Abstract
Soybean was domesticated about 5,000 to 6,000 years ago in China. Although genotyping technologies such as genotyping by sequencing (GBS) and high-density array are available, it is convenient and economical to genotype cultivars or populations using medium-density SNP array in genetic study as well as in molecular breeding. In this study, 235 cultivars, collected from China, Japan, USA, Canada and some other countries, were genotyped using SoySNP8k iSelect BeadChip with 7,189 single nucleotide polymorphisms (SNPs). In total, 4,471 polymorphic SNP markers were used to analyze population structure and perform genome-wide association study (GWAS). The most likely K value was 7, indicating this population can be divided into 7 subpopulations, which is well in accordance with the geographic origins of cultivars or accession studied. The LD decay rate was estimated at 184 kb, where r2 dropped to half of its maximum value (0.205). GWAS using FarmCPU detected a stable quantitative trait nucleotide (QTN) for hilum color and seed color, which is consistent with the known loci or genes. Although no universal QTNs for flowering time and maturity were identified across all environments, a total of 30 consistent QTNs were detected for flowering time (R1) or maturity (R7 and R8) on 16 chromosomes, most of them were corresponding to known E1 to E4 genes or QTL region reported in SoyBase (soybase.org). Of 16 consistent QTNs for protein and oil contents, 11 QTNs were detected having antagonistic effects on protein and oil content, while 4 QTNs soly for oil content, and one QTN soly for protein content. The information gained in this study demonstrated that the usefulness of the medium-density SNP array in genotyping for genetic study and molecular breeding.
Highlights
Soybean [Glycine max (L.) Merr.] is one of important crops worldwide, providing a sustainable source of high-quality protein feed and vegetable oil
Leamy et al (2017) studied seed composition traits in wild soybean (Glycine soja) and found 29 single nucleotide polymorphisms (SNPs) located on ten different chromosomes that are significantly associated with the seven seed composition traits, of which eight SNPs co-localized with quantitative trait loci (QTL) previously uncovered in linkage or association mapping studies conducted with cultivated soybean samples (Leamy et al, 2017)
Fast genotyping method e.g., using a set of core SNP array is in high demand for genetic study or molecular breeding (Chaudhary et al, 2015)
Summary
Soybean [Glycine max (L.) Merr.] is one of important crops worldwide, providing a sustainable source of high-quality protein feed and vegetable oil. Previous studies identified eleven major-effect loci affecting flowering and maturity in soybean, which have been designated as E1 to E10, and the J locus for “long juvenile period” (Bernard, 1971; Buzzell, 1971; Buzzell and Voldeng, 1980; McBlain and Bernard, 1987; Ray et al, 1995; Bonato and Vello, 1999; Cober and Voldeng, 2001; Cober et al, 2010; Kong et al, 2014; Samanfar et al, 2017) Of these genes, E1, E2, E3, E4, E6, E9, E10, and J have been cloned and functionally characterized (Liu et al, 2008; Watanabe et al, 2009, 2011; Xia et al, 2012a; Zhai et al, 2014a; Zhao et al, 2016; Lu et al, 2017; Samanfar et al, 2017). More than 30 QTN were identified under multiple environments for flowering time and maturity; while 16 consistent QTNs were detected for protein and oil contents
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