Association Between Allelic Variations in Starch Synthesis-Related Genes (SSRGs) and Grain Quality Traits of Rice Under High Temperature

Rising temperature by global warming is degenerating grain yield and quality of rice. In this study, we investigated the influence of 10 previously reported SSRG markers on the variations in grain quality traits of 187 nonglutinous Korean rice varieties under ambient and two greenhouse conditions. As temperature rose, average ripened grains percentage (RGP), head rice percentage (HRP), and amylose content (AC) decreased significantly, while average chalky grains percentage (CGP) and breakdown viscosity (BDV) increased significantly. Among 10 SSRG markers analyzed, six showed relatively high association (R²>0.1) with the variations in one or more grain quality traits in the three different environments, i.e., AGPase-L InDel (PKV, SBV, BDV), AGPase-S A/T SNP (SBV, BDV), SSIIa TT/GC SNPs (ADV), SBEI InDel (SBV, BDV), SBEIII C/G SNP (PKV, SBV, BDV), and SDBE InDel (PKV, SBV, BDV). With the changes in grain quality traits by high temperature, six markers showed significant associations, i.e., AGPase-L InDel (ΔHRP, ΔCGP, ΔBDV), AGPase-S C/T SNP (ΔHRP, ΔCGP, ΔAC), AGPase-S A/T SNP (ΔHRP, ΔCGP), SBEI InDel (ΔHRP, ΔCGP, ΔBDV), SBEIII C/G SNP (ΔHRP, ΔCGP, ΔBDV), and SDBE InDel (ΔHRP, ΔCGP). However, when the analysis was conducted after separating the two major subpopulations (japonica and Tongil), significant association was not observed in most markers or R² decreased to a large extent.