WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean
Yanjie Yao,
Erhui Xiong,
Xuelian Qu,
Junfeng Li,
Hongli Liu,
Leipo Quan,
Wenyan Lu,
Xuling Zhu,
Meiling Chen,
Ke Li,
Xiaoming Chen,
Yun Lian,
Weiguo Lu,
Dan Zhang,
Xinan Zhou,
Shanshan Chu,
Yongqing Jiao
Affiliations
Yanjie Yao
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Erhui Xiong
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Xuelian Qu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Junfeng Li
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Hongli Liu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Leipo Quan
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Wenyan Lu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Xuling Zhu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Meiling Chen
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Ke Li
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Xiaoming Chen
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Yun Lian
Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences
Weiguo Lu
Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences
Dan Zhang
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Xinan Zhou
Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences
Shanshan Chu
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Yongqing Jiao
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University
Abstract Background Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. Results In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as “Photosynthesis”, “Carbon metabolism”, and “Fatty acid metabolism”, were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. Conclusions Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.
