Objective Grain size is one of the main agronomic traits affecting rice yield. A recombinant inbred line population derived from indica rice variety V20B and slender javanica rice variety CPSLO17 was used for QTL mapping of brown rice grain size. It aims to explore the genetically-stable main effect QTLs, providing new genetic resources and scientific basis for developing high-quality and high-yield rice varieties.

Method Based on the high-density genetic linkage map of V20B/CPSLO17 genetic background, the brown rice grain size phenotype data of 150 recombinant inbred lines under four environments (Guiyang, Guizhou in 2019, Guiyang, Guizhou in 2020, Guiding, Guizhou in 2021, and Sanya, Hainan in 2021) were used for QTL scanning by the ICIM-ADD method of IciMapping 4.0 software.

Result The grain size of brown rice from parent V20B was significantly larger than that from CPSLO17, and the grain sizes of brown rice from recombinant inbred lines showed significant differences among the four environments, all exhibiting a continuous unimodal distribution. A total of 11 QTLs related to brown rice grain size distributed on 7 chromosomes were found in the four environments, with their LOD values ranging from 3.00 to 14.57. Four QTLs including qRGS5, qRGS7.1, qRGS7.2, and qRGS11.3 had a phenotypic variance explained (PVE) over 10%, of which the qRGS5 was repeatedly detected in all four environments, with its PVE of 29.71%, 28.77%, 17.27% and 12.50%, respectively. The synergistic alleles of three QTLs (qRGS2.1, qRGS2.2 and qRGS12) derived from the parent CPSLO17, while the other eight synergistic alleles (qRGS4.1, qRGS5, qRGS7.1, qRGS7.2, qRGS8, qRGS11.1, qRGS11.2 and qRGS11.3) derived from the parent V20B, and the synergistic alleles of QTL qRGS5 detected in all four environments derived from the parent V20B.

Conclusion The difference of brown rice grain size between parents V20B and CPSLO17 is extremely significant. The brown rice grain size trait is affected by the environments. The QTL qRGS5 is a genetically-stable main effect QTL that affects grain size in brown rice, which has practical value in new gene discovery for brown rice grain size and molecular breeding for high-yield and high-quality rice.