QTL Mapping for RVA Profile Characteristics in a Recombinant Inbred Line Population Derived from High-Harvest-Index Yuexiangzhan Rice

Rapid Visco Analyzer (RVA) profile characteristics are important indicators of rice (Oryza sativa L.) eating quality. In this study, based on the high-density genetic linkage map constructed under the genetic background of Yuexianghzan (YXZ) and Shengbasimiao (SBSM), combined with the RVA profile characteristic data of recombinant inbred lines (RILs) grown in two environments, QTL scanning was performed using the ridge regression analysis method. A total of 59 QTLs associated with RVA profile characteristics were detected across 11 chromosomes in the two environments, with individual QTLs explaining 0.12% to 85.16% of the phenotypic variation. Moreover, 11 QTLs were repeatedly detected in two environments with large effects. The QTL located in the 1.44–1.85 Mb interval on chromosome 6 simultaneously controlled eight RVA profile characteristics and contained the cloned waxy (Wx) gene. Additionally, the intervals 20.58–20.70 Mb on chromosome 5 and 24.96–25.42 Mb on chromosome 8 were repeatedly mapped and influenced multiple RVA characteristics. Based on gene annotation information, a total of nine candidate genes (LOC_Os05g34730, LOC_Os05g34830, LOC_Os05g34854, LOC_Os06g03910, LOC_Os06g04200, LOC_Os06g42720, LOC_Os08g39830, LOC_Os08g39850, and LOC_Os08g39860) that directly or indirectly influence the starch synthesis pathway were identified. The results of this study lay a foundation for further map-based cloning of genes related to rice RVA profile characteristics and molecular design breeding.