Mapping And Utilization Of Genes Related To Seed Coat Color In Soybean (glycine Max(l.) Merr.)

Seed coat color is one of important morphological markers for genetic andmolecular biology in soybean. Seed coat is black in most of wild soybean while yellowin cultivar for natural and artificial selection during the evolution of soybean. Therefore,it is very important to discover genes related to soybean seed coat color not only forbreeding but also for evolutionary study. Different color formation in seed coat iscaused by deposition of various anthocyanin pigments. Although the biosynthesis ofdifferent pigments had been uncovered in several plant species, most of genescontrolling natural variation in seed coat color are still unknown in soybean. In thisstudy, recombinant inbred line (RIL), which was constructed by the cross of cultivatedsoybean ZP95-5383and wild soybean NY279, was used for maping of genes related toseed coat color. Firstly, molecular markers related to seed coat color were screend byusing bulked segregation analysis (BSA) and QTLs related to seed coat color were alsodetected by composite interval mapping (CIM) method. Futhermore, the candidateregions were successfully reduced based on the population of residual heterozygosislines. In addition, candidate regions were also analyzed and verificatied by correlationanalysis in25resequencing soybeans.The main results were as follows:1. Inheritance of seed coat color is controlled by several genes in soybean. Theseparation of seed coat color was investigated during F2-F4generation of the RILpopulation. The seed coat color existed separation in offsprings of yellow, green, brown,and black lines., and the most complex separation occurred in the green lines.Meanwhile, each generation had homozygous lines, including the non-separated lines ineach generation, and the homozygous from separated lines. Therefore, seed coat colorwas regulated by multiple genes.2. Preliminary mapping revealed that two loci were related to seed coat color usingBSA method. Screening of polymorphic markers showed that17markers, which waslocated in the Chromosome8, Chromosome1and Chromosome6, were related to seedcoat color by BSA. After analysis of these markers in171individuals of F2population,two loci were detected by CIM method using Windows QTL Cartographer version V2.5software and genetic linkage maps constructed by MapManagerQTXb17software. The two loci were located in Chromosome8and Chromosome1respectively, with the LODvalues20,5and genetic variation60%,11%. The genetic distances of candidate regionswere22.17cM,15cM and the physical distance were5.5Mb,1.2Mb, respectively.4. Fine mapping of genes related seed coat color in soybean. Fine mapping wascarried out by using residual heterozygous lines and polymorphic markers betweenmakers of preliminary mapping. The candidate region in Chromosome8was reduced toa526.582-kb region between ls8-6and ls8-5and that in Chromosome1was reduced toa22-kb region between ls1-20and ls1-23. Furthermore, a marker located in this region(ls1-20) was cosegregated with yellow seed coat.5. The results of gene mapping were confirned by association analysis of the SNPdata of25re-sequenced materials in candidate regions.25re-sequenced materials,including9modern cultivars,8landraces and8wild soybeans were used for associationanalysis. These materials had different seed coat colors, including10yellow,11blackand4brown ones. The results showed that4321SNPs located on a270-kb region incandidate region of Chromosome8, which was about250kb shorter than the finemapping results, had relativly high correlation (P<1e-4) with the phenotype. Five locilocated on a224kb region, including CHS tandem repeatse, had most high correlation(P<1e-10) among them. Meanwhile,2667SNPs located on a170-kb region in candidateregion of Chromosome1also had relativly high correlation (P<1e-4) with thephenotype, which was consistent with the results of fine mapping.6. The selection efficientcy of a molecular marker related to yellow seed coat wereanalized by using soybean germplasm.355core germplasm and germplasm resourceswere used to identify the selection efficiency of ls1-22and the result showed thatselection efficiency of this marker was up to76.23%for identification of soybean withyellow seed coat.In this study, genes related to seed coat color have been fine mapped and analysed,establishing foundation for studying genetic mechanism and evolutionary relationshipof seed coat color in soybean between wild soybean and modern cultivar.