SNPs Screening and Bioinformatics Analysis of SIM1 Gene in Congjiang Pigs

In this study, Congjiang pig was served as a research object, crossbred pigs (Congjiang pig×boar), outside crossbred pigs (Duroc×Landrace×Yorkshire) as controls.Using DNA pools and direct sequencing detected polymorphism of 7 exons, part of introns and 3'untranslated region (3'-UTR) sequences of SIM1 gene for three groups.Bioinformatics software predicted what impact polymorphic loci had to mRNA secondary structure and protein primary, secondary structure of SIM1 gene.The results showed that 12 SNPs were screened in SIM1 gene of three groups, C77T located in exon 5, T29186C and A29195C located in intron 9, C63T and C225T located in exon 10, and C107T, A426G, T583C, A586C, A605C and A615C located in exon 11, G267T located in 3'-UTR. C77T, T29186C, A29195C, C63T, C225T, C107T and G267T were silent mutations, A426G, T583C, A586C, A605C and A615C were missense mutations.The five missense mutations respectively led to isoleucine (Ile) into valine (Val), leucine (Leu) into proline (Pro), glutamate (Glu) into alanine (Ala), glutamic (Glu) into aspartic (Asp), asparagine (Asn) histidine (His), and according to online software forecast, mRNA secondary structure and protein primary, secondary structure of SIM1 gene changed in mutations before and after.