Divergent genetic architecture of cold stress tolerance in aus and tropical japonica rice

Thirteen subpopulation-specfic QTL were revealed: 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 regions previously identified by our AUS × <i>temperate japonica</i> biparental mapping, further confirming the discovery of subpopulation-specific QTL. 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% encode proteins involved in signal transduction and protein homeostasis processes. Although most QTL showed that alleles from cold-tolerant parents improved the two cold tolerance traits, alleles from cold-sensitive parents enhanced these traits at several other QTL. Therefore, alleles from both cold-tolerant and cold-sensitive parents can be used in breeding efforts to generate AUS and TRJ lines with better cold tolerance potential than their respective cold-tolerant parents.