Fine mapping and validation of QTL underlying fiber content and seed coat color traits and identification of SNP markers for marker assisted selection of these traits derived from yellow seed coat (YSC) canola line YN01-429 and its lineage

Abstract

A method for identifying a quantitative trait locus associated with desirable nutritional traits in canola includes: analyzing a population of canola plants or germplasm for desirable nutritional traits; determining the genotype of the canola plants or germplasm using at least one marker selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 111; mapping the canola plants or germplasm for the presence of a quantitative trait locus (QTL) associated with the markers; and associating the QTL with the desirable nutritional trait. An isolated and / or recombinant nucleic acid includes a sequence associated with a quantitative trait locus (QTL), wherein the QTL is associated with a desirable nutritional trait in a canola plant or germplasm and wherein the QTL is further associated with at least one marker selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 111.

Description

CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 FINE MAPPING AND VALIDATION OF QTL UNDERLYING FIBER CONTENT AND SEED COAT COLOR TRAITS AND IDENTIFICATION OF SNP MARKERS FOR MARKER ASSISTED SELECTION OF THESE TRAITS DERIVED FROM YELLOW SEED COAT (YSC) CANOLA LINE 5 YN0l-429 AND ITS LINEAGE PRIORITY CLAIM This application claims the benefit of the filing date of United States Provisional Patent 10 Application Serial Number 62 / 093,963, filed December 18, 2014 for "FINE MAPPING AND VALIDATION OF QTL UNDERLYING FIBER CONTENT AND SEED COAT COLOR TRAITS AND IDENTIFICATION OF SNP MARKERS FOR MARKER ASSISTED SELECTION OF THESE TRAITS DERIVED FROM YELLOW SEED COAT (YSC) CANOLA LINE YN0l-429 AND ITS LINEAGE" 15 which is incorporated herein in its entirety. TECHNICAL FIELD The disclosure relates to fine mapping of quantitative trait loci ( QTLs) associated with low fiber content and YSC traits and identification of SNP markers for marker assisted 20 selection of these traits in Brassica napus. BACKGROUND Canola (Brassica napus L., 2n = 4x = 38, AACC), an allotetraploid formed :from diploids B. rapa (2n = 2x = 20, AA) and B. oleracea (2n = 2x = 18, CC), is one of 25 the most important vegetable oilseed crops in the world, especially in China, Canada, the European Union and Australia. Canola meal, the fraction of the seed remaining after crushing and oil extraction, is approximately 55% of the volume of canola seed. Canola meal consists of several components including protein, fiber, residual oil, 30 carbohydrates, and anti-nutritional factors. Canola meal contains approximately 75% of the protein of 48% protein soybean meal, 80% of the energy value, and 300% of the crude fiber, as well as higher levels of anti-nutritional factors such as glucosinolates, tannins, phytic acid, sinapine and erucic acid, and is sold as livestock feed at 60%-70% of the price of soybean meal. See, e.g., Hickling (2007) Canola 35 meal competitive situation and Canola Council of Canada goals, Canola Meal 1 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 Research Meeting, Saskatoon, Canada; Newkirk (2009) Canola meal feed industry guide ( 4th Edition),. The relatively high fiber content of cartola meal is a significant limiting factor for its use in monogastric animal species (Hickling, 2007; Newkirk, 2009). Since meal comprises half of the seed volume of canola, and demand for 5 biodiesel could ddve a 67% increase in rapeseed seed production from 2006 to 2015 (Hickling, 2007), there is a need to modify the compositional properties of canola meal and thereby increasing its nutritional value relative to soybean. Scientists at Agdculture and Agri-Foods Canada (AAFC) have developed yellow seed coat (YSC) lines (YN86-37, YN90-1016, YN97-262 and YN0l-429) of 10 low hull proportion with thinner seed coat, low fiber and high oil compared to the black seed coat (BSC) canola (Rakow et al., 2011). Feeding studies, compadng yellow seeded canola meal from AAFC line YN0l-429 to B. juncea, B. rapa, and brownseeded B. napus, demonstrated the advantages of YSC B. napus line such as higher protein, lower fiber, increased amino acid digestibility and metabolizable energy 15 content, and improved nutrient and energy utilization based on feed to gain ratio in broiler chickens and monogastdc animal species (Hickling, 2009; Slominski et al., 2010). The breeding of low fiber content has been greatly hampered by a poor understanding of the inheritance and stability of the low fiber content ti·aits, as well 20 as a lack of robust,high-throughput markers tightly linked to the trait. Due to allotetraploidy, effect of multiple genes, maternal effects and environmental effects, the inheritance of low fiber content trait is complex, and identification of markers tightly linked to this trait is very challenging. Somers et al, (2001) reported identification of eight random amplified polymorphic DNA (RAPD) markers for a 25 major gene (pigment]) associated with yellow seed coat trait from YSC line YN90- l O 16, the low fiber content source of YN97-262 and YN0l-429 used in the applicant's Low Fiber breeding program (Rakow et al., 2011). The major gene explained 72.3% of the variation in seed color, while two additional genes that appeared to be additive explained 21.5% of the color vadation (Somers et al., 2001). 30 It has been suggested that the low fiber content of AAFC YSC line YN0 1- 429 and its lineage might be controlled by three recessive genes (Kubik and Thompson, 2009). Current selection of lower fiber canola lines has pdmarily been 2 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 5 based on fiber content data obtained using cost and labor intensive analytical methods, or seed coat color, because of its high co1Telation with low fiber in the AAFC YSC lines YN97-262 and YN0l-429. DISCLOSURE A particular embodiment of the invention includes a method for identifying quantitative trait locus associated with desirable nutritional traits in canola. The method includes analyzing a population of canola plants or germplasm for desirable nutritional traits. The genotype of the canola plants or germplasm is determined using 10 at least one marker selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 111. The canola plants or genuplasm are mapped for the presence of a quantitative trait locus (QTL) associated with the markers. The QTL is associated with the desirable nutritional trait. Another embodiment relates to an isolated and / or recombinant nucleic acid 15 having a sequence associated with a QTL. The QTL is associated with a desirable nutritional trait in a canola plant or germplasm. The QTL is further associated with at least one marker selected from the group consisting of SEQ ID NO: 1 through SEQ IDNO:111. Yet another embodiment relates to a method for selecting a canola plant or 20 germplasm that comprises desirable nutritional traits. The method includes detecting in the canola plant or germplasm at least one marker linked with a QTL that is selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 111, wherein the QTL is associated with a desirable nutritional trait in the canola plant or germplasm. A canola plant or germplasm is then selected based on the presence of the marker. 25 The foregoing and other features will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures. BRIEF DESCRIPTION OF THE DRAWINGS 30 FIG. 1 shows the distribution of White fudex (WI) and %ADF in Nex828 x YN0l-429 (YSC) DH lines. The left figure shows the White fudex (WI) of seed coat color plotted against % of ADF in canola seed. The right figure shows the 3 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 distribution of ¾ADF among DH lines. The number in bracket indicated % of ADF in canola seed. FIG. 2 shows the distribution of White Index (WI) and ¾ADF in DN051493 x YN0l-429 (YDN) DH lines. The left figure shows White Index (WI) of seed coat 5 color plotted against% of ADF canola seed. The right figure shows the distribution of ¾ADF among DH lines. The number in bracket indicated % of ADF in canola seed. FIG. 3A shows the location (X-axis) and significance (LOD score on Yaxis) of the QTL identified on N09. FIG. 3B shows the additive effect of the QTL 10 identified on N09. FIG. 4A shows the location (X-axis) and significance (LOD score on Yaxis) of the QTL identified on Nl 1. FIG. 4B shows the additive effect of the QTL identified on N09. FIG. 5A shows the location (X-axis) and significance (LOD score on Y- 15 axis) of the QTL identified on N09. FIG. 5B shows the additive effect of the QTL identified on N09. FIG. 6A shows the location (X-axis) and significance (LOD score on Yaxis) of the QTL identified on Nl 1. FIG. 6B shows the additive effect of the QTL identified on Nl 1. 20 FIG. 7 shows a Map of the major ADF QTL interval on N09, constructed with the YDN DH population. Within the 4.9 cM QTL interval, 111 SNP markers were identified, including the flanking markers DBSNP01120 and DBSNP02172. The ADF 9 and WI_9 loci are also mapped within the interval. FIG. 8 shows a map of N09 constructed with N09 of YDN, YSC and TN 25 DH populations, showing 18 SNP markers identified within 0.0-4.9 cM to a major QTL underlying fiber content (ADF_9) and seed coat color (WI_9) on N09. DISCLOSURE Described herein are high-throughput single nucleotide polymorphism (SNP) 30 markers and high-density genetic maps for fme mapping and validation of quantitative trait loci (QTL) underlying fiber content and seed coat color traits. In some embodiments, SNP markers tightly linked to fiber content and seed coat color 4 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 traits may be used for marker-assisted selection (MAS) of desirable nutritional traits in yellow-seeded canola (YSC) lines. In particular embodiments, the YSC line may be AAFC YSC line YN0l-429 and its lineage. Also disclosed is a method of leveraging SNP markers and high-density 5 genetic maps based on fiber content and seed coat color traits from AAFC YSC line YN0l-429, using an extensive set of phenotypic data of two DH populations. In a particular embodiment, a major QTL, which explains 59.2% to 74.7% of the variance of fiber content and seed coat color traits, is described on N09 in two DH populations, and a minor QTL, which explains 1.4% to 7.2% of the variance of fiber 10 content and seed coat color traits, is described on Nl 1 in two DH populations. High correlation (R2 = 0.67-0.85) exists between seed coat color traits (WI and L) and ADP content in both populations. Also disclosed herein are 18 SNP markers within 0.0-4.9 cM of the major fiber content and seed coat color QTL on N09 (see Figure 8), and 40 SNP markers 15 within 0.0-4.1 cM of the minor fiber content and seed coat color QTL on Nll, which may be used in embodiments for marker-assisted selection of complex low fiber content and YSC traits from YSC line YN0l-429 and its lineage, and thus may improve the breeding process of canola lines with low ADP content if YN0l-429 or it lineage is used as a low fiber content source in breeding programs. 20 An Low Fiber product which aims to improve the nutritional value of commercial canola meal to 85-90% of the value of 48% protein soybean meal by increasing protein content (from 36% to 44%) and true metabolizable energy (TME) (a 16%-20% increase), and decreasing fiber content (from 15-19% to less than 10%) has been developed. These improvements are anticipated to increase the nutritive 25 value of canola meal, particularly in monogastric species, and should allow increasing dietary inclusion rates. YSC lines (YN86-37, YN90-1016, YN97-262 and YN0l-429) of low hull proportion with a thinner seed coat, low fiber and high oil as compared to black seed coat (BSC) canola (Rakow et al., 2011) also have been developed. Feeding studies 30 comparing yellow-seeded canola meal from AAFC line YN0l-429 to B. juncea, B. rapa, and brown-seeded B. napus have demonstrated the advantages of the YSC B. napus line, including higher protein, lower fiber, increased amino acid digestibility 5 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 and metabolizable energy content, and improved nutrient and energy utilization based on feed to gain ratio in broiler chickens and monogastric animal species (Hickling, 2009; Slominski et al., 2010).

