SNP-SNP Interaction Analysis on Soybean Oil Content under Multi-Environments.
Soybean oil content is one of main quality traits. In this study, we used the multifactor dimensionality reduction (MDR) method and a soybean high-density genetic map including 5,308 markers to identify stable single nucleotide polymorphism (SNP)-SNP interactions controlling oil content in soybean across 23 environments. In total, 36,442,756 SNP-SNP interaction pairs were detected, 1865 of all interaction pairs associated with soybean oil content were identified under multiple environments by the Bonferroni correction with p <3.55×10-11. Two and 1863 SNP-SNP interaction pairs detected stable across 12 and 11 environments, respectively, which account around 50% of total environments. Epistasis values and contribution rates of stable interaction (the SNP interaction pairs were detected in more than 2 environments) pairs were detected by the two way ANOVA test, the available interaction pairs were ranged 0.01 to 0.89 and from 0.01 to 0.85, respectively. Some of one side of the interaction pairs were identified with previously research as a major QTL without epistasis effects. The results of this study provide insights into the genetic architecture of soybean oil content and can serve as a basis for marker-assisted selection breeding.
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Qingshan
Q
Chen
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Xinrui
X
Mao
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Zhanguo
Z
Zhang
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Rongsheng
R
Zhu
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.|Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, People's Republic of China.
Zhengong
Z
Yin
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Yue
Y
Leng
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Hongxiao
H
Yu
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Huiying
H
Jia
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Shanshan
S
Jiang
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Zhongqiu
Z
Ni
The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150090, Heilongjiang, People's Republic of China.
Hongwei
H
Jiang
The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150090, Heilongjiang, People's Republic of China.
Xue
X
Han
The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150090, Heilongjiang, People's Republic of China.
Chunyan
C
Liu
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Zhenbang
Z
Hu
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Xiaoxia
X
Wu
The Crop Research and Breeding Center of Land-Reclamation of Heilongjiang Province, Harbin, 150090, Heilongjiang, People's Republic of China.
Guohua
G
Hu
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Dawei
D
Xin
College of Agriculture, Soybean biology Key Laboratory of the Ministry of Education, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
Zhaoming
Z
Qi
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