Unraveling the environmental regulation of soybean seed protein through WGCNA and multiWGCNA

Soybean is an agronomically important crop due to protein- and oil-rich seeds. Soybeans in Western Canada have lower seed protein content by ∼1%-5% than those from Eastern Canada, as observed over the past two decades. To elucidate the environmental influence on seed protein accumulation, 10 soybean genotypes ranging in seed protein content were planted in four locations (one east, three west) from 2018 to 2021. Multi weighted gene co-expression network analysis (multiWGCNA) identified differentially co-expressed modules with protein × region trait association from two different networks from soybeans grown in 2019 and 2021. Two protein × region modules were assessed by intramodular connectivity, eigengene expression, and functional roles. The results identified differential co-expression of genes with key roles in epigenetic regulation of gene expression, translational modulation, photosynthetic capacity, seed protein storage vacuole filling, and carbon metabolism are environmentally regulated and likely influence seed composition. In this work, WGCNA and multiWGCNA untangled complex expression and trait data, providing valuable information on environmentally influenced genetic mechanisms influencing seed protein content.