[0001] Combinations of the yellow seeded / low fiber traits from YSC lines YN97- 5 262 and YN0 1-419 with the Omega 9 fatty acid profile, as well as other desirable agronomic and seed quality attributes, have been studied. L Mapping and Validation o / Low Fiber Content and YSC Traits from YN0J-429 In a preferred embodiment, the disclosure describes a method for identifying 10 and mapping quantitative trait loci (QTL) associated with low fiber content and yellow seed coat (YSC) traits in Brassica napus using single-nucleotide polymorphism (SNP) markers. In embodiments, the QTLs are defined in YSC line YN0l-429. In some embodiments, the markers may be used for marker-assisted selection oflow fiber content and YSC traits derived from YSC line YN0l-429 and its 15 lineage SNP markers and high-density genetic maps were leveraged, and fiber content and seed coat color traits were fine mapped and validated from AAFC YSC line YN0 1-429 with an extensive set of phenotypic data from two dihaploid (DH) populations. These experiments are outlined in greater detail in Examples 1-5. Two 20 DH populations, YSC and YDN, were developed from spring canola line crosses. The 183 DH lines of the YSC population were developed from a cross between AAFC yellow seeded / low fiber line YN0I-429 and DAS Nexera black seeded / high fiber variety Nex828, and grown along with the two parents in paired row plots at the AAFC Saskatoon research farm and the DAS Rosthem research fann in Canada 25 in 2007 for phenotyping. Seed samples from two locations were analyzed by AAFC . using near-infrared spectroscopy (NIR) ADP (named ADP A in Figures 3 and 4) and using Hunter lab for seed coat color White Index (named WI_A in Figures 3 and 4) measurement in 2007. The population was also analyzed by DAS Analytical Technologies Group in Indianapolis for ADP (named ADP A in Figures 3 and 4) 30 using the AOAC reference method (AOAC Official Method 973.18) and by DAS Bioprocess Group in Indianapolis for seed coat color White Index (named WI_ D in Figures 3 and 4) and Hunter Lab Lightness Index (named L in Figures 3 and 4) 6 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 measurement in 2011. The 400 DH lines of the YDN population were developed from a cross between YN0l-429 and DAS Nexera black seeded / high fiber variety DN051493. The YDN population was grown along with the two parents at Pike Lake and Cudworth, Canada in 2011 for phenotyping. Seed samples were analyzed 5 for ADP (named ADF_Ml and ADF_M2 in Figures 5 and 6), seed coat color White Index (named WI in Figures 5 and 6) and Hunter lab Lightness Index (naii1e L in the Figures 5 and 6). A third DH population of 181 DH lines (named TN population) from a cross between Tapidor (a European winter cultivar) and Ningyou7 (a Chinese semi-winter cultivar) was added for consensus map construction in addition to YSC 10 and YDN populations for QTL mapping of fiber content and seed coat color traits; TN population did not segregate for fiber content and seed coat color traits.. The three DH populations were genotyped with 12,000 SNP markers and a consensus map was constructed with individual map of the YSC, YDN and TN populations. Composite Interval Mapping (CIM) was used for a whole genome QTL scan. After 15 QTL mapping, the SNP markers within 0.0-5.0 cM of the QTL underlying fiber content and seed coat color traits were converted, to K.ASPar assays for MAS of these traits derived from YN0l-429 and its lineage. High correlation was also observed between the seed coat color traits WI and L (R2 = 0.81-0.99) and between seed coat color traits and ADP content (R2 = 0.66- 20 0.85) .in both populations (Figures 1 and 2). Because of the large effect of the major QTL (R2= 59.2%-74.7%) on N09, and bi-modal distributions of fiber content and seed coat color traits in DH lines (Figures 1 and 2), quantitative fiber content and seed coat color traits can be treated as qualitative traits. After conversion of the quantitative traits of ADP and WI into qualitative traits, the ADP (ADF_09) and WI 25 (WI_09) were mapped to the same genomic region where the major QTL were located 011 N09 in both YSC and YDN populations. Figure 7 shows the map location of major ADP and WI QTL, ADF_09 and WI_09 on the consensus map of N09 constructed with YSC, YDN and TN populations and 323 SNP markers. Somers et al. (2001) and Rakow et al. (2011) indicated that the YSC line 30 from AAFC delivers consistently low fiber content across multiple environments, and low lignin content is always associated with the yellow seed color. The YSC genetic map was constructed witq.174 DH and 2,982 polymorphic SNP markers, a 7 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 total length of 2,515.8 cM and an average length of 0.80 cM / marker. The YDN population was constructed with 397 DH lines and 2,972 SNP markers, a total length of 2,189 cM and an average length of 0.74 cM / marker. The TN genetic map was constructed with 181 DH lines and 2,716 polymorphic SNP markers, a total 5 length of 1905.7 cM and an average length of 0.70 cM / marker. In embodiments, the disclosure describes a consensus map of 5,500 SNP markers with an average of 0.47 cM constructed with the YDN, YSC and TN populations (Figure 7). YSC and YDN populations segregated for fiber content and seed coat color traits and were used for QTL mapping, which further confinned that seed coat color 10 ti·aits and fiber content traits were highly correlated (Figures 3-6). QTL mapping indicated that a major QTL was identified on linkage group (LG) N09 and a minor QTL was identified on LG Nl l for all the seed coat color traits (WI and L) and ADF content in both populations (Figures 4-6). In the YSC population, the major QTL identified on N09 explained 71.5% of 15 ADF variance, and coincided with major QTL which explained 59.2% of WI and 60.8% of Lightness Index (L) variance at LOD scores ranged from 40 to 47 (Figure 3). The minor QTL identified on Nll explained 2.4% of ADF variance, and coincided with the minor QTL which respectively.explained 7.2% of WI and 6.3% of Lightness Index (L) variance at LOD scores ranged from 5 to 9 in Nex828 x 20 YN0l-429 population (Figure 4) .. QTL analysis of YDN population further confirmed the results from YSC population. The major QTL identified on N09 explained 73.4% of ADF variance and coincided with the major QTL which respectively explained 74.0% of WI and 74.7% of Lightness Index (L) variance at LOD score 143 (Figure 5). The minor 25 QTL identified on Nl 1 explained 1.4% of ADF variance, and coincided with the minor QTL which respectively explained 5.9% of WI and 5.7% of Lightness Index (L) variance at LOD scores ranged from 3 to 32 (Figure 6). The results were in accordance with Somers et al. (2001) results, which indicated that a major gene explained 72.3% of the variation in seed color, as well as two additional genes that 30 appeared to be additive and explained 21.5% of the color variation. Since seed coat color QTL (WI and L) perfectly coincided with QTL for fiber content and explained the almost the same percetitage of phenotypic variance (R2 = 77.4%) as QTL for 8 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 ADF content in both YN0l-429 derived DH populations, seed coat color indexes (WI and L) were good indicators for the fiber content in canola seed if YSC line YN0l-429 or its lineage is used as a low ADF content source in breeding programs .. 5 IL SNP Markers and QTL Underlying Low Fiber Content and YSC Traitsfrom YN0J-429 In some embodiments, the disclosure describes a major QTL which explains 59.2-74.7% of the phenotypic variance of fiber content and seed coat color traits in two dihaploid (DH) plant populations. In particular embodiments, a minor QTL has been 10 found to explain 1.4-7 .2% of the phenotypic variance of these traits in two dihaploid plant populations. High correlation is disclosed between seed coat color traits (WI and L) and ADF content in both populations. In an alternative embodiment, a set of high throughput markers closely linked to fiber content and seed coat color traits from YSC line YN0l-419. In other 15 embodiments, nucleic acid sequences linked to QTL's are associated with desirable nutritional traits. The sequence can be derived from yellow-seeded coat (YSC) line , YN0l-429 or its lineage. Particular embodiments related to a set of 18 SNP markers that lie within 0.0A.9 cM of the major ADF and seed color (WI) QTL identified in Nex828 x YN0l-429 (YSC) and DN051493 x YNOl-429 (YDN) DH populations. 20 In a particular embodiment, the SNP markers include those markers identified as DBSNP357222 through DBSNP22221 l 1 in Figure 7, which flanked by DSNP01120 and DSNP02172. In another embodiment, the SNP markers include DBSNP357223, DBSNP357224, DBSNP357226, DBSNP357227, DBSNP357228, DBSNP357230, DBSNP357231, DBSNP357233, DBSNP357234, DBSNP357244, 25 DBSNP357247, DBSNP357250, DBSNP357252, DBSNP357253, DBSNP357254, DBSNP357255, DBSNP357256, DBSNP357257, DBSNP357258, DBSNP357273, DBSNP357287, DBSNP357288, DBSNP357290, DBSNP357291, DBSNP357292, DBSNP357293, and DBSNP357294, as shown in Figure 7. 