Coat Color Traits Research Articles

Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses.

ABSTRACTThe Kushum is a relatively new breed of horses in Kazakhstan that was established in the middle of the 20th century through a cross between mares of Kazakhstan local horses and stallions of Thoroughbred, Trotter, and Russian Don breeds to supply military horses. To reveal the genetic characteristics of this breed, we investigated haplotypes of mitochondrial DNA (mtDNA) and single-nucleotide polymorphisms of the Y chromosome, as well as genotypes of five functional genes associated with coat color, body composition, and locomotion traits. We detected 10 mtDNA haplotypes that fell into 8 of the 17 major haplogroups of horse mtDNA, indicating a unique haplotype composition with high genetic diversity. We also found two Y-chromosomal haplotypes in Kushum horses, which likely originated from Trotter and/or Don breeds. The findings regarding the mtDNA and Y-chromosomal haplotypes are concordant with the documented maternal and paternal origins of the Kushum horses. The allele frequencies of ASIP, MC1R, and MATP associated with coat color were consistent with the coat color variations of Kushum horses. The allele frequencies of MSTN associated with endurance performance and those of DMRT3 associated with gait suggested that the observed allele frequencies of these genes were the result of selective breeding for these traits. As a result of this study, we were able to obtain useful information for a better understanding of the origin and breeding history of the Kushum horse breed using molecular markers.

True Colors: Commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential.

Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANELTM data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e-7 and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to visualize the potential historic connections between breeds that share rare alleles; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.

Assessing genetic divergence among rice germplasm based on qualitative traits

Rice is cultivated worldwide under wide range of ecological conditions and is a daily staple food crop for more than half of world’s population. The morphological characterization is usually performed to select better genotypes. This type of characterization identifies elite genotypes based on qualitative as well as quantitative traits. In present study 45 diverse rice germplasm were screened for important qualitative traits. The experiment was designed as augmented and important qualitative traits including leaf related traits, lodging, panicle shape, seed coat color and awn related traits were studied. Significant variations were observed for all the examined traits. Majority of genotypes showed resistance to lodging, and only few showed slight lodging. The brown seed coat color was found dominant among genotypes. All the studied traits included in the study were found useful for the identification of improved genotypes and these traits have direct relation with yield or yield related traits. However, to elucidate the particular responsible genes for these traits, further molecular based studies are recommended. Keywords: Genetic variability; Lodging; Morphological traits; Rice; Qualitative traits http://dx.doi.org/10.19045/bspab.2019.80056

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs.

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log2 fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.

Identification and validation of major and minor QTLs controlling seed coat color in Brassica rapa L.

Seed coat color is an important agronomic trait in Brassica rapa. Yellow seeds are a desirable trait for breeding oilseed Brassica crops. To identify quantitative trait loci (QTLs) that condition seed coat color in B. rapa, we used a population of recombinant inbred lines (RILs) derived from crossing 09A001, a standard rapid-cycling (RcBr) inbred line of B. rapa L. ssp. dichotoma with yellow seeds, with 08A061, an inbred line of heading Chinese cabbage with dark brown seeds. Using two phenotypic scoring methods, we detected a total of nine QTLs distributed on four chromosomes (Chrs.), A03, A06, A08, and A09, that explained 3.17 to 55.73% of the phenotypic variation for seed color. To validate the effects of the identified QTLs in the RIL population, chromosome segment substitution lines (CSSLs) harboring the chromosomal segment carrying the candidate QTL region from 08A061 were selected, and two co-localized major QTLs, qSC9.1 and qSCb9.1, and one minor QTL, qSC3.1, were successfully validated. The validated QTL located on Chr. A03 appears to be a new locus underlying seed coat color in B. rapa. These findings provide additional insight that will help explain the complex genetic mechanisms underlying the seed coat color trait in B. rapa.

Identification of Candidate Genes Controlling Black Seed Coat and Pod Tip Color in Cowpea (Vigna unguiculata [L.] Walp).

