The Secrets of Cold Tolerance at the Seedling Stage and Heading in Rice As Revealed By Association Mapping

Cold stress at the seedling stage limits rice (Oryza sativa L.) production in temperate regions or at high elevations in the tropics due to poor plant stand establishment and delayed maturity. At the heading stage, cold temperature causes sterility, thus decreasing grain yield. To explore the mechanism(s) underlying cold tolerance at the seedling stage via genome-wide association studies (GWAS), 420 accessions from the Rice Diversity Panel 1 (RDP1), representing the genetic diversity within the rice subspecies Indica and Japonica and their associated subpopulations, were screened for seedling vigor following a cold treatment and a warm treatment. After germination, the accessions were classified based on their coleoptile elongation as cold tolerant (>5 mm long), intermediate (<5 mm), or no germination. Using the genotypes from a high density rice array comprised of 700,000 SNP markers, GWAS identified 190 SNPs in 41 regions significantly associated with cold tolerance. These regions contained 55 a priori candidate genes, 39 genes were near the identified SNPs and the SNPs were located within 16 genes with five genes across subpopulations, seven in Japonica and four in Indica. Also, four GWAS loci mapped within previously reported QTLs, and seven near two QTLs on chromosomes 1 and 7. Annotation and homologues revealed some of the proteins/enzymes were previously associated with cold tolerance in rice or other species. To evaluate cold tolerance at heading, 235 Japonica accessions were grown in a greenhouse and exposed to nightly cold temperatures of 52^oF starting at panicle initiation and at maturity the percent sterility induced was determined. The results of GWAS at heading are being evaluated.