Genome-Wide Association Mapping for Cold Tolerance of Rice at Germination and Seedling Stages Using the Bengal and Assam Aus Panel

Abstract

Rice (Oryza Sativa L.) is an important cereal crop in many countries. Cold stress is a major abiotic constraint for rice production. Cold tolerance was evaluated using the Bengal and Assam Aus Panel (BAAP) at germination, seedling, and reproductive stages. Cold-tolerant related quantitative trait loci (QTLs) and candidate genes were identified at germination and seedling stages. Low temperature at 13°C for 14 days was selected to screen 194 aus accessions at the germination stage, and 13/8°C was selected to evaluate 160 aus accessions at the seedling stage. After that, cold tolerance was evaluated at reproductive stages at 18±2°C using six accessions. Overall, It was found that cold stress significantly delayed seed germination and reduced germination rates in seeds, reduced plant height, growth rates, dry shoot weight, and decreased chlorophyll fluorescence (Fv/Fm) in rice seedlings. In addition, it leads to spikelet sterility, delayed heading time, and loss of grain mass. ARC14855 accession was identified as cold-tolerant at the reproductive stage, highly cold-sensitive at the seedling stage, and moderately cold-tolerant at the germination stage, in contrast with Kada-68-1, which was cold sensitive at the reproductive stage and cold tolerant at germination and seedling stages. Some accessions displayed consistent cold-response, such as BR 16 and BJ 1 accessions, which consider cold tolerance at germination and seedling stages, while Padma Sail and ARC 10376 showed sensitivity to cold stress at both stages. This variability in responses highlights the complexity of the interaction of physiological processes that change under cold stress for each stage. Genome-wide association mapping was conducted, and a total of 39 and 57 putative QTLs associated with traits at the germination and seedling stages, respectively, were identified. A number of candidate genes for cold tolerance were further explored, including OsBMY10, OsPHD37, and OsANK at the germination stage, while OsFSD3, OsWRKY73, Prefoldin, and OsCPK27 at the seedling stage. By integrating transcriptomic and GWA mapping data, 28 candidate genes were identified, including OsFSD3, and OsPRMT10, which likely regulated cold tolerance at the seedling stage. Overall, this study provides valuable insight into the genetic basis of cold tolerance in different developmental stages of rice, informing molecular breeding strategies to enhance cold tolerance in rice accessions.