GWAS and haplotype analysis reveal the intricate interplay of hormones in rice seed germination under hypoxic conditions.

Genome-wide association mapping of the BAAP panel revealed 14 QTLs significantly associated with anaerobic germination tolerance (AGT), distributed across eight chromosomes. Among these, chromosome 11 emerged as a key region, harbouring two prominent QTL hotspots qAG11.1 and qAG11.2 indicating its major contribution to AGT in direct-seeded rice under flooded conditions. Candidate gene analysis revealed strong associations with key regulators of hormonal and metabolic pathways. Notably, ethylene biosynthesis and signalling genes-OsACO (LOC_Os09g39720, LOC_Os06g37590), CTR1 (LOC_Os09g39320), and ERS1 (LOC_Os03g49500) were linked to enhanced coleoptile elongation under hypoxia. EMF2B (LOC_Os09g13630), involved in ABA-mediated dormancy regulation, and KO1 (LOC_Os06g37330), a critical enzyme in GA biosynthesis, contributed to early seedling vigour. SLR1 (LOC_Os03g49990), a GA signalling repressor, was functionally linked to growth regulation under anaerobic stress. Carbohydrate mobilization genes β-amylase (LOC_Os09g39570) and TPP6 (LOC_Os08g31630) were also strongly associated with AGT performance. Haplotype analysis identified favourable alleles across multiple loci, with genotypes such as ARC 14940 and Boro Black combining superior haplotypes and exhibiting higher germination rates and shoot elongation. These findings provide a robust genetic framework and valuable markers for accelerating AGT breeding in rice through haplotype-based selection.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04422-2.