Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice.

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japónica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields lo-cated throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hdl6 and Hdl7 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hdl6 and Hdl7 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been de-tected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These re-sults led us to propose a new selection strategy to improve agronomic performance in temperate japónica rice cultivars. [ABSTRACT FROM AUTHOR]