Genome-wide association study of cold stress in rice at early young microspore 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 in fertility stage, genome-wide association study (GWAS) was conducted. Cultivated 129 rice germplasm were moved in the growth chamber under the condition of $12^{\circ}C/RH70%$(12h day/12h night when the rice plant was grown in 10 DBH(days before heading). Also, rice plant as control was moved in the green house under condition of $28^{\circ}C/RH70%$(12h day/12h night). After 4 days the plants were moved in a greenhouse. The fertility of rice plant were monitored after the grain were fully grown. The most tolerant rice germplasm to cold stress were Cheongdo-Hwayang-12 and IR38 as 63.1 and 61.8 of fertility and the most recessive rice germplasm were Danyang38 and 8 rice germplasm as 0. As a result of GWAS with re-sequencing data and fertility after cold treatment germplasm using genome association and prediction integrated tool (GAPIT), 99 single-nucleotide polymorphisms (SNPs) were observed by applying a significance threshold of -logP>4.5 determined by QQ plot. With SNPs region, 14 candidate genes responded to cold stress in fertility stage were identified.