Combining a Genome-Wide Association Study and Gene-Based Haplotype Analysis to Identify Candidate Genes for Cold Tolerance at the Bud Burst Stage in Rice (Oryza sativa L.)

Abstract

As a temperature-loving crop, rice is sensitive to low temperatures. With the popularization of direct-seeded rice, cold tolerance (CT) at the bud burst stage has become an important breeding goal. Here, we evaluated CT for 513 rice accessions at the bud burst stage. A total of 13 QTLs were detected by genome-wide association analysis using the severity of damage (SD) and survival rate of seedlings (SR) as indicators of CT. Based on analyses of LD blocks, GO enrichment, gene expression and haplotype, we identified five genes, LOC_Os01g35184, LOC_Os01g56150, LOC_Os01g73410, LOC_Os02g36740, and LOC_Os09g28180, as the most likely candidates for qSD1-1, qSD1-4, qSD1-5, qSD2-1, and qSR9-1, respectively, for CT. The accumulative effects of favorable haplotypes for the above five most likely candidate genes played an important role in the improvement of the CT of rice cultivars. Hence, this study has furnished valuable insights for advancing gene cloning and pyramiding breeding, aiming to enhance cold tolerance during the bud burst stage in rice.