qAG2.1 Is Associated with Anaerobic Germination Tolerance in Rice Seeds: Evidence from Haplotype Analysis and Marker-Assisted Breeding

Anaerobic germination tolerance (AGT) is a critical adaptive trait for rice establishment in flood-prone environments and direct-seeded systems. Here, we identified and validated the quantitative trait locus qAG2.1 for AGT and introgressed it into the elite lowland rice variety CR Dhan 801 through marker-assisted backcross breeding. The introgressed lines exhibited significantly improved germination under anaerobic conditions, demonstrating the effectiveness of qAG2.1 in a high-yielding genetic background. While CR Dhan 801 showed a low anaerobic germination percentage (17.6%), the donor ARC10424 exhibited 82.6%, and the best-performing introgressed line (22009-3) achieved 49.2%. Importantly, the improved lines maintained agronomic performance comparable to CR Dhan 801 under non-stress conditions, indicating minimal yield penalty. To gain mechanistic insight, the qAG2.1 interval was dissected in silico to prioritise candidate genes putatively associated with AGT. This analysis highlighted genes linked to ethylene biosynthesis and signalling (e.g., OsACO3, OsERF109), abscisic acid biosynthesis (OsNCED1), gibberellin homeostasis (OsGA2ox9), trehalose metabolism (OsTPS5, OsTPP1), detoxification of anaerobic by-products (OsALDH2A), and water transport (OsPIP1;3). Collectively, these results validate qAG2.1 as a further deployable locus for improving anaerobic germination in elite rice backgrounds and provide a set of putative candidate genes for future functional characterisation.