ABSTRACT
Cold stress adversely affects the growth and development of plants and limits the geographical distribution of crop plants. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. Genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with that of the single nucleotide polymorphic (SNP) loci across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate genes for cold tolerance. Investigation of at least two independent mutants for 29 of these genes identified 16 cold tolerance genes controlling diverse genetic mechanisms. This study identified five genes encoding novel leucine-rich repeat domain-containing proteins, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified cold tolerance genes, ADS2 and ACD6 are the only two cold tolerance genes identified earlier. The comparatively little overlap between the genes identified in this genome-wide association study of natural variants with those discovered previously through forward and reverse genetic approaches suggests that cold tolerance is a complex physiological process governed by a large number of genetic mechanisms.
Short Summary Cold stress adversely affects the growth and development of plants and limits the geographical distribution of crop plants. Genome-wide association study of the phenotypic variation of Arabidopsis natural variants with that of the single nucleotide polymorphic loci followed by T-DNA insertion mutant analyses of 29 candidate genes led to assigning cold tolerance function for the first time to 14 genes including three nucleotide-binding sites leucine repeat region (NB-LRR) protein genes. The comparatively little overlap between the genes identified in this study with those discovered previously suggests that cold tolerance is governed by a complex network of multiple genetic mechanisms.
