Characterization and fine mapping of qPE12, a new locus controlling rice panicle exsertion

Panicle exsertion is an important agronomic trait involved in pollination and hybrid rice seed production. The identification of genes controlling panicle exsertion will play a central role in hybrid rice breeding. C115, a chromosome segment substitution line carrying introgression segments of Nipponbare in genetic background of indica variety 9311, had significantly shortened panicle exsertion, uppermost internode length and plant height. Genetic analysis in F2 and F3 populations derived from a cross of C115 and 9311 indicated that the shortened panicle exsertion of C115 was recessive and controlled by a single Medelian factor, and the allele from Nipponbare decreased the phenotypic value. Primary mapping suggested qPE12, the Nipponbare introgression segment locating on the long arm of chromosome 12, was responsible for this phenotypic variation. Based on map-based cloning strategy, fine mapping was carried out with a total of 1130 recessive individuals selected from F2 and F3 populations, delimiting qPE12 to a 190-kb region. This result provides important information for isolation of a new gene controlling panicle exsertion in the future.