Characterization of shade tolerance gene network in soybean revealed by forward integrated reverse genetic studies

作者：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 · 发表于：Horticulture Research · 年份：2024 · DOI：10.1093/hr/uhae333 · 被引用次数：5 · 研究领域：Soybean genetics and cultivation、Plant pathogens and resistance mechanisms、Legume Nitrogen Fixing Symbiosis

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...