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In the past decades, extensive efforts have been made to develop analysis methods for mapping the QTLs (quantitative trait loci). Recently, we proposed a molecular marker regression model by using the gene marker material fitting the orthogonal layout to estimate the quantitative trait. By the same method, a locating QTL method was researched and developed by the gene marker material fitting the orthogonal layout. The results showed the recombination rate reflecting genetic distance between a marker and a QTL could affect the accuracy estimating the gene effect and allele's interaction effects by molecular marker regression model when considering the linear marker variable coefficient as relative gene effects and quadratic marker variable coefficient as the opposite of allele's interaction effects. The accuracy was reduced along with the increasing of the recombination rate between a marker and a QTL. The larger the recombination rate was, the smaller the accuracy was. The accuracy is also related to the truth of relative the gene effect and allele's interaction effects. The sampling error and truth of the gene effect and allele's interaction effects don't affect the reducing trends of estimated effect with the increasing of the recombination rate r or genetic distance between a marker and a QTL. There was a function relation between variable coefficient and recombination rate r. Finally, an approach to locate the QTL in marker maps was developed by using genetic linkage map in some Internet biological database.