Rice (Oryza sativa L.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage, sake. The grain used in sake brewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking rice. Chalky grains, such as white-core or white-belly grains, are not ideal as cooking rice. Here, we report that three grain-size quantitative trait loci (QTLs; qGL4-2, qGWh5, qGWh10), derived from the brewing cultivar, Yamadanishiki, affect grain shape, chalky grain rate, and yield, using near isogenic and pyramiding lines in the genetic background of the cooking cultivar, Koshihikari. First, these QTLs influenced multiple components of grain shape, where epistatic effects were detected between qGL4-2 and qGWh5, for grain width and thickness, and between qGL4-2 and qGWh10, for grain length. Therefore, these QTLs may coordinate to control grain shape. Second, lines harboring qGWh5 or qGWh10 at the Yamadanishiki allele exhibited increased WCE, whereas lines with qGL4-2 and qGWh10 exhibited decreased white-belly grain rate (WBR). Thus, grain shape is associated with the occurrence of chalky grain, where the chalky type depends on the QTL. Finally, we used total panicle weight of plants as a simplified rice yield index, and a promising line pyramiding qGL4-2 and qGWh5 emerged. In conclusion, qGL4-2 would be useful for the breeding of cooking rice, to decrease WBR, while qGWh5 and qGWh10 were definitely more beneficial for that of brewing rice, to increase grain weight and WCE.

稻（稻L.）在日本不仅是主食，也为日本酒精饮料的重要材料，清酒。在清酒酿造中使用的谷物与蒸煮米饭谷物具有不同的特征，包括大粒径和高白核表达率（WCE）。因为大粒谷物通常具有较重的谷物重量和较高的产量，所以此性状对于煮饭也很重要。白垩粒，例如白核或白腹粒，不适合作为煮饭。在这里，我们报告了三个晶粒大小数量性状基因座（QTL；qGL4-2，qGWh5，qGWh10）是由酿造品种Yamadanishiki衍生而来的，它会在烹饪品种Koshihikari的遗传背景中使用近等基因和金字塔形系来影响谷物形状，垩白粒率和产量。首先，这些QTL影响了晶粒形状的多个组成部分，其中在qGL4-2和qGWh5之间（对于晶粒的宽度和厚度）以及在qGL4-2和qGWh10之间（对于晶粒的长度）检测到上位性效应。因此，这些QTL可以协调以控制晶粒形状。第二，窝藏线qGWh5或qGWh10在山田锦等位基因显示出增加的WCE，而用线qGL4-2和qGWh10表现出降低的白腹纹率（WBR）。因此，颗粒形状与白垩颗粒的出现有关，其中白垩类型取决于QTL。最后，我们使用植物的总穗重作为简化的水稻产量指数，并出现了有希望的品系金字塔qGL4-2和qGWh5。总而言之，qGL4-2将有助于煮饭的育种，以降低WBR，而qGWh5和qGWh10无疑对酿造大米更有利，以增加谷物重量和WCE。