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 F 2 and F 3 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 F 2 and F 3 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.