Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3

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To identify the chromosomal regions controlling the eating quality of Koshihikari rice, we performed a quantitative trait locus (QTL) analysis using two backcross inbred lines (BILs): N-BILs (79 lines derived from a cross of Nipponbare/Koshihikari//Nipponbare) and K-BILs (89 lines derived from a cross of Nipponbare/Koshihikari//Koshihikari). We evaluated several components of the eating quality of cooked rice, namely glossiness, taste, stickiness, hardness, and overall evaluation, based on sensory tests by a trained panel, and amylose and protein contents. Ten QTLs for these components were detected in N-BILs (two regions of chromosome [chr.] 3 and one of chr. 11), and six in K-BILs (chr. 3 and chr. 6). Each QTL explained 11.6% to 32.0% of the total phenotypic variance. QTLs at the distal end of the short arm of chr. 3 were commonly identified in both BILs. The Koshihikari alleles at these QTLs increased eating quality. The genetic effect of the Koshihikari alleles was confirmed by analysis of a chromosome segment substitution line containing a Koshihikari segment of the short arm of chr. 3 in the Nipponbare background.