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Seed coat color is an important agronomic trait in soybean for morphology marker,biochemical function,and evolution.Although pigmentation process of seed coat color has been well dissected at molecular level in several plant species,genes controlling natural variation of seed coat color in soybean are still not completely understood.To study the genetic basis of seed coat color and systematically dissect genes associated with this trait in soybean,a combination of association and linkage analysis were used.Fourteen loci distributed in ten chromosomes were identified to be associated with seed coat colors by using 176,065 coding SNPs selected from resequencing of 56 soybean accessions.Four of these loci,including one novel locus were validated and narrowed using a segregating population generated from a cross of G.max ZP95-5383 and G.soja NY279,in which the complex trait of seed coat colors were further separated into simple trait pairs by continuously developing residual heterozygous lines(RHLs).Therefore,the regulation mechanism of different loci for the complex trait of seed coat color were completely illustrated by genotyping all the F2 individuals of this RIL population using flanking markers from fine-mapping regions.Our results will be useful for map-based cloning of the genes as well as for marker-assisted breeding in soybean.The information also provide a alternative strategy for systematically discovering genes controlling the complex trait by association analysis with highthroughput genome sequence data in natural population following linkage analysis onsite regions among dissected segregating populations.