Seed coat color is an important part of consumer preferences for cowpea (Vigna unguiculata [L.] Walp). Color has been studied in numerous crop species and has often been linked to loci controlling the anthocyanin biosynthesis pathway. This study makes use of available resources, including mapping populations, a reference genome, and a high-density single nucleotide polymorphism genotyping platform, to map the black seed coat and purple pod tip color traits, with the gene symbol Bl, in cowpea. Several gene models encoding MYB domain protein 113 were identified as candidate genes. MYB domain proteins have been shown in other species to control expression of genes encoding enzymes for the final steps in the anthocyanin biosynthesis pathway. PCR analysis indicated that a presence/absence variation of one or more MYB113 genes may control the presence or absence of black pigment. A PCR marker has been developed for the MYB113 gene Vigun05g039500, a candidate gene for black seed coat color in cowpea.

Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds

Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the selection signatures in six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped to the latest reference goat genome, which generated a sequencing depth ranging from 22.30 to 31.75-fold for each breed. A total of 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative SNPs were detected in Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, and Tibetan cashmere goats, respectively. Based on the genome-wide FST and expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 44, 19, and 35 outlier windows were deemed as the selection signatures in the six goat breeds. After genome annotation, several genes within the selection signals were found to be possibly associated with important traits in goats, such as coat color (IRF4, EXOC2, RALY, EIF2S2, and KITLG), high-altitude adaptation (EPAS1), growth (LDB2), and reproduction traits (KHDRBS2). In summary, we provide an improved understanding of the genetic diversity and the genomic footprints under positive selection or the adaptations to the local environments in the domestic goat genome.

Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat.

The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.

English

The study was conducted to characterize meat quality and morphology of sheep in North Shewa Zone, and to generate baseline information on the patency of Menz sheep. A total of 720 sheep were purposely selected for morphological study. The result showed that age at first kidding, age at sexual maturity, weight, height, length, hair length, tail length and age at disposal were with a mean of 5.58 months, 4.55 months, 36.62 kg, 60.44, 82.49 and 4.42 cm and above 1 year, respectively. The result revealed that all sheep in the study areas were local pure breed, most of them were hornless with smooth hair and white coat color traits. The analytical result ranges from 5.68 to 6.25 (pH), 64.06 to 74.18 (moisture), 18.26 to 25.12 (protein), 3.80 to 13.71 (fat) and 1.02 to 1.46 (ash) contents of meat. Menz district sheep showed significant change in the parameters aforementioned. Menz sheep were the best in all traits/parameters, and a need of patent right to improve Menz sheep appropriately is our recommendation. Key words: Meat quality, Menz sheep, morphology.

English

This study aimed at identifying Sheko cattle keepers&#39; preferences by way of phenotypic ranking and hypothetical choice experiment in their habitat in order to define the indigenous selection criteria. The ranking experiment report was based on 15 cows and 6 to 9 bulls. Three animals of the same sex were randomly assigned in one group that resulted into five groups for cows and two to three groups for bulls. Thirty cattle keepers belonging to another community were invited to rank the groups of experimental animals according to their own preferences and give the reasons why they had chosen the animals as 1st, 2nd, and 3rd. Then they were provided with life history of each cow, including age, milk yield, parity, calving interval and heart girth measurements; while for bulls, age, milk yield of dam, sire fertility and heart girth measurements were described to determine whether she/he would consider re-ranking them. The results of farmers&rsquo; preference for traits through both methods are not consistent. In phenotypic ranking, the results indicate that, milk yield, body conformation, body size and coat color were emphasized in the selection of cow while, body size, dairy character, draught character and coat color traits were important traits for selection of bull. Information on life history provided insight in the respondents&rsquo; ranking decisions. In choice experiments, the maximum likelihood estimates of the parameters for cow selection were significant in both lowland and midland agro-ecological zones (AEZs), except for calving interval in midland. The trait mothering ability was the most preferred trait followed by milk yield in both AEZs. For bulls the estimates were significant with the exception of growth rate in midland. It was found out that by this method breeding bulls are chosen based on milk performance of mother and temperament in both AEZs. Key words: Breeding objectives, choice experiment, lowland, midland, phenotypic ranking, Sheko. &nbsp

