| Summary: | The stigma exsertion rate (SER) is one of the important factors affecting the seed production of hybrid rice. In the genus <i>Oryza</i>, wild rice species usually show higher SERs than cultivars. We previously identified one novel SER-QTL, <i>qSERg-1b</i>, from the single-segment substitution line (SSSL) SG22 of <i>O. glumaepatula</i>. In this study, <i>qSERg-1b</i> was fine-mapped by developing the secondary SSSLs (s-SSSLs) of SG22 and substitution mapping among the s-SSSLs. A total of 11 s-SSSLs were developed and used for <i>qSERg-1b</i> fine-mapping. As a result, <i>qSERg-1b</i> was narrowed down to the 122.59 kb physical region between InDel markers M01 and M49. There were 19 genes annotated in both <i>O. glumaepatula</i> and the HJX74 genomes at the <i>qSERg-1b</i> interval. Based on the genome re-sequencing of SG22 and HJX74, and the expression levels of the annotated functional genes, multiple nucleotide variations were found in <i>LOC_Os01g53630</i>, <i>LOC_Os01g53680</i>, and <i>LOC_Os01g53710,</i> including base substitutions and insertions/deletions of the genes, and they also showed significant differences in expression levels between SG22 and HJX74. Therefore, <i>LOC_Os01g53630</i>, <i>LOC_Os01g53680</i>, and <i>LOC_Os01g53710</i> were selected as the most possible candidate genes of <i>qSERg-1b</i> for further validation. The above results laid an important foundation for <i>qSERg-1b</i> cloning and provided valuable resources for molecular breeding of SER in rice.
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