Genetic Architecture of Cold Tolerance in Rice at the Seedling Stage and Heading Determined through Genome-Wide Association Studies.

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. Initially, the Rice Diversity Panel 1 (RDP1) composed of 421 accessions, representing both the Indica and Japonica subspecies, was screened for cold tolerance at the seedling stage. The accessions were arranged in a randomized complete block design (RCBD) with three cold and two warm replications. After the cold treatment (30 days) or warm treatment (7 days) the accessions were classified based on their coleoptile length into cold tolerance (>5 mm long), intermediate (<5 mm long), or no germination. Overall, screening of the RDP1 accessions revealed only 17.7% of the Indica accessions were highly cold tolerant, whereas 51.5% of the Japonica accessions, excluding the 16 aromatic accessions, were tolerant. Subsequently, a genome-wide association study (GWAS), using the genotypes from a high density rice array (HDRA) composed of 700,000 SNPs (single nucleotide polymorphisms), identified GWA peaks co-located with 15 apriori candidate genes on 7 of the 12 rice chromosomes. Eight of these genes were significant when all accessions were analyzed together, five within Japonica accessions only, and two within Indica accessions only. Moreover, four genes were co-located with previously reported QTLs associated with cold tolerance. Recently, the 235 Japonica accessions were evaluated for cold tolerance at the heading stage and a similar GWAS is being conducted using data collected on the percent sterility induced by cold treatment. Also, a bi-parental study is underway to validate the GWAS at the seedling stage.