Genetic Dissection of Anaerobic Germination in aus Rice

This study presents a comprehensive genetic dissection of anaerobic germination (AG) potential in a panel of 185 aus rice (Oryza sativa L.) accessions using high-resolution phenotyping and genome-wide association study (GWAS). Accessions were evaluated under contrasting environments—anaerobic tray, field tank, and aerobic conditions—to assess germination efficiency, coleoptile elongation, and seedling vigour traits. Multi-environment phenotypic data revealed substantial genotypic variation and genotype × environment interactions. GWAS identified 84 QTLs associated with AG-related traits (GRP, AGI, MGR, LtD7), several of which overlapped known genes like OsTPP7, SnRK1A, and OsETOL1. Haplotype analysis of key candidate genes, including OsTPP7 and OsEE1, revealed superior allelic variants linked to enhanced germination and coleoptile elongation under anaerobic stress. This study provides novel QTLs, functional haplotypes, and promising donor genotypes for the development of climate-resilient, direct-seeded rice cultivars.