Genome-wide association study for traits related to cold tolerance and recovery during seedling stage in rice

Abstract

Rice (Oryza sativa L.), due to its tropical and subtropical origin, is adversely affected by low temperatures below 15°C, restricting growth and yield. During the seedling and vegetative stage, cold stress causes curled leaves, fewer tillers, retarded growth, chlorosis, and necrosis. Due to the significance of this trait, exploring the wealth of genetic resources from a wider pool of germplasm to identify new sources of tolerance will be a crucial step. Toward this goal, we performed a genome-wide association study (GWAS) on a novel diversity panel of 238 rice accessions using the 7K SNP Cornell-IR LD Rice (C7AIR) single nucleotide polymorphism (SNP) array. The experiment was conducted in controlled growth conditions, and rice accessions were evaluated for seven traits and four indices, which were recorded at three different time points, that is, before cold treatment, after cold treatment, and post-recovery phase. A total of 77 significant GWAS-quantitative trait loci (QTLs) were identified for 21 cold tolerance and related traits of interest. Out of these, 34 were detected after cold stress, and 43 were detected during the post-recovery phase. A total of 42 QTL regions were significant at false discovery rate (FDR) < 0.001 and −log₁₀(p-values) > 5. In addition, 31 novel GWAS-QTLs, three colocalized GWAS-QTL hotspots, and eight colocalized GWAS-QTLs for two traits sharing the same genomic location were also identified. The results of this study may help in further elucidating the molecular mechanisms underlying cold tolerance as well as aid in developing climate-smart rice varieties for chilling stress conditions.