10.3389/fpls.2018.00610.s001
Ya-ying Wang
Ya-ying
Wang
Yu-qiu Li
Yu-qiu
Li
Hong-yan Wu
Hong-yan
Wu
Bo Hu
Bo
Hu
Jia-jia Zheng
Jia-jia
Zheng
Hong Zhai
Hong
Zhai
Shi-xiang Lv
Shi-xiang
Lv
Xin-lei Liu
Xin-lei
Liu
Xin Chen
Xin
Chen
Hong-mei Qiu
Hong-mei
Qiu
Jiayin Yang
Jiayin
Yang
Chun-mei Zong
Chun-mei
Zong
De-zhi Han
De-zhi
Han
Zi-xiang Wen
Zi-xiang
Wen
De-chun Wang
De-chun
Wang
Zheng-jun Xia
Zheng-jun
Xia
Data_Sheet_1_Genotyping of Soybean Cultivars With Medium-Density Array Reveals the Population Structure and QTNs Underlying Maturity and Seed Traits.ZIP
Frontiers
2018
soybean
GWAS
flowering time
protein content
oil content
population structure
FarmCPU
2018-05-09 10:48:22
Dataset
https://frontiersin.figshare.com/articles/dataset/Data_Sheet_1_Genotyping_of_Soybean_Cultivars_With_Medium-Density_Array_Reveals_the_Population_Structure_and_QTNs_Underlying_Maturity_and_Seed_Traits_ZIP/6236663
<p>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 r<sup>2</sup> 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.</p>