Identification of QTLs for Rice Starch RVA Profile Properties in Different Ecological Sites

Two rice varieties with similar apparent amylose content, Nipponbare (Oryza sativa subsp. japonica) and 93-11 (O. sativa supbsp. indica), were used as parents to establish a recombinant inbred line population consisting of 190 lines by single seed descent method. The genetic linkage map contained 202 simple sequence repeat (SSR), cleaved-amplified polymorphism sequence (CAPS), and sequence tagged site (STS) markers. Quantitative trait loci (QTLs) were identified for 8 rice starch RVA profile properties including peak paste viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), setback viscosity (SBV), consistence viscosity (CSV), peak time (PeT), and pasting temperature (PaT) in 3 ecological sites using composite interval mapping method. A total of 57 QTLs were identified, with 1 to 14 for each trait. Thirteen stable QTLs were detected at repeated environments, among which qCPV-3, qCPV-10b, qSBV-10b, qCSV-3b, and qCSV-10b were detected in all environments, and they explained 26.9%, 29.5%, 29.7%, 25.2%, and 28.3% of phenotypic variations, respectively. Sixteen QTLs had pleiotropy with a single QTL controlling 2–6 RVA profile properties. The interval of RM25032-RM1375 on chromosome 10 harbored gene loci controlling PKV, HPV, CPV, SBV, PaT, and CSV.