30 Ill Marker-Assisted Selection (MAS) of Low Fiber Content and YSC Traitsfrom YN0J-429 9 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 Certain embodiments related to a method for selecting canola plants or germplasm for a desirable nuttitional trait associated with QTL's using marker-assisted selection (MAS). For example, the YSC line YN0l-429 may be used. Seed color measurement may be used to replace costly and time-consuming wet chemistry 5 analysis of fiber content. SNP markers disclosed to be within 4.9 cM of the major fiber content and seed coat color QTL on N09 or the minor fiber content and seed coat color QTL on Nl 1 can be used for MAS, and will greatly expedite the breeding of canola lines with low fiber content, one of the most important components of DAS Low Fiber product concept. 10 Particular embodiments describe a method for using the identified QTL in marker-assisted selection (MAS) of the complex fiber content and seed coat color traits from the YSC line YN0l-429 to facilitate breeding in Brassica and more efficient selection of desirable nutritional traits. Particular embodiments are directed to markerassi~ ted selection of canola va1ieties to increase the nuttitive value of canola meal, 15 particularly for feed animals, including monogastric animals and ruminants. According to certain embodiments, the method may be used to select canola seed or germplasm comprising, on average, at least about 44% crude protein, and not more than about 14% acid detergent fiber as detennined by NIR. on a dry mass basis. In alternative embodiments, the canola seed or germplasm may further comprise, on 20 average, at least about 49% crude protein content. In other embodiments, the canola seed or germplasm may comprise on average, not more than about 12% acid detergent fiber content. Additionally, the canola seed or germplasm selected by the disclosed method may further comprise the following traits: reduced glucosinolate content, low tannin content, and / or low residual cell wall content. 25 IV. Abbreviations ADF acid detergent fiber AME apparent metabolizable energy DAS Dow AgroSciences 30 DH di.haploid FAME fatty acid / fatty acid methyl esters NMR nuclear magnetic resonance CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 5 NIR. QTL RAPD SNP RCW near-infrared spectroscopy quantitative trait locus random amplified polymorphic DNA Single nucleotide polymorphism residual cell walls V. Terms Allotetraploid: As used herein, "allotetraploid" generally refers to a hybrid organism that has a chromosome set that is four times that of a haploid organism. 10 Canola oil: Canola oil refers to oil extracted from commercial varieties of rapeseed. To produce canola oil, seed is typically graded and blended at grain elevators to produce an acceptably uniform product. The blended seed is then crushed, and the oil is typically extracted with hexane and subsequently refined. The resulting oil may then be sold for use. Oil content is typically measured as a percentage of the 15 whole dried seed, and particular oil contents are characteristic of different varieties of canola. Oil content can be readily and routinely detennined using various analytical techniques, for example and without limitation: NMR; NIR.; and Soxhlet extraction. The percent composition of total fatty acids is typically determined by extracting a sample of oil from seed, producing methyl esters of fatty acids present in the oil 20 sample, and analyzing the proportions of the various fatty acids in the sample using gas chromatography. The fatty acid composition may also be a distinguishing characteristic of particular varieties. Elite line: As used herein, the term "elite line" means any line that has resulted from breeding and selection for superior agronomic performance. An elite plant is any 25 plant from an elite line. Enhanced canola meal: As used herein, the term "enhanced canola meal" means canola meal, produced from canola seeds, which has decreased fiber content, and may have increased protein and .true metabolizable energy content, as well as reduced anti-nutritional factors such as glucosinolates, tannins, phytic acid, sinapine 30 and erucic acid. Meal with some or all of these characteristics could allow increasing inclusion rates in the diet of animal species especially in monogastric animals. 11 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 Plant line: As used herein, a "line" refers to a group of plants that display little genetic variation (e.g., no genetic variation) between individuals for at least one trait. Inbred lines may be created by several generations of self-pollination and selection or, alternatively, by vegetative propagation from a single parent using tissue or cell culture 5 techniques. As used herein, the tenns "cultivar," "variety," and "type" are synonymous, and these terms refer to a line that is used for commercial production. Plant material: As used herein, the term "plant material" refers to any processed or unprocessed material derived, in whole or in part, from a plant. For example and without limitation, a plant material may be a plant part, a seed, a fruit, a 10 leaf, a root, a plant tissue, a plant tissue culture, a plant explant, or a plant cell. Quantitative trait: As used herein, a "quantitative trait" may refer to a trait or phenotype that is expressed in varying degrees, along a generally continuous gradient and is frequently linked to two or more genes and is affected by environment. Quantitative trait locus: As used herein, a "quantitative trait locus" refers to a 15 segment or region of DNA containing or linked to a gene or genes underlying a • quantitative trait. Seed color: In some embodiments, this disclosure refers to canola varieties (e.g., inbred canola lines and hybrids) characterized by seed color. Canela seed color rating or "seed color" is generally scored on a 1-5 scale, based on seeds obtained from 20 healthy plants at or near complete seed maturity. "l" signifies a good yellow color. "2" signifies mainly yellow with some brown. "3" indicates a mixture of brown and yellow. "4" and "5" signify brown and black, respectively. Whiteness index (WI) scores also may be used to describe canola varieties. ·For example, yellow-seeded lines YN97-262 and 9592 have whiteness index scores of-34.6 and -33.2, respectively, and 25 seed color scores of 1. Dark-seeded lines, Nex 715 and Nex 705, have whiteness index scores of -0.2 and -4.4, respectively, and seed color scores of 4. Dark-seeded lines 46A65 and Q2 have whiteness index scores of 0.3 and -3.9, respectively, and seed color scores of 5. Color of particular seeds may also be described in terms of a percentage, or other ratio, as compared to any of these lines. 30 Stability: As used herein, the term "stability," or "stable," refers to a given plant component that is maintained at substantially the same level through multiple generations. For example, a stable component may be maintained for at least three 12 generations at substantially the same level. In this context, the tenn "substantially the same" may refer in some embodiments to a component maintained to within 25% between two different generations; within 20%; within 15%; within 10%; within 5%; within 3%; within 2%); and / or within 1 %, as well as a component that is maintained 5 perfectly between two different generations. In some embodiments, a stable plant component may be, for example and without limitation, an oil component; a protein component; a fiber component; a pigment component; a glucosinolate component; and a lignin component The stability of a component may be affected by one or more environment factors. For example, the stability of an oil component may be affected by, 10 for example and without limitation: temperature; location; stress; and the time of planting. Subsequent generations of a plant having a stable component under field conditions will be expected to produce the plant component in a similar manner, for example, as set forth above. Trait or phenotype: The tenns "trait" and "phenotype" are used interchangeably 15 herein. For the purposes of the present disclosure, the traits of particular interest are low fiber content and seed coat color. Some canola varieties exhibit a yellow seed coat, while further varieties exhibit a dark (e.g., black, dark, and mottled) seed coat. A "variety" or "cultivar" is a plant line that is used for commercial production which is distinct, stable and unifonn in its characteristics when propagated. 20 Unless indicated otherwise, the terms "a'" and "an" a'l used herein refer to at least one. The references discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed a<; an admission that the inventors arc not entitled to antedate such disclosure by virtue of prior 25 invention. 