Su Yanzhu, Pan Yongpeng, Zeng Weiying, Lai Zhenguang, Guo Pengfei, Hao Xiaoshuai, Gu Shengyu, Zhang Zhipeng, Sun Lei, Li Ning, He Jianbo, Wang Wubin, Xing Guangnan, Zhang Jiaoping, Sun Zudong, Gai Junyi
Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & State Key Laboratory for Crop Genetics and Germplasm Enhancement & State Innovation Platform for Integrated Production and Education in Soybean Bio-breeding & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
Institute of Economic Crops, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China.
Hortic Res. 2024 Nov 26;12(3):uhae333. doi: 10.1093/hr/uhae333. eCollection 2025 Mar.
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.
耐荫性是玉米田套种/间作大豆品种的关键性状。我们之前对中国南方大豆种质进行的全基因组关联研究（GWAS）结果表明，耐荫性由具有多个等位基因的基因复合体赋予。为了全面了解耐荫性基因系统，我们以基因等位序列为标记进行了GWAS（命名为GASM-RTM-GWAS），该研究在两个极端亲本的重组自交系（RIL）群体中进行，以耐荫性指数（STI）和相对髓细胞长度（RCL）作为指标。总共鉴定出211个基因，其中STI相关基因99个，RCL相关基因119个（有7个共享基因），然后将这些基因注释到相似的五个生物学类别中。此外，转录组分析检测到7837个差异表达基因（DEG），表明有大量DEG参与调控/因果GWAS基因的表达。对GWAS基因和DEG进行蛋白质-蛋白质相互作用（PPI）分析和基因功能分析，结果显示有一组相互关联的因果基因和一组相互关联的DEG；前者包含在后者之中，它们的功能作为一个基因网络相互连接。为了进一步了解大豆对荫蔽胁迫的顺序响应，将六个按时间顺序排列的基因模块分为信号激活与转运、信号转导、信号放大、基因表达、调控代谢物和物质转运。从这些模块中，选择了12个关键基因作为进一步分析的切入点。我们的研究提供了耐荫性基因网络的概述，这是对复杂性状遗传系统的新见解, 而不是通常从挑选单个基因开始的方式。
