Time-Course Transcriptome, Metabolome, and Weighted Gene Co-Expression Network Analysis Reveal the Roles of the OsBELH4A Gene in Regulating Leaf Senescence and Grain Yield of Rice

Rice (<i>Oryza sativa</i> L.) is one of the major food crops. Yield and quality are affected by premature leaf senescence, a complex and tightly regulated developmental process. To elucidate the molecular regulatory mechanism controlling rice leaf senescence, the integrative transcriptome, metabolome and weighted gene co-expression network analysis (WGCNA) of flag leaves in five development stages (FL1-FL5) was performed. In this study, a total of 9412 differential expressed genes (DEGs) were identified. To further mine DEGs related to leaf senescence, a total of five stage-specific modules were characterized by WGCNA. Among them, two modules displayed continuous down-regulated and up-regulated trends from stages FL1 to FL5, which were considered to be highly negatively and positively correlated with the senescence trait, respectively. GO enrichment results showed that the genes clustered in stage-specific modules were significantly enriched in a vast number of senescence-associated biological processes. Furthermore, large numbers of senescence-related genes were identified, mainly participating in transcription regulation, hormone pathways, degradation of chlorophyll, ROS metabolism, senescence-associated genes (SAGs), and others. Most importantly, a total of 40 hub genes associated with leaf senescence were identified. In addition, the metabolome analysis showed that a total of 309 differential metabolites (DMs) were identified by WGCNA. The integrative transcriptome and metabolome analysis identified a key hub gene <i>OsBELH4A</i> based on the correlation analysis conducted between 40 hub genes and 309 DMs. The results of function validation showed that <i>OsBELH4A</i> overexpression lines displayed delayed leaf senescence, and significantly increased grain number per plant and grain number per panicle. By contrast, its knockout lines displayed premature leaf senescence and reduced grain yield. Exogenous hormone treatment showed that <i>OsBELH4A</i> significantly responded to SA and auxin. These findings provide novel insights into leaf senescence, and further contribute to providing genetic resources for the breeding of crops resistant to premature senescence.