Abstract 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.

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