Genome-Wide Association Study for Cold Tolerance in Rice Seedlings under Cold-Water Treatment

Rice is a temperature-sensitive crop, its yield is severely affected by low temperature, especially cold stress at the seedling stage will delay heading. To understand the genetic basis of cold tolerance, we evaluated the cold tolerance at the seedling stage of 136 rice accessions. To evaluate cold tolerance, we treated rice seedlings with cold water irrigation for ten days and scored the cold tolerance on a 1-9 scale, based on their low-temperature response and subsequent recovery. The genome-wide association study for cold tolerance revealed seven QTLs on chromosomes 1, 3, 6, 7, 10, and 12. The genomic region of the qCWS7 on chromosome 7 overlapped with a previously reported QTL associated with cold tolerance in the germinating stage. Similarly, qCWS1-1, qCWS1-2, qCWS3, qCWS6, and qCWS10 overlapped with a previously reported QTL associated with drought-stress tolerance. Subsequent bioinformatic and haplotype analyses suggested that five candidate genes affect cold tolerance: Os01g0228600 encoding a cytosolic hydroxypyruvate reductase, Os03g0115000 encoding a cupredoxin domain containing protein, Os06g0612800 encoding a stress-associated protein (SAP) gene family, Os12g0552500 encoding a universal stress protein (USP), and Os10g0482900 encoding a thioredoxin fold domain containing protein.