Identification of genetic loci conferring seed coat color based on a high-density map in soybean

Abstract

Seed coat color is a typical evolutionary trait. Identification of the genetic loci that control seed coat color during the domestication of wild soybean could clarify the genetic variations between cultivated and wild soybean. We used 276 F10 recombinant inbred lines (RILs) from the cross between a cultivated soybean (JY47) and a wild soybean (ZYD00321) as the materials to identify the quantitative trait loci (QTLs) for seed coat color. We constructed a high-density genetic map using re-sequencing technology. The average distance between adjacent markers was 0.31 cM on this map, comprising 9,083 bin markers. We identified two stable QTLs (qSC08 and qSC11) for seed coat color using this map, which, respectively, explained 21.933 and 26.934% of the phenotypic variation. Two candidate genes (CHS3C and CHS4A) in qSC08 were identified according to the parental re-sequencing data and gene function annotations. Five genes (LOC100786658, LOC100801691, LOC100806824, LOC100795475, and LOC100787559) were predicted in the novel QTL qSC11, which, according to gene function annotations, might control seed coat color. This result could facilitate the identification of beneficial genes from wild soybean and provide useful information to clarify the genetic variations for seed coat color in cultivated and wild soybean.

Construction of a high-density genetic map for faba bean (Vicia faba L.) and quantitative trait loci mapping of seed-related traits

“…The results of the correlation analysis among seed traits showed that seed coat color was positively correlated with FC and StC, and negatively correlated with LC. Mendel first proposed that the seed coat color of peas is controlled by a pair of genes and considered a qualitative trait ( Myers, 2004 ), while the seed coat color of soybeans is controlled by multiple genetic loci ( Choung et al., 2001 ), and more than 30 molecular marker loci on different chromosomes that control seed coat color in soybean have been detected ( Yuan et al., 2022 ). However, few studies on the QTLs for seed coat color in faba bean have been reported.…”

Construction of the first ultra-dense genetic map for faba bean (Vicia faba L.) and quantitative trait loci mapping for seed-related traits

“…The results of the correlation analysis among seed traits showed that seed coat color was positively correlated with FC and StC, and negatively correlated with LC. Mendel rst proposed that the seed coat color of peas is controlled by a pair of genes and considered a qualitative trait (Myers JR 2004), while the seed coat color of soybeans is controlled by multiple genetic loci (Choung et al 2001), and more than 30 molecular marker loci on different chromosomes that control seed coat color in soybean have been detected (Yuan et al 2022). However, few studies on the QTLs for seed coat color in faba bean have been reported.…”

Research Advances on the Hard Seededness Trait of Soybean and the Underlying Regulatory Mechanisms

“…~5000 years ago, in the eastern half of north China and disseminated to Europe and America in the 18th century [3,4]. Compared to their wild relatives, cultivated soybeans have undergone significant changes in growth habits, plant architecture, seed morphology, and composition under long-term targeted selection and improvement [5][6][7]. Cultivated soybeans display a bush-type growth habit with a stout primary stem and sparse branches, bearing large seeds that are generally prone to water absorption and germination.…”