Abstract：Investigating patterns of linkage disequilibrium(LD) is helpful for a more in-depth understanding of the genome-wide mechanisms for the genetic variation response to the natural and artificial selection in model and domestic animals. LD analysis for the candidate genes on fatness in chickens can provide more important information about the genetic control of fat deposition and make the molecular markers associated with fatness more powerful. In this study, polymorphisms of perpxisome proliferator-activated receptor-γ (PPARγ), apolipoprotein B(ApoB), uncoupling protein(UCP) and other 10 candidate genes on chicken fatness among individuals were detected by DNA sequencing, denaturing high performance liquid chromatography(DHPLC), single-strand conformation polymorphism(SSCP), restriction fragment length polymorphism(RFLP) and labelled primers(LP) methods. LD investigation among the polymorphisms of the candidate genes was performed in the 8th generation populations of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content, two common measures of LD, |D'| and r2, were used in this study. The results showed that the value of |D'| and r2 often did not match very much within the candidate genes. The value of |D'| usually was larger than value of r2, sometimes even |D'|=1, while r2 was close to zero. Furthermore, in different genes, even within the same gene, LD patterns of different regions were usually different, and there was no a linear correlation between physical distance and the value of |D'| or r2. In addition, in some genes, such as ApoB, the values of |D'| and r2 between nonadjacent polymorphisms were much larger than those between the adjacent polymorphisms. Finally, there were different LD patterns of polymorphisms in some genes, such as PPAR-γ between lean and fat chicken lines. The results in this study also suggested, as a LD measure parameter, r2 is more useful than |D'|in population genetics analysis.
