Good-eating-quality QTLs detected in two breeding populations by genome-wide association mapping increase eating quality of the Japanese rice cultivar ‘Koshihikari’

Abstract

To identify QTLs controlling the eating quality of ‘Akidawara’, ‘Satojiman’, and ‘Ikuhikari’ rice, we performed a genome-wide association mapping analysis using two breeding populations in 2013 and 2014 de‍rived from crosses between these and another parental line. Through sensory tests by a trained panel, we evaluated five components of the eating quality of cooked rice. Fifty-eight QTLs for these components were detected in breeding lines in 2013 (seven regions of chromosome [chr.] 1, 4, and 11) and 2014 (ten of chr. 1, 2, 4, 8, 9, and 11). The Akidawara, Satojiman, or Ikuhikari alleles at these QTLs increased eating quality. QTLs on the short arm of chr. 4, the middle of the long arm of chr. 4, the distal end of the long arm of chr. 4, and the short arm of chr. 11, were identified in both years. The genetic effects of the Satojiman alleles at QTLs on the distal end of the long arm of chr. 4 and on the short arm of chr. 11 were confirmed by analysis of two chromosome segment substitution lines containing a Satojiman segment in the ‘Koshihikari’ background in 2016 and 2017, in which the Satojiman alleles increased the level of eating quality of Koshihikari.