Study on Rice Submergence Germination Through the Combination of RNA-Seq and Genome Resequencing Strategies

Submergence during germination is a major barrier to the adoption of direct-seeded rice (DSR). Despite its importance in overcoming this barrier, the genetic architecture underlying the rapid coleoptile elongation under submergence remains largely elusive. Through screening among 20 different rice cultivars, a submergence-tolerant cultivar Xian133 and a sensitive cultivar Chang15 were obtained. Comparative transcriptomics and whole-genome resequencing were conducted between these two cultivars. The results show that rapid germination under flooding is driven primarily by transcriptional reprogramming rather than by antagonistic gene regulation. Transcriptome-wide analyses revealed a significant enrichment of the amino sugar and nucleotide sugar metabolism pathway in tolerant cultivar. This was further supported by the fact that promoter variants at the key loci OscPGM and OsAGPL1 modulate the expression of these genes and emerge as principal determinants of coleoptile elongation capacity under hypoxia. The identified single-nucleotide polymorphisms (SNPs) within these regulatory regions provide promising molecular targets for marker-assisted breeding of DSR cultivars.