Genetic Analysis and Fine Mapping of QTLs for Stigma Exsertion Rate in Rice

Stigma exsertion rate (SER) is a crucial trait that influences the seed production of hybrid rice by determining the outcrossing ability of male sterile lines (MSLs). However, the molecular genetic mechanisms underlying SER are still poorly understood. In this study, we identified 14 quantitative trait loci (QTLs) using a recombinant inbred line (RIL) population derived from B805D-MR-16-8-3 (B805D) and Hua6S. Two major QTLs, qSE1 and qSE9, were validated for their effects in the residual heterozygous line (RHL) background. The RHL carrying homozygous qSE1 region from Hua6S increased dual stigma exsertion rate (DSE) by 14.67% and 15.04%, and increased total stigma exsertion rate (TSE) by 11.73% and 13.04%, in F₁₀ and F₁₁ progeny, respectively. Conversely, the RHL carrying homozygous qSE9 region from B805D showed a substantial increase of 22.72% and 14.45% in single stigma exsertion rate (SSE), an increase of 13.46% and 8.30% in TSE, and an increase in percentage of spikelets with exserted stigma (PSE) by 24.82% and 15.57%, respectively, in F₁₀ and F₁₁ progeny. Furthermore, examination of floral organ traits revealed that both the Hua6S allele of qSE1 and the B805D allele of qSE9 increased pistil size to improve SER, but they had contrasting effects on spikelet shape. Subsequently, qSE1 and qSE9 were fine-mapped to intervals of 246.5 kb and 341.4 kb, respectively. A combination of sequencing, expression and haplotype analysis revealed that a single nucleotide variation (T to C) in the 5'UTR region of LOC_Os01g72020 (OsBOP1) was likely to be the functional variation for qSE1. Collectively, our work has laid a foundation for cloning the genes responsible for SER, and demonstrated that the Hua6S allele of qSE1 and the B805D allele of qSE9 can effectively increase SER, which could make important contributions to the genetic improvement of MSLs aimed at improving hybrid seed production.