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Effect of genetic background on detection of quantitative trait locus (QTL) and QTL by environment interaction governing yield related traits (filled grain number, total spikelet number, thousand grain weight, panicle number, grain yield) was studied using two sets of reciprocal introgression lines (ILs) and recombinant inbred lines (RILs) derived from a cross between a japonica variety Lemont and an indica variety Teqing.