Genome-Wide Association Study of Cold Stress in Rice Seedling Stage (Oryza sativa L.)

Cold stress is one of the most influenced factors to rice yield. In order to identify genes related to cold stress, genome-wide association study (GWAS) was implemented. Seedlings of 137 rice germplasms were cultivated 2 week in green house. We transferred to chamber was set up to 12℃ of temperature and 70% of relative humidity and treated one week. We scored treated rice seedlings 2days after transferring to greenhouse. Rice seedlings were scored 0 to 10 through the comparison between control and treatment. The normal rice seedlings were scored 0 and the withered rice seedlings were scored 10. Score of these rice germplasm were normally distributed. Oc-chung and Dongoh were the most tolerant to chilling stress but Dharial and Mala were the most sensitive. As a result of GWAS with re-sequencing data of rice germplasms and phenotype data, 187single-nucleotide polymorphism (SNP) markers were observed under stress condition by applying a significance threshold of -logP>6. The related gene to cold stress is on the chromosome 5 and 8.