Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2017
Publication Date: 3/10/2017
Citation: Shakiba, E., Edwards, J., Jodari, F., Duke, S.E., Baldo, A.M., Korniliev, P., Mccouch, S.R., Eizenga, G.C. 2017. Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis. PLoS One. doi:10.1371/journalpone.0172133. Interpretive Summary: Cold or cool temperatures are detrimental to rice at germination and at the seedling stage because it causes poor germination and injures the young seedlings which results in poor stand establishment. At the reproductive stage cold or cool temperatures affect the grain development and seed quality which decreases seed yield and acceptability by the consumer. We screened a collection of over 400 diverse rice cultivars from around the world for cold tolerance at germination and identified 83 cultivars which were more cold tolerant than the check cultivar. Using the genotypes of all the rice cultivars we identified 42 chromosomal regions associated with cold tolerance at germination. Eleven of these regions had been previously identified in other studies of cold tolerance. For cold tolerance at the reproductive stage we screened a subset of 186 cultivars from the same collection and identified seven cultivars which were cold tolerant for all the traits evaluated. Two of the seven cultivars also were classified as cold tolerant at germination. Based on the genotypes of these cultivars, 29 regions associated with reproductive cold tolerance were identified and ten of these regions had been previously reported. The next step will be to validate the cold tolerance in the “cold tolerant” cultivars with more detailed evaluations. Once the cold tolerance is confirmed in these cultivars, DNA markers will be developed for the most tolerant cultivars for use by rice breeders in varietal improvement programs to improve cold tolerance at the germination and/or reproductive stage.
Technical 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 trait 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. Fifteen of these QTLs co-localized with 13 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. Nine co-localized with previously reported QTLs for yield components. Candidate gene ontology searches revealed these QTLs were associated with significant enrichment for genes related to 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 at both growth stages. DNA markers linked to these genes or QTL will be used by rice breeders in varietal improvement programs to improve cold tolerance at the germination and/or reproductive stage.