Molecular Network Analysis of Gene Co-Expression Driving Seed Oil Content in Soybean

Soybean seed composition is governed by an inverse correlation between protein and oil, a relationship complicated by environmental factors. In Canada, western grown soybeans consistently have lower seed protein than eastern grown soybeans, a pattern driven by genotype by environment interactions that modulate the protein–oil balance. To uncover the transcriptional networks behind these differences, a multi-year Weighted Gene Co-Expression Network Analysis (WGCNA) was performed on leaf transcriptomes from ten soybean genotypes cultivated in contrasting eastern and western environments. The analysis identified oil-associated co-expression modules preserved across years and environments; their eigengenes showed significant, consistent correlations with seed oil content each year. A core set of recurring hub genes formed the backbone of this network, many of which co-localize with major seed composition Quantitative Trait Loci. Notably, a key hub lies adjacent to the protein–oil trade-off regulator on chromosome 20, while additional hubs map within a QTL on chromosome 10 linked to a more favorable protein–oil balance. The relationship between module expression and oil content displayed a genotype by environment interaction, providing a molecular basis for phenotypic differences between eastern and western regions. These hub transcription factors are prime candidates for breeding soybean cultivars with improved seed composition.