Skip to main content
ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #325052

Title: Dissecting cold tolerance in rice as revealed by association mapping

item SHAKIBA, EHSAN - University Of Arkansas
item JODARI, FARMAN - California Cooperative Rice Research Foundation
item Edwards, Jeremy
item Baldo, Angela
item Duke, Sara
item KORNILIEV, PAVEL - Cornell University
item MCCOUCH, SUSAN - Cornell University
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 2/1/2016
Publication Date: 7/2/2017
Citation: Shakiba, E., Jodari, F., Edwards, J., Baldo, A.M., Duke, S.E., Korniliev, P., McCouch, S.R., Eizenga, G.C. 2017. Dissecting cold tolerance in rice as revealed by association mapping. Proc. 36th Rice Technical Working Group Meeting Proceedings. pp. 64-65. 1-4 March 2016. CDROM.

Interpretive Summary:

Technical Abstract: Cold stress 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. Identification of genetic sources of tolerance to cold stress in rice could have a positive impact on production of rice in regions where temperature limits rice yield. A collection of genotypically and geographically diverse rice accessions known as the Rice Diversity Panel 1 (RDP1) was screened to identify the genetic sources of cold tolerance at the seedling and reproductive stages. For the seedling stage, the experiment was arranged in a randomized complete block design (RCBD) with three cold replications and two warm replications. After treatment, the accessions were categorized based on coleoptile length into three groups, high tolerance (coleoptile length >5 mm long), intermediate tolerance (coleoptile length <5 mm long) or no germination. This screening revealed only 17.7% of the Indica accessions were highly cold tolerant, whereas 51.5% of the Japonica accessions were tolerant. For the reproductive stage, 191 Japonica accessions were grown in a greenhouse, modified to test for cold tolerance. The plants were arranged in a RCBD with two replications and several agronomic traits were measured after cold treatment including category of seed blanking (no seed produced), seed weight and seed weight per panicle. A Genome Wide Association Study (GWAS) was conducted to identify the genetic variation associated with cold stress. The RDP1 accessions were categorized in five groups, temperate japonica, tropical japonica, Japonica (both temperate and tropical japonica subpopulations), Indica (both indica and aus subpopulations), and the complete RDP1. The RDP1 was genotyped using a high density rice array (HDRA) which contained 700,000 single nucleotide polymorphism (SNP) markers. These genotypes were used in a GWAS pipeline, composed of Python (v2.6-2.7) and R (v2.15) scripts for conducting the linear mixed model analysis using the EMMA eXpedited (EMMAX) algorithm. Candidate gene discovery was conducted using the UCSC Genome Browser and the MSU7 annotation of the Nipponbare genome. Haplotype blocks were constructed for each of the five subpopulations across the genome to help evaluate candidate genes proximal to the GWAS hits. The GWAS results revealed 28 regions including four in temperate japonica, five in tropical japonica, five in Japonica, five in Indica and nine in all RDP1, associated with cold tolerance at the seedling stage. Several of these regions co-localized with previously reported QTLs associated with seedling cold tolerance. The GWA analysis at the reproductive stage detected nine regions including four associated with seed weight, two with the seed weight per panicle ratio, and three associated with blanking (no seed produced). Of the nine regions identified by GWA mapping at the reproductive stage, six were co-localized with previously reported QTLs for yield components. In summary, GWAS proved to be a powerful tool for exploring the genetic variation that underlies cold tolerance and GWAS can be used for complex quantitative traits like cold tolerance. These results also provide information that plant breeders can utilize in developing a new generation of cold tolerant rice cultivars.