Haplotype diversity in MC1R locus between the Min and white-haired pig breeds

ABSTRACTIn this article, we investigated the genetic variations in the coding region of porcine melanocortin receptor 1 (MC1R) gene in three pig breeds (Min, Yorkshire and Landrace) with black and white coat colors. Six polymorphic sites were found to be significantly associated with coat color. Two blocks were identified in the linkage disequilibrium map, the haplotypes in the first block are nt67/68indelCC and nt67/68indel--, and the haplotypes in the second block are ACCGA and GTTAG. The median-joining network diagram of MC1R haplotypes showed most Min pigs and other Asia domestic breeds own similar haplotypes to ACCGA, while the haplotypes of Europe pig breeds are similar to GTTAG. The phylogenetic analysis of the MC1R CDS further showed Min pigs are close to Laiwu pigs (Shandong, China), which indicated that the black coat color trait of Min pig might be originated and evolved from the black pig breed in Shandong Peninsula of China.

Identifying candidate positive selection genes in Korean imported pig breeds

Domestication and artificial selection have modified the genome landscape of the pig. The identification of selection signatures in the genome can help to elucidate the selection mechanisms and uncover the causal genes related to the phenotypic variations between domestic pig breeds. We scanned the genomes of Korean imported pig breeds against native breeds using Z-transformed Fst (ZFST) and Heterozygosity (ZHp) statistics to search for the signatures of positive selection. We identified 411 (ZFST = 175; ZHp = 256) putatively selected genes in commercial breeds. The gene regions identified were harboring those related to immunity, coat color, reproduction function and other traits. Several genes (e.g., PLSCR4, AGTR1 and CORIN) were related to reproduction traits such as fertility, ovulation rate, and uterine function. This study revealed genes which improve our understanding of the biological mechanisms of higher litter sizes, the phenotype of interest, in higher litter pig breeds.

Candidate Gene Identification of Feed Efficiency and Coat Color Traits in a C57BL/6J × Kunming F2 Mice Population Using Genome-Wide Association Study.

Feed efficiency (FE) is a very important trait in livestock industry. Identification of the candidate genes could be of benefit for the improvement of FE trait. Mouse is used as the model for many studies in mammals. In this study, the candidate genes related to FE and coat color were identified using C57BL/6J (C57) × Kunming (KM) F2 mouse population. GWAS results showed that 61 and 2 SNPs were genome-wise suggestive significantly associated with feed conversion ratio (FCR) and feed intake (FI) traits, respectively. Moreover, the Erbin, Msrb2, Ptf1a, and Fgf10 were considered as the candidate genes of FE. The Lpl was considered as the candidate gene of FI. Further, the coat color trait was studied. KM mice are white and C57 ones are black. The GWAS results showed that the most significant SNP was located at chromosome 7, and the closely linked gene was Tyr. Therefore, our study offered useful target genes related to FE in mice; these genes may play similar roles in FE of livestock. Also, we identified the major gene of coat color in mice, which would be useful for better understanding of natural mutation of the coat color in mice.

Fine Mapping and Whole-Genome Resequencing Identify the Seed Coat Color Gene in Brassica rapa.

