubate standard solutions. Results are reported as pirubate μmol per gram of tissue weight (μmol / g).

[0131] The validation results confirmed that in the spiciness-reducing strains, the spiciness-reducing haplotype (referred to as the "B" allele) was enriched, and strains with lower average pirubate values ​​and less variability in pirubate levels had a lower abundance of the high-pirubate ("A") allele (Table 7). In all spiciness-reducing materials, the soluble solids content (SSC) measured by Brix exceeded 7%, and there was no correlation with the pirubate level (R 2 = 0.2 (negative slope).

[0132] The linkage groups described herein were mapped to known markers to determine which chromosome number corresponds to each linkage group. Thus, 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.

[0133] [Table 7] JPEG2026065039000008.jpg246156

Claims

1. A method for identifying and / or selecting an onion plant or plant part, comprising determining the presence or absence of one or more markers suitable for determining the presence of one or more QTLs that confer a reduced pirubate level in the onion plant or plant part, wherein the markers are A marker linked to a reduction pirubate-conducting QTL located between markers isotig30225_1454 and isotig32865_1404 on chromosome 2; a marker linked to a reduction pirubate-conducting QTL located between markers isotig32772_1413 and isotig33099_885 on chromosome 1; and A marker linked to a reduced pirubate-contributing QTL located between markers isotig28625_2789 and isotig41937_218 on chromosome 7. A method selected from the group consisting of the following.

2. The method according to claim 1, wherein the marker is a fragment length polymorphism (RFLP) marker, a cleavage-amplified polymorphism sequence (CPAS) marker, a microsatellite marker, a restriction enzyme fragment length polymorphism (RFLP) marker, a randomly amplified polymorphic DNA (RAPD) marker, an amplified fragment length polymorphism (AFLP) marker, or a single nucleotide polymorphism (SNP) marker, preferably an SNP marker.

3. The markers linked to the reduced pirubate-contributing QTL located on chromosome 2 are: SNP_11, which contains adenine in nucleotide 51 of SEQ ID NO: 21 or in a sequence having at least 95% identity with SEQ ID NO: 21; SNP_12, which contains cytosine in nucleotide 51 of SEQ ID NO: 23 or in a sequence having at least 95% identity with SEQ ID NO: 23; SNP_13, which contains thymine in nucleotide 51 of SEQ ID NO: 25 or in a sequence having at least 95% identity with SEQ ID NO: 25; SNP_14, which contains adenine in nucleotide 51 of SEQ ID NO: 27 or in a sequence having at least 95% identity with SEQ ID NO: 27; SNP_01, which contains thymine in nucleotide 51 of SEQ ID NO: 1 or in a sequence having at least 95% identity with SEQ ID NO: 01; and SNP_01, which contains thymine in nucleotide 51 of SEQ ID NO: 3 or in a sequence having at least 95% identity with SEQ ID NO:

3. The method according to claim 2, wherein the SNP marker is selected from the group consisting of: SNP_02 having adenine in sequence nucleotide 51; SNP_03 having cytosine in nucleotide 51 of sequence number 5 or a sequence having at least 95% identity with sequence number 5; SNP_04 having thymine in nucleotide 51 of sequence number 7 or a sequence having at least 95% identity with sequence number 7; SNP_15 having guanine in nucleotide 51 of sequence number 29 or a sequence having at least 95% identity with sequence number 29; isotig30225_1454 having cytosine in nucleotide 61 of sequence number 51 or a sequence having at least 95% identity with sequence number 51; and isotig32865_1404 having guanine in nucleotide 61 of sequence number 53 or a sequence having at least 95% identity with sequence number 53.

4. The markers linked to the reduced pirubate-contributing QTL located on chromosome 1 are: SNP_16, which contains adenine in nucleotide 51 of SEQ ID NO: 31 or in a sequence having at least 95% identity with SEQ ID NO: 31; SNP_17, which contains adenine in nucleotide 51 of SEQ ID NO: 33 or in a sequence having at least 95% identity with SEQ ID NO: 33; and nucleotide 51 of SEQ ID NO: 9 or in a sequence having at least 95% identity with SEQ ID NO:

