title: Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis.
abstract: Cold temperature is an important abiotic stress which negatively affects morphological development and seed production in rice (Oryza sativa L.). At the seedling stage, cold stress causes poor germination, seedling injury and poor stand establishment; and at the reproductive stage cold decreases seed yield. The Rice Diversity Panel 1 (RDP1) is a global collection of over 400 O. sativa accessions representing the five major subpopulations from the INDICA and JAPONICA varietal groups, with a genotypic dataset consisting of 700,000 SNP markers. The objectives of this study were to evaluate the RDP1 accessions for the complex, quantitatively inherited cold tolerance traits at the germination and reproductive stages, and to conduct genome-wide association (GWA) mapping to identify SNPs and candidate genes associated with cold stress at these stages. GWA mapping of the germination index (calculated as percent germination in cold divided by warm treatment) revealed 42 quantitative trait loci (QTLs) associated with cold tolerance at the seedling stage, including 18 in the panel as a whole, seven in temperate japonica, six in tropical japonica, 14 in JAPONICA, and nine in INDICA, with five shared across all subpopulations. Twenty-two of these QTLs co-localized with 32 previously reported cold tolerance QTLs. GWA mapping of cold tolerance at the reproductive stage detected 29 QTLs, including seven associated with percent sterility, ten with seed weight per panicle, 14 with seed weight per plant and one region overlapping for two traits. Fifteen co-localized with previously reported QTLs for cold tolerance or yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to with lipid metabolism, response to stimuli, response to biotic stimuli (suggesting cross-talk between biotic and abiotic stresses), and oxygen binding. Overall the JAPONICA accessions were more tolerant to cold stress than INDICA accessions.
authors.affiliation: University of Arkansas, Rice Research and Extension Center, Stuttgart, Arkansas, United States of America.
authors.forename: Ehsan
authors.initials: E
authors.lastname: Shakiba
authors.affiliation: USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America.
authors.forename: Jeremy D
authors.initials: JD
authors.lastname: Edwards
authors.affiliation: Rice Experiment Station (RES), Biggs, California, United States of America.
authors.forename: Farman
authors.initials: F
authors.lastname: Jodari
authors.affiliation: USDA/ARS Plains Area, College Station, Texas, United States of America.
authors.forename: Sara E
authors.initials: SE
authors.lastname: Duke
authors.affiliation: USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America.
authors.forename: Angela M
authors.initials: AM
authors.lastname: Baldo
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Pavel
authors.initials: P
authors.lastname: Korniliev
authors.affiliation: School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, United States of America.
authors.forename: Susan R
authors.initials: SR
authors.lastname: McCouch
authors.affiliation: USDA/ARS Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America.
authors.forename: Georgia C
authors.initials: GC
authors.lastname: Eizenga
mesh_terms: D000704:Analysis of Variance; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000737:chemistry / Q000378:metabolism; D003080:Cold Temperature; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D018525:Germination / Q000235:genetics; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D036226:Seedlings / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics