Divergent genetic architecture of cold stress tolerance in Aus and Tropical Japonica rice

Georgia C Eizenga^1*Yami Santamaria²Aaron Jackson¹Huy Phan²Melissa H. Jia¹Quynh P.-H. Grunden¹Jeremy D Edwards¹Ed Himelblau²Michael R. Schlappi^2*

• ¹Dale Bumpers National Rice Research Center, Agricultural Research Service (USDA), Stuttgart, United States
• ²Marquette University, Milwaukee, United States

Exploring natural genetic variation to facilitate breeding of improved rice seedling cold tolerance will allow the crop to be planted earlier in the growing season, thus taking advantage of spring rainfall and decreasing exposure to high summer nighttime temperatures which decrease grain quality. To uncover genomic regions in rice managing cold stress tolerance response mechanisms in the cold sensitive aus (AUS) and the relatively cold tolerant tropical japonica (TRJ) subpopulations and to identify cold tolerance genes, AUS and TRJ recombinant inbred line populations developed from crosses between cold tolerant and cold sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after one week of cold exposure quantified as percent electrolyte leakage (EL), and percent low-temperature seedling survivability (LTSS) after one week of recovery growth. This revealed 13 subpopulation-specific QTL: three EL and four LTSS QTL for AUS, and two EL and four LTSS QTL for TRJ, with no overlap between AUS and TRJ QTL. Only two AUS QTL overlapped with QTL regions previously uncovered by our AUS x temperate japonica biparental mapping approaches, further indicating that subpopulation-specific QTL were uncovered. Based on high impact genomic differences between the cold tolerant and cold sensitive parents, 35 cold tolerance candidate genes were identified, 23 in AUS and 12 in TRJ, of which about 50% code for proteins involved in signal transduction and protein homeostasis processes. Although for most QTL, alleles from the cold tolerant parents improved the two cold tolerance traits, alleles from the cold sensitive parents enhanced the traits at several other QTL. Therefore, alleles from both the cold tolerant and cold sensitive parents can be used in breeding efforts to generate AUS and TRJ lines with better cold tolerance potentials than their respective cold tolerant parents.