The Transcriptome Landscape of Multiple Tissues in Soybean Under Shade

ABSTRACT Dense planting represents a significant strategy for enhancing soybean yield. However, the shade avoidance response elicited by such planting density may hinder further yield enhancements. To acquire a comprehensive understanding of the spatiotemporal responses of soybean to shading signals, we segmented the shading treatment into three distinct periods and performed transcriptomic analyses on soybean apical tissues, the first internode, hypocotyl, petiole, and leaves during these intervals. Enrichment analysis indicated that hormone signalling networks are substantially modulated by shading signals, predominantly involving hormones such as auxins, gibberellins, and brassinosteroids. Through weighted correlation network analysis and motif enrichment analyses, we identified several gene groups and transcription factors that may be implicated in the shade avoidance response in soybeans. Furthermore, utilizing a transient gene expression system, we validated the functions of key genes, discovering that GmGA20ox , GmUGT73C2 , and GmWRKY75c are involved in the regulation of soybean hormone homoeostasis, thereby reinforcing the validity of our analytical findings. This study delineates a transcriptomic framework of soybean responses to shade avoidance, highlighting clusters of essential regulatory genes that govern hormone homoeostasis and plant architecture. The findings provide critical insights for breeding strategies pertinent to dense planting and intercropping systems.