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Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits

文献类型： 外文期刊

作者： Wang, Ya-ying 1 ; Li, Yu-qiu 1 ; Wu, Hong-yan 1 ; Hu, Bo 1 ; Zheng, Jia-jia 1 ; Zhai, Hong 1 ; Lv, Shi-xiang 1 ; Liu, Xin 1 ;

作者机构： 1.Chinese Acad Sci, Northeast Inst Geog & Agroecol, Key Lab Soybean Mol Design Breeding, Harbin, Heilongjiang, Peoples R China

2.Univ Chinese Acad Sci, Beijing, Peoples R China

3.Jilin Acad Agr Sci, Soybean Res Inst, Changchun, Jilin, Peoples R China

4.Heilongjiang Acad Agr Sci, Harbin, Heilongjiang, Peoples R China

5.Jiangsu Acad Agr Sci, Nanjing, Jiangsu, Peoples R China

6.Huaiyin Inst Agr Sci Xuhuai Reg Jiangsu Prov, Huaian, Peoples R China

7.Heilongjiang Acad Agr Sci, Mudanjiang Branch, Mudanjiang, Peoples R China

8.Heilongjiang Acad Agr Sci, Heihe Branch, Heihe, Peoples R China

9.Michigan State Univ, Dept Plant Soil & Microbial Sci, E Lansing, MI 48824 USA

关键词： soybean; GWAS; flowering time; protein content; oil content; population structure; FarmCPU

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2018 年 9 卷

页码：

收录情况： SCI

摘要： 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 El 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.

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