Variation in domesticated rice inflorescence architecture revealed by principal component analysis and quantitative trait locus analysis

To isolate the factors that define variation in domesticated rice (Oryza saliva L.) inflorescence architecture, we performed a principal component analysis (PCA) using 292 accessions (136 indica and 156 japonica). The first component accounted for 40.6% of the total variance, and its main components were interpreted as lengthening of the stage in which secondary branch primordia were formed. The second component accounted for 23.4%, and its main components were explained by formation of more primordia on the rachis and primary branches. Indica tended to have more primary branches and their lateral organs, whereas japonica tended to have a longer rachis with more lateral organs, suggesting that there were heterochronic differences in panicle development. Quantitative trait locus (QTL) analyses for panicle traits and heading date were performed in 5 F-2 populations and a set of backcross inbred lines; these were derived from crosses between Koshihikari and six other accessions, including the top three for number of spikelets per panicle. A total of 174 QTLs were detected for 10 panicle traits. Only the QTLs on chromosomes 3, 6, and 7 were shared, and only by two or three populations, suggesting that variation in domesticated rice inflorescence architecture is determined by many genes.