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WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean

Authors :
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
Source :
BMC Genomics, Vol 24, Iss 1, Pp 1-17 (2023)
Publication Year :
2023
Publisher :
BMC, 2023.

Abstract

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.

Details

Language :
English
ISSN :
14712164
Volume :
24
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
edsdoj.ff13f50fb9a54d0a8a6d1635a4656974
Document Type :
article
Full Text :
https://doi.org/10.1186/s12864-023-09617-6