Identification of hub genes involved in GA-regulated coleoptile elongation under submerged germinations in rice.

Submergence stress hinders the direct seeding in rice cultivation. Rapid elongation of rice seed coleoptiles to reach the water surface enables rice to survive submergence stress. Gibberellin (GA) positively influences rice growth. However, the molecular mechanisms underlying GA-regulated coleoptile elongation under submergence conditions remain unclear. Here, we performed a WGCNA analysis to preliminarily investigate the mechanisms. Our results identify four key modules with a high correlation to the GA regulation of rice submergence tolerance. The genes within these modules are mainly involved in Golgi apparatus and carbohydrate metabolic pathways, suggesting involvement of these biological processes in enhancing rice submergence tolerance. Moreover, natural variation analysis reveals that the hub genes, specifically, Os03g0337900, Os03g0355600, and Os07g0638400, exhibited a strong correlation with the subspecies divergence of the coleoptile elongation phenotype. Mutation of Os07g0638400 results in a lower germination potential and a stronger inhibition of coleoptile elongation under submergence conditions in rice, indicating the reliability of the analyses. The hub genes identified in this study provide deep insights into understanding the molecular mechanisms underlying GA-dependent submergence stress tolerance in rice and provide a theoretical basis for innovating rice germplasm for direct seeding application.