QTL Analysis of White Core Grain in a Rice Cultivar, “Yamadanishiki” for Brewing Japanese Rice Wine

Japanese rice wine (sake) is made from brewing rice cultivars that have characteristic traits, differing from cooking rice cultivars. In sake brewing, the steamed rice is fermented with koji (Aspergillus oryzae) and yeast (Saccharomyces cerevisiae). In the processes, white core grain is very useful. White core is opaque in the central rice grain and yields fast water absorption and amylolysis efficiency. Thus, it is important for brewing rice breeding to elucidate the genetic mechanism of white core expression. We report the QTLs for white core expression in the most popular brewing cultivar, “Yamadanishiki” in Japan. First, QTL analysis was conducted with the recombinant inbred lines derived from Koshihikari/Yamadanishiki in 2013 and 2014. Koshihikari is the main cooking rice cultivar in Japan with low white core expression rate (WCR, <10%) whereas Yamadanishiki has high WCR (about 70%). Five QTLs were detected on chromosomes 1, 3, 6 and 10, and the Yamadanishiki alleles at all QTLs increased WCR. The QTL on chromosome 6 was stably detected in both years. Next, to verify the candidate QTL on chromosome 6, we developed the backcrossed lines carrying the Yamadanishiki chromosomal segment including the QTL region with the Koshihikari genetic background. The WCRs of the candidate lines were significantly higher than Koshihikari. Therefore, this QTL was identified for WCR, and we also demonstrated that the QTL was affected by environmental factors. This QTL is designated as qWCY6 (QTL of White Core expression rate for Yamadanishiki allele on chromosome 6).