Stage- and Temperature-Dependent Coleoptile Elongation Under Submergence in Thai indica Rice (Oryza sativa L.)

Direct-seeded rice offers agronomic and economic advantages, but early-season flooding creates hypoxic conditions around germinating seeds and young seedlings, limiting crop establishment. Understanding genotypic variation in early submergence responses is therefore important for improving tolerance during anaerobic germination (AG) and anaerobic seedling development (ASD). This study aimed to characterize submerged coleoptile elongation in Thai rice germplasm and identify genetic factors associated with this response. We screened 192 Thai indica rice accessions with submergence imposed before or after germination to evaluate AG and ASD responses under naturally varying ambient temperatures. Underwater coleoptile length and elongation index showed substantial genotypic variation, while responses under AG and ASD were only weakly correlated (r = 0.29), indicating that tolerance differs between developmental stages. Across trials, coleoptile elongation under submergence was strongly influenced by the environment, with higher ambient temperature associated with reduced elongation and genotype-dependent sensitivity to the ambient temperature–dissolved oxygen (DO) gradient. Controlled-temperature experiments further showed that elevated temperature was associated with lower DO concentrations and reduced underwater coleoptile elongation. Genome-wide association analysis using mixed-model-adjusted phenotypes identified four quantitative trait loci (QTLs) for coleoptile length and three for elongation index under AG, along with one QTL for coleoptile length under ASD. Integrative analysis of a chromosome 12 QTL combining local linkage disequilibrium, public RNA-seq data, and haplotype variation prioritized OsSWEET13, OsNAM, and OsARF24 as candidate genes for coleoptile elongation under submergence. Together, these findings show that developmental stage, temperature, and genetic background shape submerged coleoptile elongation in Thai indica rice.