9. SNP_05 containing cytosine; SNP_06 containing adenine in nucleotide 51 of sequence number 11 or in a sequence having at least 95% identity with sequence number 11; SNP_07 containing cytosine in nucleotide 51 of sequence number 13 or in a sequence having at least 95% identity with sequence number 13; SNP_08 containing thymine in nucleotide 51 of sequence number 15 or in a sequence having at least 95% identity with sequence number 15; SNP_05 containing cytosine in sequence number 35 SNP_18 comprising thymine in nucleotide 51 of a sequence having at least 95% identity with creotide 51 or sequence number 35; SNP_19 comprising thymine in nucleotide 51 of sequence number 37 or sequence number 37 having at least 95% identity with sequence number 37; SNP_20 comprising guanine in nucleotide 51 of sequence number 39 or sequence number 39 having at least 95% identity with sequence number 39; SNP_18 comprising thymine in nucleotide 51 of sequence number 41 or sequence number 41 having at least 95% identity with sequence number 41 The method according to claim 2, wherein the SNP marker is selected from the group consisting of SNP_21 having cytosine in nucleotide 51 of a sequence having 5% identity; isotig32772_1413 having guanine in nucleotide 61 of SEQ ID NO: 55 or of a sequence having at least 95% identity with SEQ ID NO: 55; and isotig33099_885 having thymine in nucleotide 61 of SEQ ID NO: 57 or of a sequence having at least 95% identity with SEQ ID NO:

57.

5. The markers linked to the reduced pirubate-contributing QTL located on chromosome 7 are: SNP_22, which contains thymine in nucleotide 51 of SEQ ID NO: 43 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 43; SNP_23, which contains thymine in nucleotide 51 of SEQ ID NO: 45 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 45; SNP_24, which contains cytosine in nucleotide 51 of SEQ ID NO: 47 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 47; SNP_25, which contains guanine in nucleotide 51 of SEQ ID NO: 49 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 49; and the nucleotide of SEQ ID NO: 17 The method according to claim 2, wherein the SNP marker is selected from the group consisting of: SNP_09 comprising thymine in rheotide 51 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 17; SNP_10 comprising guanine in nucleotide 51 of SEQ ID NO: 19 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 19; isotig28625_2789 comprising guanine in nucleotide 61 of SEQ ID NO: 59 or in nucleotide 61 of a sequence having at least 95% identity with SEQ ID NO: 59; and isotig41937_218 comprising guanine in nucleotide 61 of SEQ ID NO: 61 or in nucleotide 61 of a sequence having at least 95% identity with SEQ ID NO:

61.

6. The method according to any one of claims 1 to 5, comprising determining the presence or absence of at least one marker located on chromosome 2 and linked to a reduced pirubate-granting QTL, at least one marker located on chromosome 1 and linked to a reduced pirubate-granting QTL, and at least one marker located on chromosome 7 and linked to a reduced pirubate-granting QTL in the plant or plant part.

7. The method according to claim 6, wherein the marker on chromosome 2 is SNP_03, which comprises cytosine in nucleotide 51 of SEQ ID NO: 5 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 5; the marker on chromosome 1 is SNP_07, which comprises cytosine in nucleotide 51 of SEQ ID NO: 13 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO: 13; and the marker on chromosome 7 is SNP_10, which comprises guanine in nucleotide 51 of SEQ ID NO: 19 or in nucleotide 51 of a sequence having at least 95% identity with SEQ ID NO:

19.

8. The method according to any one of claims 1 to 7, wherein one or more QTLs that impart the reduced pirubate level are present in a plant whose seeds are deposited under accession number PTA-9053, a plant whose seeds are deposited under accession number PTA-9054, or a plant whose seeds are deposited under accession number PTA-9055.

9. A fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 1 or sequence number 1; A fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 3; A fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 5; A fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 7; A fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 9; The fragment comprising at least 15 nucleotides, including sequence number 11 or nucleotide 51 of sequence number 11; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 13; The fragment comprising at least 15 nucleotides, including sequence number 15 or nucleotide 51 of sequence number 15; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 17; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 19; The fragment comprising at least 15 nucleotides, including sequence number 21 or nucleotide 51 of sequence number 21; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 23; The fragment comprising at least 15 nucleotides, including sequence number 25 or nucleotide 51 of sequence number 25; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 27; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 29; A fragment comprising at least 15 nucleotides, including sequence number 31 or nucleotide 51 of sequence number 31; The fragment comprising at least 15 nucleotides, including sequence number 33 or nucleotide 51 of sequence number 33; The fragment comprising at least 15 nucleotides, including sequence number 35 or nucleotide 51 of sequence number 35; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 37; The fragment comprising at least 15 nucleotides, including nucleotide 51 of sequence number 39; A fragment comprising at least 15 nucleotides, including sequence number 41 or nucleotide 51 of sequence number 41; A fragment comprising at least 15 nucleotides, including sequence number 43 or nucleotide 51 of sequence number 43; The fragment comprising at least 15 nucleotides, including sequence number 45 or nucleotide 51 of sequence number 45; The fragment comprising at least 15 nucleotides, including sequence number 47 or nucleotide 51 of sequence number 47; and The fragment consists of at least 15 nucleotides, including sequence number 49 or nucleotide 51 of sequence number 49. Isolated nucleic acids comprising nucleotide sequences selected from the group consisting of, or comprising complementary nucleotide sequences thereof.

