To dissect the genetic basis of yield and its related traits, the QTLs controlling whole growth period (WGP), plant height (PH), number of panicles per plant (PN), number of grains per panicle (GN), hundredkernel weight (HKW), grain yield (GY) and biomass yield (BY) were detected by unconditional and conditional approaches with the recombinant inbred lines derived from a cross between two japonica varieties, Xiushui 79 and C Bao in three environments. Fourtythree maineffect QTLs and 29 pairs of epistatic QTLs were detected. By the unconditional method, 37 maineffect QTLs and 26 pairs of epistatic QTLs were detected. Three maineffect QTLs, qGY1.2, qGY7.1 and qGY9, were found for GY while no epistatic QTL was found for GY. By the conditional method, 9 maineffect QTLs and 3 pairs of epistatic QTLs for GY including the three maineffect QTLs detected by unconditional methods were detected. qGY9, in the interval RM6570-RM5652 on the long arm of chromosome 9, could be detected by unconditional method and conditional method when WGP, PH, PN, GN and HKW were at the same levels, but the additive effect and the variance explained were different. The allele of qGY9 contributed by C Bao could increase GY through increasing PH, HKW and PN. The alleles at the interval RM7097-RM448 on the long arm of chromosome 3 and the interval RM162-RM5753 on the long arm of chromosome 6 detected by the conditional method which could increase GY had negative effects on PH and WGP.
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