13 Date Re9ue / Date Received 2022-04-19 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 5 EXAMPLES The following Examples are provided to illustrate certain particular features and / or aspects. These Examples should not be construed to limit the disclosure to the particular features or aspects described. Example 1: Plant material and DNA extraction For fine mapping and validation of low fiber content and seed coat color traits from yellow seed coat (YSC) line YN0l-429, two dihaploid (DH) populations, YSC and YON, were developed from crosses between spring canola lines in 2007 and 2010, 10 respectively. The 176 DH lines of YSC population were developed from a cross between the Agriculture and Agri-Food Canada (AAFC) yellow seeded, low fiber line YN0l-429 and the DAS Nexera black seeded,high fibervarietyNex828. The 399 DH lines of the YON population were developed from a cross between YN0l-429 and DAS Nexera black seeded, high fiber variety DN051493. The DH population, TN, 15 was derived from a cross between the European winter cultivar Tapidor and the Chinese semi-winter cultivar Ningyou7. This population was a reference mapping population widely used for trait mapping and genomics studies by the international canola research community (Shi et al. 2009), and was not segregating for fiber content and seed coat color traits. It was used for consensus map construction along withthe 20 YSC and YON populations to identify more Single Nucleotide Polymorphic (SNP) markers tightly linked to the fiber content and seed coat color traits. Genomic DNA for the populations was extracted from 8 leaf punches per sample using the DAS Biocel extraction method (Bohl eta!. 2009). DNA samples were quantified with Quant-iT™ PicoGreen® Quantification Kit (Invitrogen, Carlsbad, 25 CA) using the manufacturer's instructions or with the Nanodrop 8000 Spectrophotometer (Thenno Scientific, Waltham, MA) per manufacturer's instructions. Example 2: Phenotypic data The 176 DH lines from the YSC population were grown along with the two 30 parents as checks in paired row plots at the AAFC Saskatoon research farm and the DAS Rosthern research farm at Canada in 2007 forphenotyping. Seed samples from all established plots were collected from both locations and analyzed by AAFC using 14 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 Near Infrared Spectroscopy (NIR) for Acid Detergent Fiber (ADF) and seed coat color White Index (WI). The population was also analyzed for ADF using the AOAC reference method (AOAC Official Method 973.18) in 2007 and for seed coat color White Index and Hunter Lab Lightness Index (L) in 2011. 5 The YDN population was grown along with the two parents as checks in paired row plots at Pike Lake and Cudworth, Canada in 2011 for phenotyping. Seed samples from 361 DH lines were analyzed for ADP using two NIR models and for seed coat color White Index and the HunterLab Lightness Index in 2011. Significant differences were observed between the two mapping parents for 10 fiber content and seed coat color for both populations, as illustrated in Table 1. Distributions of fiber content in DH lines revealed bi-modal distributions skewed towards the higher fiber range in both populations (Figures 1 and 2). High correlation was observed between the seed coat color traits WI and L (R2 = 0.81-0.99) and between seed coat color traits and fiber content traits (R2 = 0.66-0.85) in both 15 populations (Figures 1 and 2). Table 1: The %ADP and seed coat color data, WI and L of the parents and DH lines in YSC and YDN populations. 20 YSC population YDN population DH lines DH lines with DH lines with YNOl- Nex828 with YN0l- DN0514 YN0l- DN051493 Trait Nex828 429 alleles 429 alleles 93 429 alleles 14.0± %ADF 15.6% 9.1% 1.6% 10.0 ± 1.0% 19.0% 12.6% 18.5 ± 1.4% WI 68.0 145.6 67.1 ±4.2 100.4 ± 19.2 67.9 159.3 68.0 ± 5.0 L 74.4 157.7 73.1 ± 5.0 109.9 ± 20.8 74.4 172.1 74.1 ± 5.9 Example 3: Genotypic data The three DH populations, YSC, YDN, and TN, were genotyped with 12,000 SNP markers developed at DAS on two Illumina lnfinium chips on the BeadStation 500 G per manufacturer's protocol (Illumina, San Diego, CA). Genotypic data was 25 analyzed using the GenomeStudio Genotyping Analysis Module vl.8.4 (Illumina, San Diego, CA), which converts fluorescent signals for each SNP into A and B signals whose values reflect the relative abundance of arbitrarily assigned A and B alleles. 15 DH lines with YN0l- 429 alleles 12.8 ± 0.9% 123.5 ± 19.6 134.8 ± 20.8 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 5 Signal is converted into polar coordinates, using the Manhattan distance metric for the intensity R, and with ThetaE[ 0, 1] representing angle E[O, 90] degrees. Each marker is clustered in Cartesian coordinates, and the genotypes {AA, AB, BB} are assigned to samples in clusters close to Theta={O, ½,]}. Example 4: Linkage map and consensus map construction The individual maps of the YSC, YDN and TN populations were constructed with MAPMAKER / EXP 3.0 (Lander et al. 1987; Lincoln et al. 1992) at LOD score 10.0 and Haldane's mapping function, and the consensus map was constructed with 10 Phenomap Enterprise 3.0 (GeneFlow Inc., Centreville, VA). The YSC genetic map was constructed with 176 DH lines and 2,982 polymorphic SNP markers, and had a total length of 2,515.8 cM and an average length of0.80 cM / marker. The YDN genetic map was constructed with 399 DH lines and 2,972 SNP markers, and had a total length of2,189 cM and an average of0.74 15 cM / marker. The TN genetic map was constructed with181 DH lines and 2,716 polymorphic SNP markers, and had a total length of 1905.7 cM and an average of 0.70 cM / marker. A consensus map of 5,500 SNP markers was constructed with the YDN, YSC and TN populations. 20 Example 5: QTL mapping The Composite Interval Mapping (CIM), as implemented in QTL Cartographer V2.5 (Wang et al. 2011), was used for QTL mapping. A LOD score of 3.0 was used as threshold to identify genomic regions significantly affecting the seed coat color and fiber content traits. 25 Table 2 shows the details of the QTLs identified for seed coat color and fiber content. Results indicated that a major QTL was identified on linkage group (LG) N09 and a minor QTL was identified on Nl 1 for the seed coat color traits, WI and L, and fiber content trait ADF, in both YSC and YDN populations. In the YSC population, the major QTL identified for ADF on N09 coincided with a major QTL for WI and L at 30 LOD scores ranging from 40 to 47. The minor QTL identified for ADF on Nl 1 coincided with a minor QTL for WI and L at LOD scores ranging from 3 to 9 in the YSC population. QTL analysis of the YDN population further confirmed the results 16 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 from the YSC population. For the YDN population, the major QTL identified for ADF on N09 coincided with the major QTL for WI and Lat LOD scores ranged from 136 to 143. The minor QTL identified for ADF on Nl 1 coincided with the minor QTL for WI and Lat LOD scores ranging from 7 to 26. s Table 2: The phenotypic variance explained (R2) by significant QTL underlying ADF content and seed coat color traits (WI and L) in YSC and YDN populations with LOD scores~ 3. Linkage % of Variance Population Trait Group Explained (R.2) LOD YSC (n=176) Seed coat color L N09 60.8 Seed coat color WI N09 59.2 Fiber content ADF N09 71.5 Seed coat color L Nll 6.3 Seed coat color WI Nll 7.2 Fiber content ADF Nll 2.4 YDN (n=399) Seed coat color L N09 74.7 Seed coat color WI N09 74 Fiber content ADF N09 73.4 Seed coat color L Nll 5.7 Seed coat color WI Nll 5.9 Fiber content ADF Nll 1.4 10 Example 6: Mapping of ADF and seed coat color as qualitative traits Because of the large effect of the major QTL (R2= 59.2%-74.7%) on N09, and the bi-modal distributions of fiber content and seed coat color traits in the DH lines (Figures 1 and 2), quantitative fiber content and seed coat color 1:J.·aits can be treated as qualitative 1:J.·aits. Based on their ADF content and seed coat color WI, DH lines of both 15 populations were divided into two groups, one with low fiber / high WI and homozygous YN0 1-429 alleles and the other group with high fiber / low WI and homozygous Nex828 or DN051493 alleles (Figures 1 and 2). In the YSC population, the DH lines with YN0l-429 alleles had an average of 10.0 ± 1.0% of ADF and the DH lines with Nex828 alleles had an average of 14.0 ± 20 1.6% ofADF in canola seeds (Figure 1). In the YDN population, the DH lines with YN0l-429 alleles had an average of 12.8 ± 0.9% of ADF and the DH lines with DN051493 alleles had an average of 18.5 ± 1.4% of ADF in canola seeds (Figure 2). 