Uncovering Major and Minor QTLs Generating Natural Variation in Heading Date Among Asian Rice Cultivars

Heading date is one of crucial factors determining regional and seasonal adaptation in rice (Oryza sativa L.). Heading date therefore has been a major target of selection in breeding programs. To genetically dissect naturally occurring variation in rice heading date, we detected quantitative trait loci (QTLs) in advanced backcrossed populations derived from multiple crosses of the japonica rice cultivar Koshihikari, as a common parental line, with eleven rice diverse accessions (five of indica, three of Aus, and three of japonica) that originate from various regions in Asia. QTL analyses of over 14,000 backcrossed individuals revealed a total of 255 QTLs located widely across rice genome. Among the detected QTLs for heading date, 128 QTLs corresponded well with the genomic positions of the rice heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected on different chromosome regions with the rice heading date genes above mentioned. Advanced backcross progeny allowed detecting these QTLs with relatively small additive effects. These results indicate that natural variation in rice heading date could be generated by combinations among different alleles both of large effect QTLs and small effect QTLs. These QTLs could be of great significance in rice breeding for allowing adjustment to certain cultivation conditions under a wide range of temperature and day-length conditions by fine-tuning of heading date.