10. Nucleotide sequences or fragments thereof selected from the group consisting of SEQ ID NOs: 1-50 and SEQ ID NOs: 51-62, for marker-assisted selection of onion plants or plant parts. (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 to 50; or The fragment consists of at least 15 nucleotides, each containing nucleotide 61 of the nucleotide sequence selected from the group consisting of SEQ ID NOs. 51 to 62. The use of one or more of the above, or one or more complementary sequences from the nucleotide sequences.

11. SNP_01 of chromosome 2, comprising thymine in nucleotide 51 of sequence number 1 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 1; SNP_02 of chromosome 2, comprising nucleotide 51 of sequence number 3 or a sequence having at least 95% identity with sequence number 3, with nucleotide 51 containing adenine; SNP_03 of chromosome 2, having cytosine in nucleotide 51 of sequence number 5, or in nucleotide 51 of a sequence having at least 95% identity with sequence number 5; SNP_04 of chromosome 2, having thymine in nucleotide 51 of sequence number 7 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 7; SNP_05 of chromosome 1, comprising cytosine in nucleotide 51 of sequence number 9 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 9; SNP_06, of chromosome 1, having adenine in nucleotide 51 of sequence number 11 or in a sequence having at least 95% identity with sequence number 11; SNP_07, of chromosome 1, having cytosine in nucleotide 51 of sequence number 13 or in a sequence having at least 95% identity with sequence number 13; SNP_08, of chromosome 1, having thymine in nucleotide 51 of sequence number 15 or in a sequence having at least 95% identity with sequence number 15; SNP_09 of chromosome 7, having thymine in nucleotide 51 of sequence number 17 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 17; SNP_10 on chromosome 7, containing guanine in nucleotide 51 of sequence number 19 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 19; SNP_11 on chromosome 2, containing adenine in nucleotide 51 of sequence number 21 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 21; SNP_12 on chromosome 2, containing cytosine in nucleotide 51 of sequence number 23 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 23; SNP_13 on chromosome 2, containing thymine in nucleotide 51 of sequence number 25 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 25; SNP_14, of chromosome 2, containing adenine in nucleotide 51 of sequence number 27 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 27; SNP_15, of chromosome 2, containing guanine in nucleotide 51 of sequence number 29 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 29; SNP_16, of chromosome 1, containing adenine in nucleotide 51 of sequence number 31 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 31; SNP_17, of chromosome 1, containing adenine in nucleotide 51 of sequence number 33 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 33; SNP_18, of chromosome 1, containing thymine in nucleotide 51 of sequence number 35 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 35; SNP_19 of chromosome 1, having thymine in nucleotide 51 of sequence number 37 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 37; SNP_20, of chromosome 1, containing guanine in nucleotide 51 of sequence number 39 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 39; SNP_21, of chromosome 1, containing cytosine in nucleotide 51 of sequence number 41 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 41; SNP_22, of chromosome 7, containing thymine in nucleotide 51 of sequence number 43 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 43; SNP_23 of chromosome 7, having thymine in nucleotide 51 of sequence number 45 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 45; SNP_24 of chromosome 7, having cytosine in nucleotide 51 of sequence number 47 or in nucleotide 51 of a sequence having at least 95% identity with sequence number 47; and SNP_25, which contains guanine in nucleotide 51 of chromosome 7, or in nucleotide 51 of a sequence having at least 95% identity with sequence number 49. Selected from the group consisting of A marker for identifying onion plants that produce bulbs with reduced pirubate levels, comprising one or more SNPs.

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