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The efficiency of hybrid seed production can be improved by increasing the percentage of exserted stigma, which is closely related to the stigma length in rice. In the chromosome segment substitute line (CSSL) population derived from Nipponbare (recipient) and Kasalath (donor), a single CSSL (SSSL14) was found to show a longer stigma length than that of Nipponbare. The difference in stigma length between Nipponbare and SSSL14 was controlled by one locus ( qSTL3 ). Using 7,917 individuals from the SSSL14/Nipponbare F 2  population, the  qSTL3  locus was delimited to a 19.8-kb region in the middle of the short arm of chromosome 3. Within the 19.8-kb chromosome region, three annotated genes ( LOC_Os03g14850 ,  LOC_Os03g14860  and  LOC_Os03g14880 ) were found in the rice genome annotation database. According to gene sequence alignments in  LOC_Os03g14850 , a transition of G (Nipponbare) to A (Kasalath) was detected at the 474-bp site in CDS. The transition created a stop codon, leading to a deletion of 28 amino acids in the deduced peptide sequence in Kasalath. A T-DNA insertion mutant (05Z11CN28) of  LOC_Os03g14850  showed a longer stigma length than that of wild type (Zhonghua 11), validating that  LOC_Os03g14850  is the gene controlling stigma length. However, the Kasalath allele of  LOC_Os03g14850  is unique because all of the alleles were the same as that of Nipponbare at the 474-bp site in the CDS of  LOC_Os03g14850  among the investigated accessions with different stigma lengths. A gene-specific InDel marker LQ30 was developed for improving stigma length during rice hybrid breeding by marker-assisted selection.

Fine Mapping and Candidate Gene Analysis of qSTL3, a Stigma Length-Conditioning Locus in Rice (Oryza sativa L.)