Genomic Dissection of Anaerobic Germination in Nested Association Mapping Population Using ddRAD Sequencing

Anaerobic germination is a crucial trait for rice cultivation, especially in regions prone to flooding and waterlogging immediately after sowing under direct-seeded conditions. In this study, we used a nested association mapping population of 384 breeding lines to identify genomic regions associated with anaerobic germination. We identified 19 significant marker-trait associations, including 12 for percent seed germination under anaerobic conditions, distributed across six chromosomes (3, 4, 5, 6, 7, and 9). This research provides important insights into the genetic basis of anaerobic germination and highlights the potential of direct-seeded rice (DSR) as a sustainable alternative to traditional puddled transplanting, particularly in flood-prone areas.