Characterization of shade tolerance gene network in soybean revealed by forward integrated reverse genetic studies
文献类型： 外文期刊
作者： Su, Yanzhu 1 ; Pan, Yongpeng 1 ; Zeng, Weiying 7 ; Lai, Zhenguang 7 ; Guo, Pengfei 1 ; Hao, Xiaoshuai 1 ; Gu, Shengyu 1 ; Zhang, Zhipeng 1 ; Sun, Lei 1 ; Li, Ning 1 ; He, Jianbo 1 ; Wang, Wubin 1 ; Xing, Guangnan 1 ; Zhang, Jiaoping 1 ; Sun, Zudong 7 ; Gai, Junyi 1 ;
作者机构： 1.Nanjing Agr Univ, Soybean Res Inst, Nanjing 210095, Jiangsu, Peoples R China
2.Nanjing Agr Univ, MARA Natl Ctr Soybean Improvement, Nanjing 210095, Jiangsu, Peoples R China
3.Nanjing Agr Univ, MARA Key Lab Biol & Genet Improvement Soybean, Nanjing 210095, Jiangsu, Peoples R China
4.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China
5.Nanjing Agr Univ, State Innovat Platform Integrated Prod & Educ Soyb, Nanjing 210095, Jiangsu, Peoples R China
6.Nanjing Agr Univ, Jiangsu Collaborat Innovat Ctr Modern Crop Prod, Nanjing 210095, Jiangsu, Peoples R China
7.Inst Econ Crops, Guangxi Acad Agr Sci, Nanning 530007, Guangxi, Peoples R China
期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）
ISSN： 2662-6810
年卷期： 2025 年 12 卷 3 期
页码：
收录情况： SCI
摘要： Shade tolerance is a key trait for cultivars in inter/relay-cropped soybeans in maize fields. Our previous genome-wide association study (GWAS) results on southern China soybean germplasm revealed that the shade tolerance was conferred by a complex of genes with multiple alleles. To complete our understanding of the shade tolerance gene system, GWAS with gene-allele sequences as markers (designated GASM-RTM-GWAS) was conducted in a recombinant inbred line (RIL) population between two extreme parents using the shade tolerance index (STI) and relative pith cell length (RCL) as indicators. Altogether, 211 genes, comprising 99 and 119 genes (seven shared) for STI and RCL, respectively, were identified and then annotated into a similar set of five biological categories. Furthermore, transcriptome analysis detected 7837 differentially expressed genes (DEGs), indicating plentiful DEGs involved in the expression of regulatory/causal GWAS genes. Protein-protein interaction (PPI) analysis and gene functional analysis for both GWAS genes and DEGs showed a group of interrelated causal genes and a group of interrelated DEGs; the former were included in the latter and their functions were interconnected as a gene network. For further understanding of the response of soybean to shade stress in a sequential connection, six chronological gene modules were grouped as signal activation and transport, signal-transduction, signal amplification, gene expression, regulated metabolites, and material transport. From the modules, 12 key genes were selected as entry points for further analysis. Our study provides an overview of the shade tolerance gene network as a new insight into a complex-trait genetic system, rather than the usual way of starting from a hand-picked single gene.
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