A yellow seed coat is a desirable agronomic trait in the seeds of oilseed-type Brassica crops. In this study, we identified a candidate gene for seed coat color in Dahuang, a landrace of Brassica rapa. A previous study of Dahuang mapped the seed coat color gene Brsc1 to a 2.8-Mb interval on chromosome A9 of B. rapa. In the present study, the density of the linkage map for Brsc1 was increased by adding simple sequence repeat (SSR) markers, and the candidate region for Brsc1 was narrowed to 1.04 Mb. In addition, whole-genome resequencing with bulked segregant analysis (BSA) was conducted to identify candidate intervals for Brsc1. A genome-wide comparison of SNP profiles was performed between yellow-seeded and brown-seeded bulk samples. SNP index analyses identified a major candidate interval on chromosome A9 (A09:18,255,838–18,934,000, 678 kb) containing a long overlap with the target region recovered from the fine mapping results. According to gene annotation, Bra028067 (BrTT1) is an important candidate gene for Brsc1 in the overlapping region. Quantitative reverse transcription (qRT)-PCR revealed that BrTT1 mainly functions in the seed. Point mutations and small deletions in BrTT1 were found between yellow- and brown-seeded Dahuang plants. Collectively, the expression and sequence analysis results provide preliminary evidence that BrTT1 is a candidate gene for the seed coat color trait in Dahuang.

Prevalence, risk factors and genetic parameters of cresty neck in Pura Raza Español horses.

Cresty neck is a relatively common morphological defect in Pura Raza Español horses and other Baroque type horse breeds, which adversely affects the breeding industry. To establish the within-breed prevalence, possible associated factors and heritability of cresty neck in Pura Raza Español horses. Cross-sectional analysis of a large worldwide database of Pura Raza Español horses. The database included evaluations of 10,929 Pura Raza Español horses from 24 countries. Cresty neck score, on a 9 point scale, girth-to-height ratio, height at the withers, length of neck, head-neck junction and neck-body junction were recorded. A Bayesian genetic animal model included the following systematic effects: girth-to-height ratio, age, sex, coat colour and geographical area of the stud. Animal and residual effects were included as random effects. Within this Pura Raza Español population, 8.91% had a cresty neck score ≥5, which is the threshold for penalty or disqualification in the studbook of the breed. The age, sex, coat colour and stud geographical area were significantly associated with cresty neck score. The estimated heritability coefficient for cresty neck score was 0.37 (s.d. = 0.034) and genetic correlation between cresty neck score and other conformational traits ranged from -0.06 (height-at-withers) to -0.21 (neck-body junction). Cresty neck is a prevalent defect in Pura Raza Español horses, associated with age, sex, coat colour and other conformational traits, with a moderate level of heritability. Breeding to select against this condition may therefore be beneficial in this breed.

The MC1R and ASIP Coat Color Loci May Impact Behavior in the Horse.

Shared signaling pathways utilized by melanocytes and neurons result in pleiotropic traits of coat color and behavior in many mammalian species. For example, in humans polymorphisms at MC1R cause red hair, increased heat sensitivity, and lower pain tolerance. In deer mice, rats, and foxes, ASIP polymorphisms causing black coat color lead to more docile demeanors and reduced activity. Horse (Equus caballus) base coat color is primarily determined by polymorphisms at the Melanocortin-1 Receptor (MC1R) and Agouti Signaling Protein (ASIP) loci, creating a black, bay, or chestnut coat. Our goal was to investigate correlations between genetic loci for coat color and temperament traits in the horse. We genotyped a total of 215 North American Tennessee Walking Horses for the 2 most common alleles at the MC1R (E/e) and ASIP (A/a) loci using previously published PCR and RFLP methods. The horses had a mean age of 10.5 years and comprised 83 geldings, 25 stallions, and 107 mares. To assess behavior, we adapted a previously published survey for handlers to score horses from 1 to 9 on 20 questions related to specific aspects of temperament. We utilized principle component analysis to combine the individual survey scores into 4 factors of variation in temperament phenotype. A factor component detailing self-reliance correlated with genotypes at the ASIP locus; black mares (aa) were more independent than bay mares (A_) (P = 0.0063). These findings illuminate a promising and novel animal model for future study of neuroendocrine mechanisms in complex behavioral phenotypes.

Revealing Seed Coat Colour Variation and Their Possible Association with Seed Yield Parameters in Common Vetch (Vicia sativaL.)

