Regulatory Architecture of Cellulose Biosynthesis in Soybean Revealed by Integrated Network Analysis

Cellulose biosynthesis is a fundamental process governing plant cell wall integrity, mechanical strength, and stress response, yet its regulatory architecture remains poorly understood in soybean (Glycine max). Through integrated transcriptomic, regulatory-network, and population-genetic analyses, we dissected the cellulose biosynthesis regulatory network, uncovering a complex regulatory landscape. Expression profiling across diverse soybean accessions revealed heterogeneous expression patterns, with CTL1, KORRIGAN, and some CESA genes showing high expression while others displayed moderate to low expression, suggesting functional specialization within the pathway. Our multi-algorithm Gene Regulatory Network (GRN) analysis identified 1829 transcription factors targeting 126 cellulose synthesis-related genes, with MYB, NAC, and MYB-related TFs emerging as key candidate regulators co-targeting 59 genes. Functional enrichment analysis underscored the central roles of phytohormone signaling and transcriptional activation. Weighted Gene Co-expression Network Analysis (WGCNA) identified a purple module strongly correlated with cellulose content, featuring hub genes Glyma.11G074900, Glyma.05G008302, and Glyma.01G168500. Haplotype analysis revealed the CESA gene family may have been a target of selection during soybean domestication. These findings provide a useful foundation for improving soybean growth through targeted cellulose pathway manipulation.