Effects of different markers frequency for marker assisted introgression efficiency

The objective of this study was to analyze the effect of non-unique marker on marker-assisted introgression efficiency to compare the effects of the flanking markers selection and mblup selection on marker-assisted introgression efficiency,and to provide the reference for implementing marker-assisted introgression in practice. the results showed that as for flanking markers selection,introgression qtl frequency was increased with the marker allele frequencies. and as for mblup selection,introgression qtl frequency did not change with the marker allele frequencies. even when the marker allele frequencies in the basic group were very low,the very high introgression qtl frequency was still obtained. when the allele marker frequency was 0.5/0.5,after athwart cross for 5 generations,introgression qtl frequencies still reached 0.9629. therefore,when the marker alleles are distributed in two basic groups with a certain frequency,mblup method is suggested for foreground selection. copyright 2016 zoological society of pakistan.