Analysis on Mapping of Rice Grain Thickness QTLs under Multiple Environments

Abstract

【Objective】Grain thickness is one of the controlling factors affecting rice yield and taste quality of rice. QTL mapping for grain thickness in rice was conducted by using recombinant inbred lines (RIL) with the indica-japonica cross (V20B/CPSLO17) genetic background and major QTLs of grain thickness were obtained, providing a scientific basis for the discovery of new grain thickness genes and the development of functional molecular markers.【Method】Based on the highdensity genetic linkage map and the indica-japonica cross genetic background of RIL populations, combined with the grain thickness phenotype data of RIL populations under three different ecological environments (Guiyang, Guizhou in 2020; Guiding, Guizhou in 2021; Sanya, Hainan in 2021), QTL mapping and genetic effect analysis were performed by the ICIM-ADD method of IciMapping 4.0 software.【Result】The study showed that the grain thickness trait in rice exhibited a continuous unimodal distribution under all three ecological environments and was not affected by planting environmental factors significantly. Five grain thickness QTLs (qGT3-1, qGT5-1, qGT5-2, qGT8-1, and qGT10-1) were detected on chromosomes 3, 5, 8, and 10 in rice under the three different ecological environments. The beneficial alleles of these five QTLs were all from the parent V20B, with LOD values ranging from 3.431 to 14.081 and a range of phenotypic contribution rates from 5.479% to 26.483%. Two QTLs (qGT5-1 and qGT5-2) had a phenotypic contribution rate greater than 10%, with qGT5-2 being the only one repeatedly detected in two planting environments (Guiyang, Guizhou in 2020 and Sanya, Hainan in 2021), explaining 26.483% and 14.933% of the population's phenotypic variance, respectively. The physical distance of QTL qGT5-2 on the chromosome was about 3.9 kb, with only one candidate gene (LOC_Os05g07920); the physical distance of qGT8-1 was about 2.3 kb, with only one candidate gene (LOC_Os08g10360).【Conclusion】Grain thickness in rice is a quantitative genetic trait regulated by multiple genes. qGT5-2 is major QTL with stable heredity and high contribution rate for grain thickness, which has significant application potential in the discovery of grain thickness regulatory genes and the breeding of new high-quality and high-yield rice varieties.

Keywords

• grain thickness
• recombinant inbred line
• genetic linkage map
• multi-environment
• qtl
• genetic effect