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Characterization of shade-tolerance gene network in soybean revealed by forward integrated reverse genetic studies
Horticulture Research ( IF 7.6 ) Pub Date : 2024-11-26 , DOI: 10.1093/hr/uhae333 Yanzhu Su, Yongpeng Pan, Weiying Zeng, Zhenguang Lai, Pengfei Guo, Xiaoshuai Hao, Shengyu Gu, Zhipeng Zhang, Lei Sun, Ning Li, Jianbo He, Wubin Wang, Guangnan Xing, Jiaoping Zhang, Zudong Sun, Junyi Gai
Horticulture Research ( IF 7.6 ) Pub Date : 2024-11-26 , DOI: 10.1093/hr/uhae333 Yanzhu Su, Yongpeng Pan, Weiying Zeng, Zhenguang Lai, Pengfei Guo, Xiaoshuai Hao, Shengyu Gu, Zhipeng Zhang, Lei Sun, Ning Li, Jianbo He, Wubin Wang, Guangnan Xing, Jiaoping Zhang, Zudong Sun, Junyi Gai
Shade-tolerance is a key trait for cultivars in inter/relay-cropped soybeans in maize field. 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 on shade-tolerance gene system, the GWAS with gene-allele sequences as markers (designated GASM-RTM-GWAS) was conducted in a recombinant inbred lines (RILs) population between two extreme parents using shade-tolerance index (STI) and relative pith-cell length (RCL) as indicators. Altogether, 211 genes, including 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 7,837 differentially expressed genes (DEGs), indicating plentiful DEGs involved in the expression of regulatory/causal GWAS-genes. The 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 with that of the former including in the latter and their functions 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 characterizes with overview of shade tolerance gene network as a new insight into the complex trait genetic system, rather than the usual way starting from a handpicked single gene.
更新日期：2024-11-26
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