Neutral Selection Analysis And Genetic Differentiation Analysis Of Coding Sequence Of MDA5 And LGP2 In Chickens

Avian influenza virus and its associated resistance genes became the hotspot of biological and genetic researches recently. As the lack of the RIG-1 gene against influenza,other two genes MDA5 and LGP2 of the same family in chickens, have been widely studied.Neutral test is also important in recent genetic research. Using the Neutral Theory as the null hypothesis, neutral selection can be tested based on some parameters, then the selection type of target region was received. This study combines neutral selection with genetic research to analyze coding sequence of MDA5 and LGP2, to find candidate sites. In this experiment, White Recessive Rock, Qingyuan, Yuehuang, Silkies, Xinghua, Wenchang,Qilin, Houdan and Muscovy duck were used. Polymorphic sites of two genes were 12 and17, respectively and among them 1 site for each gene was predicted to be the potential function mutation by SIFT, and the percent of intolerant sites of chicken is more than Muscovy duck's. Results showed that the MDA5 gene of Houdan chicken was highly conserved and homozygous. F statistic(Fst) was also used to perform population structure analysis between breeds. Results showed that there is great genetic difference between Houdan chicken and other breeds, in which all the Fst are bigger than 0.5. Linkage disequilibrium analysis shows that there is haplotype block in LGP2, and it becomes linkage disequilibrium with the other four sites. There are three sites become LD in MDA5,these sites could be candidate site of gene function studies. In addition, Tajima, Fu and Li test were used to analyze intraspecific result in neutral selection. Results showed that the DFL and FFL of Silkies are significantly greater than zero, indicating that it may be in positive selection or balancing selection. We also used Ka/Ks to analyze interspecific result in neutral selection, and Ka/Ks are significantly less than 1. Results showed that MDA5 and LGP2 of chicken were in purifying selection(negative selection). Based on the results, thedifference between tolerance and negative selection of MDA5 and LGP2 may be the important causes of the different reaction between chicken and Muscovy duck after AIV infection.