title: New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis.
abstract: In order to understand cold adaptability and explore additional genetic resources for the cold tolerance improvement of rice, we investigated the genetic variation of 529 rice accessions under natural chilling and cold shock stress conditions at the seedling stage using genome-wide association studies; a total of 132 loci were identified. Among them, 12 loci were common for both chilling and cold shock tolerance, suggesting that rice has a distinct and overlapping genetic response and adaptation to the two stresses. Haplotype analysis of a known gene OsMYB2, which is involved in cold tolerance, revealed indica-japonica differentiation and latitude tendency for the haplotypes of this gene. By checking the subpopulation and geographical distribution of accessions with tolerance or sensitivity under these two stress conditions, we found that the chilling tolerance group, which mainly consisted of japonica accessions, has a wider latitudinal distribution than the chilling sensitivity group. We conclude that the genetic basis of natural chilling stress tolerance in rice is distinct from that of cold shock stress frequently used for low-temperature treatment in the laboratory and the cold adaptability of rice is associated with the subpopulation and latitudinal distribution.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Lv
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Zilong
authors.initials: Z
authors.lastname: Guo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Xiaokai
authors.initials: X
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Ye
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Xianghua
authors.initials: X
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.|National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
authors.forename: Lizhong
authors.initials: L
authors.lastname: Xiong
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000531:Altitude; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D003080:Cold Temperature; D060146:Ecotype; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D005843:Geography; D006239:Haplotypes / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D040641:Quantitative Trait Loci / Q000235:genetics; D019655:Quantitative Trait, Heritable; D036226:Seedlings / Q000502:physiology
keywords: GWAS; chilling tolerance; cold shock tolerance; geographical distribution; rice; subpopulation distribution