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Title: Using GWAS to identify SNPs associated with rice seedling cold tolerance

item SHAKIBA, EHSAN - University Of Arkansas
item HANCOCK, TERESA - University Of Arkansas
item Jackson, Aaron
item Duke, Sara
item KORNILIEV, PAVEL - Cornell University
item McClung, Anna
item MEZEY, JASON - Cornell University
item MCCOUCH, SUSAN - Cornell University
item Eizenga, Georgia

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/2/2014
Publication Date: 12/15/2014
Citation: Shakiba, E., Hancock, T.A., Jackson, A.K., Duke, S.E., Korniliev, P., McClung, A.M., Mezey, J.G., McCouch, S.R., Eizenga, G.C. 2014. Using GWAS to identify SNPs associated with rice seedling cold tolerance. Proc. 35th Rice Tech. Work. Group Meet., New Orleans, LA, pp. 55-56. Feb. 18-21, 2014. CDROM.

Interpretive Summary:

Technical Abstract: Cold tolerance at the seedling stage is important for stand establishment when rice (Oryza sativa L.) is planted in cold water or under the cool temperatures that occur early in the growing season in temperate regions or at high elevations in the tropics. The Rice Diversity Panel 1 (RDP1) represents the five major subpopulations of rice including aus and indica representing the Indica subspecies, and aromatic (Group V), tropical japonica and temperate japonica representing the Japonica subspecies. The objectives of this study were to 1) screen the RDP1 for seedling cold tolerance using the “ragdoll” method, 2) measure the coleoptile elongation of the Japonica RDP1 accessions under cold stress, and 3) conduct genome-wide association studies (GWAS) to identify SNP (single nucleotide polymorphism) markers associated with seedling cold tolerance. Screening of the accessions grown in warm and cool temperatures with the ragdoll method in a RCBD revealed only 17.7% of the Indica accessions were highly cold tolerant, having coleoptile lengths greater than 5 mm, whereas 51.5% of the Japonica accessions, excluding the aromatic (Group V) accessions, were highly tolerant. GWA analysis was conducted using TASSEL software with SNP genotypes based on 36,901 high quality SNP revealed marker-trait associations on chr. (chromosome) 1S (short arm) and 2S. In Indica, marker-trait associations were found on chr. 2S, 8S, 9S and 12S and in Japonica, excluding aromatic (Group V) on chr. 1L (long arm), 2L, 4L and 12S. Many of these associations were located in the region of previously reported QTLs for cold tolerance. To further dissect the cold tolerance in the Japonica accessions which exhibited more tolerance overall, 235 accessions were germinated in germination paper placed in test tubes following an RCBD under both warm and cool temperatures. When the incubation time was complete, a digital image was taken of the germinated seed by accession. The coleoptile length of each seed was measured digitally using ImageJ. The mean coleoptile length for each accession in the cold treatment was adjusted for germination using the signal to noise ratio. GWA mapping revealed marker-trait associations on chr. 1L and 2S. Additional GWAS will be conducted using the 700,000 SNP genotypes generated from the high density rice array to confirm these associations.