从江香猪SIM1基因SNPs筛查及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2015.09.002

《中国畜牧兽医》---唯一指定的官方网站 ›› 2015, Vol. 42 ›› Issue (9): 2224-2232.doi: 10.16431/j.cnki.1671-7236.2015.09.002

从江香猪SIM1基因SNPs筛查及生物信息学分析

李俊, 张勇, 杨红, 张雄

贵州大学动物科学学院, 贵州大学高原山地动物遗传育种与繁殖省部共建教育部重点实验室, 贵州省动物遗传育种与繁殖重点实验室, 贵阳 550025

收稿日期:2015-02-02 出版日期:2015-09-20 发布日期:2015-09-25
通讯作者: 张勇 E-mail:as.yzhang@gzu.edu.com
作者简介:李俊(1989-),男,贵州遵义人,硕士生,研究方向:动物遗传育种与种质资源创新,E-mail:15285116484@163.com
基金资助:
贵州大学引进人才科研项目《提高香猪产仔数及仔猪成活率关键技术研究与应用》(贵大人基合字[2013]21号)

SNPs Screening and Bioinformatics Analysis of SIM1 Gene in Congjiang Pigs

LI Jun, ZHANG Yong, YANG Hong, ZHANG Xiong

Guizhou Key Laboratory of Animal Genetics, Breeding and Reproduction, Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China

Received:2015-02-02 Online:2015-09-20 Published:2015-09-25

摘要/Abstract

摘要： 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。

关键词: 从江香猪; SIM1基因; SNPs; 生物信息学

Abstract: 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.

Key words: Congjiang pigs; SIM1 gene; SNPs; bioinformatics

中图分类号:

李俊, 张勇, 杨红, 张雄. 从江香猪SIM1基因SNPs筛查及生物信息学分析[J]. 《中国畜牧兽医》---唯一指定的官方网站, 2015, 42(9): 2224-2232.

LI Jun, ZHANG Yong, YANG Hong, ZHANG Xiong. SNPs Screening and Bioinformatics Analysis of SIM1 Gene in Congjiang Pigs[J]. , 2015, 42(9): 2224-2232.

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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

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