Genome-wide association study reveals that enolase gene OsEE1 regulates coleoptile elongation in rice under anaerobic conditions

Submergence can induce anaerobic stress on germinating seedlings in direct seeded rice paddy fields, limiting the practice of direct seeding. Longer coleoptiles improves the anaerobic tolerance of rice seedlings under submerged conditions. In a search for genes that could be beneficial for developing submergence-tolerant varieties 148 non-repetitive SNP loci were detected in on a genome-wide association study (GWAS) of coleoptile length (CL), coleoptile surface area (CSA), coleoptile volume (CV), and coleoptile diameter (CD) of 591 rice accessions subjected to 4 d of anaerobic conditions. Integration of GWAS results and gene expression data identified OsEE1 , an early embryogenesis-specific enolase 1 gene associated with coleoptile length (CL) in rice grown in anaerobic conditions. Disruption of OsEE1 caused reduced CL in plants seeded under anaerobic conditions, whereas CL of OE- OsEE1 overexpression lines was significantly increased compared with the wild type. Functional analysis revealed that OsEE1 affects coleoptile length by modulating the glycolysis and tricarboxylic acid cycle pathways. Transcriptome sequencing of ko-osee1-1 knock out mutants highlighted enrichment in energy and carbohydrate metabolism, glycolysis, amino acid metabolism, and hormone signal transduction. Metabolite analysis indicated decreased levels of key metabolites in the tricarboxylic acid cycle and glycolysis pathways in ko-osee1-1 mutants compared to the wild type under anaerobic conditions. Overall, these findings shed light on the role of OsEE1 in determination coleoptile length of rice seedlings under anaerobic conditions.