17 41 40 47 8 9 3 143 141 136 26 26 7 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 After conversion of the quantitative traits of ADF and WI into qualitative traits, the ADF (ADF_09) and WI (WI_09) were mapped to the same genomic region where the major QTL were located on N09 in both the YSC and YDN populations. Figure 7 shows the map location of the major ADF and WI QTL, ADF _ 09 and WI_ 09, on the s YDN population map ofN09. Example 7: Fine-mapping of the major QTL on N09 The YDN population was later used for fine mapping and validation of the major QTL on N09. A new genetic map ofN09 was constructed with 1387 SNPs. 10 Flanking markers DBSNP0l 120 and DBSNP02172 defined a QTL interval of 4.9 cM, corresponding to 0.46 Mb on the B. napus reference genome, DH12075, which was sequenced at AAFC through an industry consortium. The major QTL has an R2 of 75% on N09. Blind screenings of the markers within the QTL interval with multiple DAS proprietary DH populations from the breeding program con:fumed that the 15 concordance between marker-predicated phenotype and actual phenotype was 2:: 98%. Figure 3 shows the genetic map of the ADF QTL interval along with the ADF _ 09 and WI 09 loci. Within the 4.9 cM QTL interval on N09, 111 SNP markers were identified, including the flanking markers DBSNP0l 120 and DBSNP02172. Table 3 lists the 20 SNPs, their genetic positions in cM, the YN0l-429 allele as well as the physical positions of the SNPs on the B. napus reference genome (DH12075). 18 Table 3: SNP markers within the 4.9 cM QTL interval for ADF mapped on N09 with the YDN population. :;; 0 N 0 SEQ ID Map Position YN01429 'a"",,' -- SNP Name NO: (cM) SNP Type SNP Forward genotype Physical Pos on Ref Genome (bp) '0" "' 0 DBSNP01120 1 117.4 SNP [TIG] GG N9:35982462 .. 35983088 QC) QC) (,,; DBSNP357202 2 117.4 SNP [CIG] GG N9:35982582 .. 35984072 DBSNP357203 3 117.4 SNP [TIG] TT N9:35982826 .. 35984316 DBSNP222203 4 117.4 SNP [A / C] AC N9:35987647 .. 35987947 DBSNP357208 5 117.4 SNP [TIG] GG N9:35994219 .. 35995219 DBSNP357214 6 117.7 SNP [A / G] AA N9:36025967 .. 36026963 DBSNP222206 7 117.7 SNP [A / G] AA N9:36027874 .. 36028174 DBSNP357215 8 118.2Q INDEL [-IA] AA N9:36030593 .. 36031612 ~ DBSNP357216 9 118.2Q SNP [TIG] TG N9:36030597 .. 36031616 0 N> ""'' "' '""' [ +I ATCACGCACC ATCACGCACCT .u.., I.O _, DBSNP357217 10 118.2Q INDEL TGCAAATGT] GCAAATGT N9:36030617 .. 36031636 N> Ø . DBSNP357218 11 118.2Q SNP [A / G] GG N9:36030736 .. 36031756 _, I 0 "' DBSNP357219 12 118.7 SNP [A / G] GG N9:36030916 .. 36031808 I Ø . DBSNP357221 13 119 SNP [CIG] cc N9:36038430 .. 36039006 DBSNP357222 14 119 SNP [TIG] TT N9:36038430 .. 36039335 DBSNP357223 15 119 SNP [A / G] GG N9:36038516 .. 36039516 DBSNP357224 16 119 SNP [TIC] cc "N9:36038712 .. 36039712 DBSNP222208 17 119 SNP [TIC] cc N9:36039152 .. 36039272 DBSNP357226 18 119 SNP [CIG] GG N9:36039465 .. 36040465 "'d ("") DBSNP357227 19 119 SNP [A / C] cc N9:36039710 .. 36040708 ""'3 ' -- DBSNP357228 20 119 SNP [TIC] cc N9: 3 603 973 8 .. 3 6040726 ('.j 00 N DBSNP357229 21 119.3 SNP [TIG] GG N9:36040629 . .36041743 0 'U""t' DBSNP357230 22 119.8 SNP [TIC] cc N9:36041302 .. 36042269 -- 0 a,, DBSNP357231 23 119.8 SNP [A / G] AA N9:36041326 .. 36042293 a,, QC) '""' DBSNP357232 24 119.8 SNP [TIC] cc N9:36041431..36042398 (,,; DBSNP357233 25 119.8 SNP [TIC] cc N9:36041470 .. 36042437 DBSNP357234 26 119.8 SNP [TIC] cc N9:36041587 .. 36042554 :;; 0 DBSNP357235 27 119.8 SNP [A / T] AA N9:36042193 .. 36043188 N 0 DBSNP357236 28 119.8 INDEL [+ / TT] TT N9:36042318 .. 36043314 a"",", -- DBSNP357237 29 119.8 SNP [TIC] TT N9:36042320 .. 36043316 "0" " 0 QC) DBSNP357238 30 119.8 SNP [A / T] TT N9:36042626 .. 36043621 QC) (,,; DBSNP357239 31 119.8 SNP [TIC] TT N9:36042629 .. 36043624 DBSNP357240 32 119.8 INDEL [+ / A] + N9:36042765 .. 36043760 DBSNP357241 33 119.8 SNP [A / G] AG • N9:36043110 .. 36044110 DBSNP357242 34 119.8 INDEL [-IT] T N9:36043117 .. 36044117 DBSNP357244 35 119.8 SNP [TIC] TT N9:36043219 .. 36044219 DBSNP357245 36 119.8 SNP [TIC] cc N9:36043480 .. 36044475 DBSNP357246 37 119.8 SNP [A / T] TT N9:36044691..36045691 ~ 0 DBSNP357247 38 119.8 SNP [A / T] TT N9:36045200 .. 36046200 N> ""'' [TIC] "' N DBSNP04324 39 119.8 SNP cc N9:36046568 .. 36047839 .u.., 0 _, DBSNP357249 40 119.8 SNP [A / G] AA N9:36046761..36047762 N> Ø . 41 119.8 SNP [A / G] AA N9:36046762 .. 36047763 _, DBSNP357250 I 0 "' DBSNP357251 42 119.8 SNP [A / G] AA N9:36046778 .. 36047779 I Ø . DBSNP357252 43 119.8 SNP [A / G] GG N9:36046868 .. 36047869 DBSNP357253 44 119.8 SNP [A / G] GG N9:36046920 .. 36047921 DBSNP357254 45 119.8 INDEL [+IT] + N9:36047652 .. 36048534 DBSNP357255 46 119.8 SNP [TIC] TT N9:36047710 .. 36048534 DBSNP357256 47 119.8 SNP [A / G] GG N9:36047752 .. 36048534 DBSNP357257 48 119.8 SNP [TIC] cc N9:36047876 .. 36048534 "'d ("") DBSNP357258 49 119.8 SNP [A / G] AA N9:3604 7941..36048534 ""'3 -('-.j DBSNP357259 50 119.8 SNP [TIC] TT N9:36048002 .. 36048534 00 N DBSNP357260 51 119.8 SNP [C / G] GG N9:36048012 .. 36048534 0 U"""t DBSNP357262 52 119.8 INDEL [+ / A] + N9:36048530 .. 36049322 -0 - a,, a,, DBSNP357263 53 119.8 SNP [A / T] TT N9:36048530 .. 36049347 QC) """ DBSNP357264 54 119.8 SNP (,,; [A / T] TT N9:36048530 .. 36049442 DBSNP357265 55 119.8 SNP [A / G] AG N9:36048530 .. 36049520 :;; 0 DBSNP357266 56 119.8 SNP [A / G] AA N9:36048564 .. 36049565 N 0 DBSNP357267 57 119.8 SNP [CIG] CG N9:36048641 . .36049642 a"",", -- DBSNP357268 58 119.8 SNP [A / C] cc N9:36048645 .. 36049646 ·"o"" 0 DBSNP357269 59 119.8 SNP [TIC] TC N9:36048651 .. 36049652 QC) QC) (,,; DBSNP357270 60 119.8 SNP [CIG] cc N9:36048792 .. 36049793 DBSNP357271 61 119.8 SNP [TIC] cc N9:36048794 .. 36049795 DBSNP357272 62 119.8 INDEL [+IA] + N9:36048932 .. 36049933 DBSNP357273 63 119.8 SNP [A / T] TT N9:36048985 .. 36049986 DBSNP357274 64 119.8 SNP [A / G] AG N9:36049082 .. 36050083 DBSNP357275 65 119.8 SNP [TIC] TC N9:36049455 .. 36050457 DBSNP357276 66 119.8 SNP [A / G] AA N9:36049482 .. 36050484 ~ [CIG] 0 DBSNP357278 67 119.8 SNP cc N9:36049554 .. 36050556 N> ""'' DBSNP357280 68 119.8 SNP [TIG] TT N9:36049653 .. 36050643 "' N .u.., """ _, DBSNP357282 69 119.8 SNP [TIG] TT N9:36049758 .. 36050643 N> 0 .... DBSNP357286 70 119.8 SNP [A / G] AA N9:36054018 .. 36055018 _, I 0 "' DBSNP222210 71 119.8 SNP [A / G] AG N9:36054461 .. 36054578 I 0 .... DBSNP357287 72 119.8 SNP [A / T] TT N9:36054757 .. 36055757 DBSNP357288 73 119.8 SNP [A / G] GG N9:36054789 .. 36055789 DBSNP357289 74 119.8 SNP [TIC] cc N9:36054810 .. 36055810 DBSNP357290 75 119.8 SNP [A / G] AA N9:36054813 .. 36055813 DBSNP357291 76 119.8 SNP [A / C] AA N9:36054956 .. 36055956 DBSNP357292 77 119.8 SNP [CIG] cc N9:36054966 .. 36055966 "'d ("") DBSNP357293 78 119.8 SNP [TIC] TT N9:36054983 .. 36055983 ""'3 -('-.j DBSNP357294 79 119.8 SNP [TIC] TT N9:36055008 .. 36056008 00 N DBSNP84508 80 119.8 SNP [A / C] AC N9:36055121 .. 36055879 0 U"""t DBSNP222211 81 119.8 SNP [A / G] GG N9:36060768 .. 36060968 -0 - a,, a,, DBSNP222212 82 119.8 SNP [A / G] GG N9:36061805 .. 36061924 QC) "(,","; DBSNP222214 83 119.8 SNP [A / G] AA N9:36076182 .. 36076301 SNP :;; 0 DBSNP222219 84 119.8 (dominant) [TIG] -- N9:36096659 .. 36096732 N 0 SNP a"",", -- DBSNP222220 85 119.8 (dominant) [A / C] -- N9:36096733 .. 36096814 "0" " 0 QC) DBSNP240715 86 119.8 SNP [A / G] AG N9:36100799 .. 36100917 QC) (,,; DBSNP222222 87 119.8 SNP [A / G] GG N9:36119793 .. 36119830 DBSNP38295 88 119.8 SNP [A / G] GG N9:36132536 .. 36133536 DBSNP222225 89 119.8 SNP [A / G] GG N9:36132936 .. 36133136 DBSNP222226 90 119.8 SNP [A / G] AA N9:36136254 .. 36136558 DBSNP08212 91 119.8 SNP [A / G] AA N9:36143105 .. 36143329 DBSNP08214 92 119.8 SNP [TIG] TT N9:36143105 .. 36143329 DBSNP222228 93 119.8 SNP [TIC] cc N9:36147820 .. 36147940 ~ N9:36156553 .. 36156673 0 DBSNP222229 94 120.1 SNP [A / G] AA N> ""'' 120.1 SNP [TIG] GG N9:36157370 .. 36158339 "' N DBSNP42126 95 .u.., N _, DBSNP222231 96 120.1 SNP [TIC] TT N9:36165969 .. 36166169 N> 0 .... DBSNP222233 97 120.6 SNP [A / G] AA N9:36175905 .. 36176121 _, I 0 "' DBSNP222235 98 120.6 SNP [A / G] AA N9:36190213 .. 36190333 I 0 .... DBSNP146598 99 120.6 SNP [TIC] TC N9:36207823 .. 36208597 DBSNP147032 100 120.6 SNP [A / G] AG N9:36212362 .. 36213110 DBSNP94819 101 120.6 SNP [TIG] TG N9:36213988 .. 36214561 DBSNP158066 102 120.6 SNP [A / T] TA N9:36214885 .. 36215409 DBSNP158078 103 120.6 SNP [TIC] cc N9:36214926 .. 36215606 DBSNP63288 104 121.4 SNP [TIG] TG N9:36278558 .. 36279063 "'d ("") DBSNP52362 105 121.4 SNP [TIC] + N9:36279239 .. 36280186 ""'3 -- DBSNP222241 106 121.4 SNP [TIC] N9:36291810 .. 36291930 ('.j -- 00 N DBSNP222242 107 121.4 SNP [TIC] TT N9:36308543 .. 36308663 0 U"""t DBSNP189108 108 121.4 SNP [TIC] TC N9:36308946 .. 36309355 -0 - a,, a,, DBSNP222244 109 121.7 SNP [TIC] cc N9:36353147 .. 36353447 QC) """ DBSNP222246 110 122 SNP [TIG] TT N9:36372163 .. 36372403 (,,; WO 2016 / 100883 i \0 00 ~ \0 C": 0\ .(.'.<..) t-- tj- -tj- \0 (") 0\ z uu .......... ...... CA 02969547 2017-06-01 PCT / 0S2015 / 066813 23 CA 02969547 2017-06-01 WO 2016 / 100883 PCT / 0S2015 / 066813 Within the 4.9 cm ADF QTL interval, flanked by DBSNP0 1120 and DBSNP02172, a sub-interval was defined in which the markers are most desired for marker assisted selection. Flanking markers DBSNP35722 and DBSNP222211 define a 0.5 cM sub-interval haplotype region unique to the donor YN0 1-429. The DBSNP35722 and DBSNP222211 flanking markers 5 and the markers within the sub-interval can be used for marker assisted selection to track the QTL on N09 when breeding for enhanced ACM attributes. 24

