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. 2022 Aug 1:13:968618.
doi: 10.3389/fpls.2022.968618. eCollection 2022.

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

Baoqi Yuan  1   2 , Cuiping Yuan  2 , Yumin Wang  2 , Xiaodong Liu  3 , Guangxun Qi  2 , Yingnan Wang  2 , Lingchao Dong  2 , Hongkun Zhao  2 , Yuqiu Li  2 , Yingshan Dong  1   2
Affiliations

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

Baoqi Yuan et al. Front Plant Sci. .

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.

Keywords: QTL; high-density genetic map; re-sequencing; seed coat color; soybean.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
The soybean high-density genetic map. Bin markers are distributed on 20 chromosomes. The black bars in each linkage group represent the mapped bin markers. The linkage group number is shown on the x-axis and genetic distance is shown on the y-axis (cM is the unit).
FIGURE 2
FIGURE 2
Phenotypic identification of parents and RIL populations. (A) The characteristics of the seed coat color of JY47 and ZYD00321 and RIL populations. (B) Frequency distribution of seed coat color for the 276 RILs.
FIGURE 3
FIGURE 3
Fine mapping of two QTLs. (A) Mapping of QTLs for seed coat color on Chr08. The curves indicate the physical position of markers against the LOD score of the QTLs detected on Chr08. (B) Mapping of the QTLs for seed coat color on Chr11. The curves indicate the physical position of the markers against the LOD score of the QTLs detected on Chr11. (C) Distribution of tightly linked markers and plausible candidate genes for seed coat color on qSC08 in soybean. (D) SNP/InDels variants based on re-sequencing data from both parents of GLYMA_08G110300 and GLYMA_08G110700.
FIGURE 4
FIGURE 4
Analysis of SNPs and InDels between two parents in qSC08 (A) and qSC11 (B). Strip-shape charts show the distribution of SNPs and InDels in different genomic regions. The upstream and downstream represent the 5 kb within the region of transcription start and stop sites, respectively. Pie charts show the effects of SNP (upside) and InDel (underside) in the intragenic regions. And the corresponding quantity of SNP or InDel is labeled near the pie chart.
FIGURE 5
FIGURE 5
Distribution of the five candidate genes for seed coat color on qSC11. (A) Distribution of the candidate genes on qSC11. (B) Variation distribution of the candidate genes on qSC11. The upstream and downstream represent the 5 kb within the region of transcription start and stop sites, respectively. The regions are markers of different colors. Each white line represents one SNP/InDel variant.
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