Association Study,Positive Selection Analysis Of Different Candidate Genes And Transcriptomic Study In Goat

Haemonchus contortus(H.contortus)is a blood sucking gastrointestinal(GI)parasite that causes heavy production losses in small ruminants due to their poor immune response and rapid development of anthelmentic resistance.Identifying genes,involving in immune related pathways against GI nematode infection,will assist in better responding and curing the ill effects of infection with H.contortus.In current study,four goats populations were included which are Yichang white(YCW),Hybrid white yellow(HYW),Nanjing yellow(NJY)and Enshi black goat(ENB).Fecal sample was collected from each goat for fecal egg count(FEC)of H.contortus and also ear tissue was collected for the extraction of genomic DNA.Four genes were found to be associated with FEC analysis and further two genes were selected for evolution studies.1.A total of 25 single nucleotide polymorphisms(SNPs)were identified in four genes,e.g.the dopamine receptor binding 1(DRB-1),IL-32,insulin-like growth factor1(IGF-1)and IL-33.Five SNPs were missense mutations.These missense SNPs change amino acid composition of the proteins which may have influence on their function in host innate immunity to GI nematode infection.2.Seven of the SNPs showed significant association with fecal egg count(FEC)trait(P<0.02),including 2,3,1 and 1 SNPs respectively in DRB-1,IL-32,IL-33 and IGF-1 genes.The comparative analysis among species showed that missense mutations leads to change in amino acid might be affecting the function of genes.On the bases of results,immune related genes and genetic markers of these genes may play a key role against H.contortus infection.3.The phylogenetic tree revealed that goat IL-32 and DRB-1 was in close resemblance with sheep IL-32 and DRB-1.The coding nucleotide sequences of IL-32 and DRB-1 were compared among 11 and 8 species respectively and it was found that the goat IL-32 gene shared identity with sheep(96%),bison(91%),camel(58%),cat,buffalo and human(56%)and DRB-1 shared(98%)identity with sheep,(47%)with rat and mouse,(46%)with horse,(44%)with camel and human and(41%)with dog.4.IL-32 and DRB-1 is involved in many biological processes,however,its role for the immune response against various diseases in mammals is poorly understood.Therefore,the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphism in IL-32 and DRB-1 gene.By using FST based method,IL-32(9375)and DRB-1(37)gene were found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and Fixation index(Fst).Using 11 and 8 nucleotide sequences of mammalian species of IL-32 and DRB-1 from NCBI database,the evolutionary selection of IL-32 and DRB-1 gene was determined using Maximum likelihood model method through four models(M1a,M2 a,M7 and M8)in Codeml program of PAML,which revealed that this gene was under purified selection.5.In transcriptome study comparative analysis of the four tissue contrasts,i.e.Testis,Lymph node,Liver and Leg muscle differential variation at the gene,isoform,and transcription start site(TSS),level showed that several of the genes differed with each other.Interestingly,the comparison of testis and lymph node is highly expressed.