Claims

25 CLAIMS What is claimed is:

1. A method for identifying Brassica napus plant or germplasm thereof comprising a quantitative trait locus (QTL), the method comprising: analyzing a population of Brassica napus plants or germplasm for the presence or absence of at least one marker selected from the group consisting of SEQ ID NOs:1-110 and 111; and identifying one or more of the Brassica napus plants or germplasm thereof having the QTL based on the presence of the at least one marker allele, wherein the marker allele and the QTL are the same as that of Brassica napus line YN01-429.

2. The method according to claim 1, wherein the at least one marker comprises a single-nucleotide polymorphism (SNP).

3. The method according to claim 1, wherein the QTL is from Brassica napus line YN01-429 or its progeny.

4. An isolated or recombinant nucleic acid for use detecting a marker in Brassica napus, wherein the isolated nucleic acid is selected from the group consisting of SEQ ID NOs:1- 110 and 111.

5. The isolated or recombinant nucleic acid of claim 4 for use detecting a SNP marker in Brassica napus.

6. A method for selecting a Brassica napus plant or germplasm that comprises a QTL, the method comprising: genotyping the Brassica napus plant or germplasm to detect the presence of a QTL comprising at least one marker selected from the group consisting of SEQ ID NOs:1-110 and 111; and selecting a Brassica napus plant or germplasm based on the presence of the at least one marker allele, wherein the marker allele and the QTL are the same as Brassica napus line YN01- 429. CA 2969547 Date reçue / Received date 2024-07-11 26 7. The method according to claim 6, wherein the Brassica napus plant or germplasm has an acid detergent fiber (ADF) content of 15% or less.

8. The method according to claim 6, wherein the QTL is the QTL is from Brassica napus line YN01-429 or its progeny.

9. A method of identifying a Brassica napus plant the method comprising isolating a sample comprising genomic DNA from the Brassica napus plant genotyping the sample to detect a chromosomal interval comprising marker alleles selected from the group consisting of SEQ ID NOs:1-110 and 111, wherein the marker alleles are the same as Brassica napus line YN01-429.

10. The method of claim 9, wherein the chromosomal interval is the chromosomal interval comprising and flanked by DBSNP35722 (SEQ ID NO:14) and DBSNP222211 (SEQ ID NO:81) of Brassica napus line YN01-429 or its progeny.

11. A method of identifying a Brassica napus plant or germplasm, the method comprising isolating a sample comprising genomic DNA from the Brassica napus plant genotyping the sample to detect a haplotype in the Brassica napus plant or the germplasm, wherein the haplotype comprises marker alleles selected from the group consisting of SEQ ID NOs:1-111 and the marker alleles are the same as Brassica napus line YN01-429.

12. The method of claim 11, wherein the chromosomal interval is the chromosomal interval comprising and flanked by DBSNP01120 (SEQ ID NO:1) and DBSNP02172(SEQ ID NO:111) of Brassica napus line YN01-429 or its progeny.

13. A method of marker assisted Brassica napus plant selection comprising: CA 2969547 Date reçue / Received date 2024-07-11 27 a. genotyping a population of Brassica napus plants to determine the presence or absence of the one or more marker alleles selected from the group consisting of SEQ ID NOs:1- 110 and 111 that are the same as those of Brassica napus line YN01-429; and b. selecting one or more of the plants that possess the one or more marker alleles.

14. The method of claim 13, wherein the marker alleles are located within a chromosomal interval comprising and flanked by DBSNP357221 (SEQ ID NO:13) and DBSNP222231 (SEQ ID NO:23).

