从江香猪SIM1基因SNPs筛查及生物信息学分析

SNPs Screening and Bioinformatics Analysis of SIM1 Gene in Congjiang Pigs

本研究以从江香猪为研究对象,二元杂交猪(从江香猪×野猪)、外三元杂交猪(杜×长×大)为对照,采用DNA池和直接测序技术对3个群体的SIM1基因7个外显子、部分内含子以及3′非翻译区序列进行多态性检测;利用生物信息学软件预测多态位点对SIM1基因mRNA二级结构和蛋白质一级、二级结构的影响。结果表明,在3个群体的SIM1基因中筛查到12个SNPs,C77T位于第5外显子,T29186C、A29195C位于第9内含子,C63T、C225T位于第10外显子,C107T、A426G、T583C、A586C、A605C、A615C位于第11外显子,G267T位于3′非翻译区。其中C77T、T29186C、A29195C、C63T、C225T、C107T、G267T为同义突变,A426G、T583C、A586C、A605C、A615C为错义突变;5个错义突变分别导致异亮氨酸(Ile)变为缬氨酸(Val)、亮氨酸(Leu)变为脯氨酸(Pro)、谷氨酸(Glu)变为丙氨酸(Ala)、谷氨酸(Glu)变为天冬氨酸(Asp)、天冬酰胺(Asn)变为组氨酸(His);根据在线软件预测,突变前后的SIM1基因mRNA二级结构和蛋白质一级、二级结构均会发生改变。

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 7exons,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,C77 Tlocated in exon 5,T29186 Cand A29195Clocated in intron 9,C63 Tand C225Tlocated in exon 10,and C107 T,A426G,T583 C,A586C,A605 Cand A615Clocated in exon 11,G267 T located in 3′-UTR.C77 T,T29186C,A29195 C,C63T,C225 T,C107T and G267 T were silent mutations,A426 G,T583C,A586 C,A605Cand A615 Cwere 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.