Effect and identification of different allele combinations of SSIIa and Wx on rice eating and cooking quality

Rice eating and cooking quality (ECQ) is one of the most important qualities and it has attracted more and more interests of consumers and breeders. SSIIa and Wx are the major genes affecting rice ECQ, and several alleles of SSIIa and Wx have been identified. In this study, the effects of different allele combinations of SSIIa and Wx on rice ECQ were explored by analyzing amylose content (AC), gelatinization temperature (GT), and Rapid Viscosity Analyzer (RVA) profile properties of one natural population which is composed of 30 glutinous rice varieties and 342 non-glutinous varieties. Nine allele combinations of SSIIa and Wx were identified in all the non-glutinous varieties. The allele combination of SSIIa^c/Wx^b harbored higher BDV, lower SBV, intermediate AC, and higher GT, which means better taste quality but more cooking time. For non-glutinous rice, stepwise regression analysis showed that RVA profile properties are mainly controlled by polymorphic loci of Wx-Int1(G/T) and Wx-EX10(C/T); AC, PV, BDV, and SBV are mainly controlled by Wx-Int1(G/T); HPV, CPV, and CSV are mainly controlled by Wx-EX10(C/T); GT is mainly controlled by SSIIa-EX8(GC/TT). Regression equation models also confirmed that SSIIa^c/Wx^b had better ECQ compared to other allele combinations, indicating its potential to improve rice quality. Our results may provide useful clues for elite alleles of SSIIa and Wx for introgression to other rice varieties to improve rice ECQ.