15. The method of claim 13, wherein chromosomal interval is of Brassica napus line YN01-429 or its progeny.

16. The method according to claim 1, wherein the at least one marker allele is a thymine (T) at position 501 of SEQ ID NO:14, a guanine (G) at position 501 of SEQ ID NO:15, a cytosine (C) at position 501 of SEQ ID NO:16, a C at position 61 of SEQ ID NO:17, a G at position 501 of SEQ ID NO:18, a C at position 501 of SEQ ID NO:19, a C at position 501 of SEQ ID NO:20, a G at position 501 of SEQ ID NO:21, a C at position 501 of SEQ ID NO:22, an adenine (A) at position 501 of SEQ ID NO:23, a C at position 501 of SEQ ID NO:24, a C at position 501 of SEQ ID NO:25, a C at position 501 of SEQ ID NO:26, an A at position 501 of SEQ ID NO:27, a TT at position 502 of SEQ ID NO:28, a T at position 501 of SEQ ID NO:29, a T at position 501 of SEQ ID NO:30, a T at position 501 of SEQ ID NO:31, a T at position 502 of SEQ ID NO:32, a T at position 501 of SEQ ID NO:34, a T at position 501 of SEQ ID NO:35, a C at position 501 of SEQ ID NO:36, a T at position 501 of SEQ ID NO:37, a T at position 501 of SEQ ID NO:38, a C at position 536 of SEQ ID NO:39, an A at position 501 of SEQ ID NO:40, an A at position 501 of SEQ ID NO:41, an A at position 501 of SEQ ID NO:42, a G at position 501 of SEQ ID NO:43, a G at position 501 of SEQ ID NO:44, an A at position 502 of SEQ ID NO:45, a T at position 501 of SEQ ID NO:46, a G at position 501 of SEQ ID NO:47, a C at position 501 of SEQ ID NO:48, an A at position 501 of SEQ ID NO:49, a T at position 501 of SEQ ID NO:50, a G at position 501 of SEQ ID NO:51, a C at position 502 of SEQ ID NO:52, a T at position 501 of SEQ ID NO:53, a T at position 501 of SEQ ID NO:54, an A at position 501 of SEQ ID NO:56, a C at position 501 of SEQ ID NO:58, a C at position 501 of SEQ ID NO:60, CA 2969547 Date reçue / Received date 2024-07-11 28 a C at position 501 of SEQ ID NO:61, a C at position 502 of SEQ ID NO:62, a T at position 501 of SEQ ID NO:63, an A at position 501 of SEQ ID NO:66, a C at position 501 of SEQ ID NO:67, a T at position 501 of SEQ ID NO:68, a T at position 501 of SEQ ID NO:69, an A at position 501 of SEQ ID NO:70, a T at position 501 of SEQ ID NO:72, a G at position 501 of SEQ ID NO:73, a C at position 501 of SEQ ID NO:74, an A at position 501 of SEQ ID NO:75, an A at position 501 of SEQ ID NO:76, a C at position 501 of SEQ ID NO:77, a Tat position 501 of SEQ ID NO:78, a T at position 501 of SEQ ID NO:79, or a G at position 101 of SEQ ID NO:

81.

17. The method of claim 1, wherein the at least one marker allele is a guanine (G) at position 283 of SEQ ID NO:1, a guanine (G) at position 501 of SEQ ID NO:2, a thymine (T) at position 501 of SEQ ID NO:3, a G at position 501 of SEQ ID NO:5, an adenine (A) at position 501 of SEQ ID NO:6, an A at position 151 of SEQ ID NO:7, an A at position 501 of SEQ ID NO:8, a 19 nucleotide insertion at position 502 of SEQ ID NO:10, a G at position 501 of SEQ ID NO:11, a G at position 501 of SEQ ID NO:12, a cytosine (C) at position 501 of SEQ ID NO:13, a G at position 61 of SEQ ID NO:82, an A at position 61 of SEQ ID NO:83, a G at position 61 of SEQ ID NO:87, a G at position 501 of SEQ ID NO:88, a G at position 101 of SEQ ID NO:89, an A at position 151 of SEQ ID NO:90, an A at position 153 of SEQ ID NO:91, a T at position 48 of SEQ ID NO:92, a C at position 61 of SEQ ID NO:93, an A at position 61 of SEQ ID NO:94, a G at position 501 of SEQ ID NO:95, a T at position 101 of SEQ ID NO:96, an A at position 151 of SEQ ID NO:97, an A at position 61 of SEQ ID NO:98, a C at position 328 of SEQ ID NO:103, a Tat position 61 of SEQ ID NO:107, a C at position 151 of SEQ ID NO:109, a Tat position 151 of SEQ ID NO:110, and a C at position 848 of SEQ ID NO:

111.

18. The method according to claim 9, wherein the at least one marker allele is a thymine (T) at position 501 of SEQ ID NO:14, a guanine (G) at position 501 of SEQ ID NO:15, a cytosine (C) at position 501 of SEQ ID NO:16, a C at position 61 of SEQ ID NO:17, a G at position 501 of SEQ ID NO:18, a C at position 501 of SEQ ID NO:19, a C at position 501 of SEQ ID NO:20, a G at position 501 of SEQ ID NO:21, a C at position 501 of SEQ ID NO:22, an adenine (A) at position 501 of SEQ ID NO:23, a C at position 501 of SEQ ID NO:24, a C at position 501 of SEQ ID NO:25, a C at position 501 of SEQ ID NO:26, an A at position 501 of CA 2969547 Date reçue / Received date 2024-07-11 29 SEQ ID NO:27, a TT at position 502 of SEQ ID NO:28, a T at position 501 of SEQ ID NO:29, a T at position 501 of SEQ ID NO:30, a T at position 501 of SEQ ID NO:31, a T at position 502 of SEQ ID NO:32, a T at position 501 of SEQ ID NO:34, a T at position 501 of SEQ ID NO:35, a C at position 501 of SEQ ID NO:36, a T at position 501 of SEQ ID NO:37, a T at position 501 of SEQ ID NO:38, a C at position 536 of SEQ ID NO:39, an A at position 501 of SEQ ID NO:40, an A at position 501 of SEQ ID NO:41, an A at position 501 of SEQ ID NO:42, a G at position 501 of SEQ ID NO:43, a G at position 501 of SEQ ID NO:44, an A at position 502 of SEQ ID NO:45, a T at position 501 of SEQ ID NO:46, a G at position 501 of SEQ ID NO:47, a C at position 501 of SEQ ID NO:48, an A at position 501 of SEQ ID NO:49, a T at position 501 of SEQ ID NO:50, a G at position 501 of SEQ ID NO:51, a C at position 502 of SEQ ID NO:52, a T at position 501 of SEQ ID NO:53, a T at position 501 of SEQ ID NO:54, an A at position 501 of SEQ ID NO:56, a C at position 501 of SEQ ID NO:58, a C at position 501 of SEQ ID NO:60, a C at position 501 of SEQ ID NO:61, a C at position 502 of SEQ ID NO:62, a T at position 501 of SEQ ID NO:63, an A at position 501 of SEQ ID NO:66, a C at position 501 of SEQ ID NO:67, a T at position 501 of SEQ ID NO:68, a T at position 501 of SEQ ID NO:69, an A at position 501 of SEQ ID NO:70, a T at position 501 of SEQ ID NO:72, a G at position 501 of SEQ ID NO:73, a C at position 501 of SEQ ID NO:74, an A at position 501 of SEQ ID NO:75, an A at position 501 of SEQ ID NO:76, a C at position 501 of SEQ ID NO:77, a Tat position 501 of SEQ ID NO:78, a T at position 501 of SEQ ID NO:79, or a G at position 101 of SEQ ID NO:

81.

19. The method according to claim 9, wherein the at least one marker allele is a guanine (G) at position 283 of SEQ ID NO:1, a guanine (G) at position 501 of SEQ ID NO:2, a thymine (T) at position 501 of SEQ ID NO:3, a G at position 501 of SEQ ID NO:5, an adenine (A) at position 501 of SEQ ID NO:6, an A at position 151 of SEQ ID NO:7, an A at position 501 of SEQ ID NO:8, a 19 nucleotide insertion at position 502 of SEQ ID NO:10, a G at position 501 of SEQ ID NO:11, a G at position 501 of SEQ ID NO:12, a cytosine (C) at position 501 of SEQ ID NO:13, a G at position 61 of SEQ ID NO:82, an A at position 61 of SEQ ID NO:83, a G at position 61 of SEQ ID NO:87, a G at position 501 of SEQ ID NO:88, a G at position 101 of SEQ ID NO:89, an A at position 151 of SEQ ID NO:90, an A at position 153 of SEQ ID NO:91, a T at position 48 of SEQ ID NO:92, a C at position 61 of SEQ ID NO:93, an A at position 61 of CA 2969547 Date reçue / Received date 2024-07-11 30 SEQ ID NO:94, a G at position 501 of SEQ ID NO:95, a T at position 101 of SEQ ID NO:96, an A at position 151 of SEQ ID NO:97, an A at position 61 of SEQ ID NO:98, a C at position 328 of SEQ ID NO:103, a Tat position 61 of SEQ ID NO:107, a C at position 151 of SEQ ID NO:109, a Tat position 151 of SEQ ID NO:110, and a C at position 848 of SEQ ID NO:

111.

