Fine mapping and candidate gene analysis of qSTL3, a stigma length-conditioning locus in rice (Oryza sativa L.)

Abstract

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-Os03g14850is the gene controlling stigma length. However, the Kasalath allele of LOC-Os03g14850is unique because all of the alleles were the same as that of Nipponbare at the 474-bp site in the CDS of LOC-Os03g14850among 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.