Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

Shade tolerance is essential for soybeans in inter/relay cropping systems. A genome-wide association study (GWAS) integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance. An improved GWAS procedure, restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers (GASM-RTM-GWAS), identified 140 genes and their alleles associated with shade-tolerance index (STI), 146 with relative pith cell length (RCL), and nine with both. Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes, of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages. From the identified genes, three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network. Altogether, both STI and RCL gene systems worked for shade-tolerance with genes interacted each other, this confirmed that shade-tolerance is regulated by more than single group of interacted genes, involving multiple biological functions as a gene network.