Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean

Abstract

Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.

Genetic diversity patterns and domestication origin of soybean

“…Interestingly, the peak on chromosome 13 is located on the W1 locus that influences seed-coat color in a case of the homozygous recessive it genotypes (Palmer et al 2004 ). Considering such a wide range of soybean seed-coat color variations, the detection of numerous minor peaks is not surprising, as reported by Song et al ( 2016 ), although it is still surprising to detect this large number of significant peaks using binary phenotyping data. Nevertheless, we think that some of those minor peaks are inevitably false because the limited number of conditional SNPs could not correct for all inflation of the statistic caused by population substructure.…”

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high‐density linkage mapping

“…Importantly, our analysis identified all known alleles ( I , i i and i ) of I locus containing a cluster of chalcone synthase genes involved in an anthocyanin pathway. The other two loci ( T and R ) associated with seed coat colour were not observed in our analysis and it could be due to the mapping parents used in present study carries only I locus associated with yellow/black seed coat colour whereas T and R locus black/brown seed coat colour (Gillman et al ., ; Song et al ., ; Toda et al ., ).…”

“…Statistical significance was assessed using unpaired two-tailed Student's t tests (P > 0.05). , 16, 1939-1953 associated with yellow/black seed coat colour whereas T and R locus black/brown seed coat colour (Gillman et al, 2011;Song et al, 2016;Toda et al, 2002).…”

Phytochemicals and Antioxidant Activity of Korean Black Soybean (Glycine max L.) Landraces

“…Soybean coat color is an important attribute determining the outward appearance of the soybean seed, which exists in a range of colors from yellow, green, brown, and black, to bicolored [5]. USA).…”