The seed coat colour variation of 70 common vetch genotypes were determined by using uniform colour scale(L⁎a⁎b⁎)and their possible correlation with seed yield parameters including the number of pods per plant, the number of seeds per pod, pod dimension, and seed yield (kg/da) was determined. The results revealed presence of highly significant (p&lt;0.01) variations for both the seed yield and the seed coat colour parameters measured. The number of pods per plant, the number of seeds per pod, and seed yield ranged from 5.8 to 16.03, from 5.2 to 7.66, and from 143.37 to 531.1, respectively. The lightness value varied from 19.00 to 40.28 while chromaticitya⁎andb⁎values ranged from −0.16 to 8.99 and from 0.79 to 22.11, respectively. The highest correlation coefficients were determined betweenb⁎andL⁎(r=0.73), anda⁎andL⁎(r=0.55). The seed coat colour traits and seed yield parameters generally showed weak negative correlations. Seed yellowness (b⁎) and seed yield had correlation coefficient of −0.25, while correlation betweenL⁎and seed yield was determined as −0.23. The results indicated that lightness and yellowness of seed coat may be used as an important parameter to prescreen high yield genotypes of common vetch.

An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds.

This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.

Identification of QTL for seed coat colour and oil content inBrassica napusby association mapping using SSR markers

Qu, C., Hasan, M., Lu, K., Liu, L., Zhang, K., Fu, F., Wang, M., Liu, S., Bu, H., Wang, R., Xu, X., Chen, L. and Li, J. 2015. Identification of QTL for seed coat colour and oil content in Brassica napus by association mapping using SSR markers. Can. J. Plant Sci. 95: 387–395. Association mapping identifies quantitative trait loci (QTL) based on the strength of linkage disequilibrium (LD) between markers and functional polymorphisms across a set of diverse germplasms. In this study, we used association mapping to detect QTL and genome-wide simple sequence repeat (SSR) markers linked to seed coat colour and oil content in a population of 217 oilseed rape (Brassica napus L.) accessions. We corrected for the population structure of B. napus using 389 genome-wide SSR markers. In total, 25 and 11 SSR markers linked to seed coat colour and oil content were detected, respectively, and these two sets of markers were in different linkage groups. Nine of these markers for seed coat colour spanned the major QTL region for seed coat colour, and been mapped to chromosome A9. Six of these markers showed high levels of association with both seed coat colour and oil content, and markers H081N08.8 and KS20291 were mapped to the major QTL region for seed coat colour on chromosome A9. Another marker, CB10364, was in high LD with all determined seed coat colour and oil content traits, and was mapped to the co-localized QTL region for them on chromosome A8. These data indicate that seed coat colour was found to be an important contributor to seed oil content. Further, we show that association mapping using a heterogeneous set of genotypes is a suitable approach for complementing and enhancing previously obtained QTL information for marker-assisted selection.

Rapid identification of major-effect genes using the collaborative cross.

The Collaborative Cross (CC) was designed to facilitate rapid gene mapping and consists of hundreds of recombinant inbred lines descended from eight diverse inbred founder strains. A decade in production, it can now be applied to mapping projects. Here, we provide a proof of principle for rapid identification of major-effect genes using the CC. To do so, we chose coat color traits since the location and identity of many relevant genes are known. We ascertained in 110 CC lines six different coat phenotypes: albino, agouti, black, cinnamon, and chocolate coat colors and the white-belly trait. We developed a pipeline employing modifications of existing mapping tools suitable for analyzing the complex genetic architecture of the CC. Together with analysis of the founders’ genome sequences, mapping was successfully achieved with sufficient resolution to identify the causative genes for five traits. Anticipating the application of the CC to complex traits, we also developed strategies to detect interacting genes, testing joint effects of three loci. Our results illustrate the power of the CC and provide confidence that this resource can be applied to complex traits for detection of both qualitative and quantitative trait loci.