20. The method according to claim 11, wherein the haplotype comprises a plurality of the following marker alleles: a thymine (T) at position 501 of SEQ ID NO:14, a guanine (G) at position 501 of SEQ ID NO:15, a cytosine (C) at position 501 of SEQ ID NO:16, a C at position 61 of SEQ ID NO:17, a G at position 501 of SEQ ID NO:18, a C at position 501 of SEQ ID NO:19, a C at position 501 of SEQ ID NO:20, a G at position 501 of SEQ ID NO:21, a C at position 501 of SEQ ID NO:22, an adenine (A) at position 501 of SEQ ID NO:23, a C at position 501 of SEQ ID NO:24, a C at position 501 of SEQ ID NO:25, a C at position 501 of SEQ ID NO:26, an A at position 501 of SEQ ID NO:27, a TT at position 502 of SEQ ID NO:28, a T at position 501 of SEQ ID NO:29, a T at position 501 of SEQ ID NO:30, a T at position 501 of SEQ ID NO:31, a T at position 502 of SEQ ID NO:32, a T at position 501 of SEQ ID NO:34, a T at position 501 of SEQ ID NO:35, a C at position 501 of SEQ ID NO:36, a T at position 501 of SEQ ID NO:37, a T at position 501 of SEQ ID NO:38, a C at position 536 of SEQ ID NO:39, an A at position 501 of SEQ ID NO:40, an A at position 501 of SEQ ID NO:41, an A at position 501 of SEQ ID NO:42, a G at position 501 of SEQ ID NO:43, a G at position 501 of SEQ ID NO:44, an A at position 502 of SEQ ID NO:45, a T at position 501 of SEQ ID NO:46, a G at position 501 of SEQ ID NO:47, a C at position 501 of SEQ ID NO:48, an A at position 501 of SEQ ID NO:49, a T at position 501 of SEQ ID NO:50, a G at position 501 of SEQ ID NO:51, a C at position 502 of SEQ ID NO:52, a T at position 501 of SEQ ID NO:53, a T at position 501 of SEQ ID NO:54, an A at position 501 of SEQ ID NO:56, a C at position 501 of SEQ ID NO:58, a C at position 501 of SEQ ID NO:60, a C at position 501 of SEQ ID NO:61, a C at position 502 of SEQ ID NO:62, a T at position 501 of SEQ ID NO:63, an A at position 501 of SEQ ID NO:66, a C at position 501 of SEQ ID NO:67, a T at position 501 of SEQ ID NO:68, a T at position 501 of SEQ ID NO:69, an A at position 501 of SEQ ID NO:70, a T at position 501 of SEQ ID NO:72, a G at position 501 of SEQ ID NO:73, a C at position 501 of SEQ ID NO:74, an A at position 501 of SEQ ID NO:75, an A at position 501 of SEQ ID NO:76, a C at position 501 CA 2969547 Date reçue / Received date 2024-07-11 31 of SEQ ID NO:77, a Tat position 501 of SEQ ID NO:78, a T at position 501 of SEQ ID NO:79, or a G at position 101 of SEQ ID NO:

81.

21. The method according to claim 11, wherein the haplotype comprises a plurality of the following marker alleles: a guanine (G) at position 283 of SEQ ID NO:1, a guanine (G) at position 501 of SEQ ID NO:2, a thymine (T) at position 501 of SEQ ID NO:3, a G at position 501 of SEQ ID NO:5, an adenine (A) at position 501 of SEQ ID NO:6, an A at position 151 of SEQ ID NO:7, an A at position 501 of SEQ ID NO:8, a 19 nucleotide insertion at position 502 of SEQ ID NO:10, a G at position 501 of SEQ ID NO:11, a G at position 501 of SEQ ID NO:12, a cytosine (C) at position 501 of SEQ ID NO:13, a G at position 61 of SEQ ID NO:82, an A at position 61 of SEQ ID NO:83, a G at position 61 of SEQ ID NO:87, a G at position 501 of SEQ ID NO:88, a G at position 101 of SEQ ID NO:89, an A at position 151 of SEQ ID NO:90, an A at position 153 of SEQ ID NO:91, a T at position 48 of SEQ ID NO:92, a C at position 61 of SEQ ID NO:93, an A at position 61 of SEQ ID NO:94, a G at position 501 of SEQ ID NO:95, a T at position 101 of SEQ ID NO:96, an A at position 151 of SEQ ID NO:97, an A at position 61 of SEQ ID NO:98, a C at position 328 of SEQ ID NO:103, a Tat position 61 of SEQ ID NO:107, a C at position 151 of SEQ ID NO:109, a Tat position 151 of SEQ ID NO:110, and a C at position 848 of SEQ ID NO:

111.

22. The method according to claim 13, wherein the one or more marker alleles are one or more of a thymine (T) at position 501 of SEQ ID NO:14, a guanine (G) at position 501 of SEQ ID NO:15, a cytosine (C) at position 501 of SEQ ID NO:16, a C at position 61 of SEQ ID NO:17, a G at position 501 of SEQ ID NO:18, a C at position 501 of SEQ ID NO:19, a C at position 501 of SEQ ID NO:20, a G at position 501 of SEQ ID NO:21, a C at position 501 of SEQ ID NO:22, an adenine (A) at position 501 of SEQ ID NO:23, a C at position 501 of SEQ ID NO:24, a C at position 501 of SEQ ID NO:25, a C at position 501 of SEQ ID NO:26, an A at position 501 of SEQ ID NO:27, a TT at position 502 of SEQ ID NO:28, a T at position 501 of SEQ ID NO:29, a T at position 501 of SEQ ID NO:30, a T at position 501 of SEQ ID NO:31, a T at position 502 of SEQ ID NO:32, a T at position 501 of SEQ ID NO:34, a T at position 501 of SEQ ID NO:35, a C at position 501 of SEQ ID NO:36, a T at position 501 of SEQ ID NO:37, a T at position 501 of SEQ ID NO:38, a C at position 536 of SEQ ID NO:39, an A at position 501 CA 2969547 Date reçue / Received date 2024-07-11 32 of SEQ ID NO:40, an A at position 501 of SEQ ID NO:41, an A at position 501 of SEQ ID NO:42, a G at position 501 of SEQ ID NO:43, a G at position 501 of SEQ ID NO:44, an A at position 502 of SEQ ID NO:45, a T at position 501 of SEQ ID NO:46, a G at position 501 of SEQ ID NO:47, a C at position 501 of SEQ ID NO:48, an A at position 501 of SEQ ID NO:49, a T at position 501 of SEQ ID NO:50, a G at position 501 of SEQ ID NO:51, a C at position 502 of SEQ ID NO:52, a T at position 501 of SEQ ID NO:53, a T at position 501 of SEQ ID NO:54, an A at position 501 of SEQ ID NO:56, a C at position 501 of SEQ ID NO:58, a C at position 501 of SEQ ID NO:60, a C at position 501 of SEQ ID NO:61, a C at position 502 of SEQ ID NO:62, a T at position 501 of SEQ ID NO:63, an A at position 501 of SEQ ID NO:66, a C at position 501 of SEQ ID NO:67, a T at position 501 of SEQ ID NO:68, a T at position 501 of SEQ ID NO:69, an A at position 501 of SEQ ID NO:70, a T at position 501 of SEQ ID NO:72, a G at position 501 of SEQ ID NO:73, a C at position 501 of SEQ ID NO:74, an A at position 501 of SEQ ID NO:75, an A at position 501 of SEQ ID NO:76, a C at position 501 of SEQ ID NO:77, a Tat position 501 of SEQ ID NO:78, a T at position 501 of SEQ ID NO:79, or a G at position 101 of SEQ ID NO:

81.

23. The method according to claim 13, wherein the one or more marker alleles are one or more of a guanine (G) at position 283 of SEQ ID NO:1, a guanine (G) at position 501 of SEQ ID NO:2, a thymine (T) at position 501 of SEQ ID NO:3, a G at position 501 of SEQ ID NO:5, an adenine (A) at position 501 of SEQ ID NO:6, an A at position 151 of SEQ ID NO:7, an A at position 501 of SEQ ID NO:8, a 19 nucleotide insertion at position 502 of SEQ ID NO:10, a G at position 501 of SEQ ID NO:11, a G at position 501 of SEQ ID NO:12, a cytosine (C) at position 501 of SEQ ID NO:13, a G at position 61 of SEQ ID NO:82, an A at position 61 of SEQ ID NO:83, a G at position 61 of SEQ ID NO:87, a G at position 501 of SEQ ID NO:88, a G at position 101 of SEQ ID NO:89, an A at position 151 of SEQ ID NO:90, an A at position 153 of SEQ ID NO:91, a T at position 48 of SEQ ID NO:92, a C at position 61 of SEQ ID NO:93, an A at position 61 of SEQ ID NO:94, a G at position 501 of SEQ ID NO:95, a T at position 101 of SEQ ID NO:96, an A at position 151 of SEQ ID NO:97, an A at position 61 of SEQ ID NO:98, a C at position 328 of SEQ ID NO:103, a Tat position 61 of SEQ ID NO:107, a C at position 151 of SEQ ID NO:109, a Tat position 151 of SEQ ID NO:110, and a C at position 848 of SEQ ID NO:

111. CA 2969547 Date reçue / Received date 2024-07-11