猪SLA-DRA基因SNP位点筛选及其生物信息学分析

doi:10.3969/j.issn.1004-1524.2017.07.04

浙江农业学报 ›› 2017, Vol. 29 ›› Issue (7): 1077-1085.DOI: 10.3969/j.issn.1004-1524.2017.07.04

猪SLA-DRA基因SNP位点筛选及其生物信息学分析

刘丽霞, 张丽, 田晓静, 陈红, 寸海霞, 金丽, 谭小音, 谢德琼

西北民族大学生命科学与工程学院,甘肃兰州 730030

收稿日期:2016-11-16 出版日期:2017-07-20 发布日期:2017-07-24
作者简介:刘丽霞(1983—),女,甘肃陇南人,博士,高级实验师,主要从事动物遗传育种研究。E-mail:skllx@xbmu.edu.cn
基金资助:
甘肃省农牧厅生物技术专项(GNSW-2008-04); 西北民族大学引进人才项目(xbmuyjrc201408); 西北民族大学中央高校基本科研业务费专项资金资助项目(31920170029)

SNP screening and bioinformatics analysis of SLA-DRA gene in pigs

LIU Lixia, ZHANG Li, TIAN Xiaojing, CHEN Hong, CUN Haixia, JIN Li, TAN Xiaoyin, XIE Deqiong

College of Life Science and Engineering, Northwest University for Nationalities, Lanzhou 730030, China

Received:2016-11-16 Online:2017-07-20 Published:2017-07-24

摘要/Abstract

摘要： 以八眉猪、蕨麻猪和甘肃黑猪为研究对象,利用PCR-SSCP和测序方法对SLA-DRA基因4个外显子进行SNP位点筛选,并利用生物信息学软件预测各SNP位点对DRA基因mRNA二级结构、蛋白质二级结构和三级结构的影响。结果在3个猪种中共检测到6个DRA基因SNP位点,分别为外显子1的A¹⁷⁷G,外显子2的A³⁰⁹³C,以及外显子4的A⁴¹⁶⁷G、A⁴²⁴⁶G、C⁴²⁸²T和G⁴²⁹³A,其中A³⁰⁹³C、A⁴¹⁶⁷G和G⁴²⁹³A为错义突变,分别导致甲硫氨酸(Met)变为亮氨酸(Leu)、谷氨酰胺(Gln)变为精氨酸(Arg)和精氨酸(Arg)变为组氨酸(His)。以3个错义SNP位点为基础,构建了6种DRA单倍型,其中H1、H3和H6为主要单倍型,频率分别为0.25、0.21和0.21。生物信息学分析表明,三个猪种DRA基因单倍型的mRNA二级结构、蛋白质二级结构和三级结构与野生型均存在一定的差异。研究结果可为八眉猪、蕨麻猪和甘肃黑猪的保种和抗病育种提供理论依据。

关键词: 猪, SLA-DRA, SNP位点, 生物信息学

Abstract: The single nucleotide polymorphism (SNP) site of four exons of SLA-DRA gene in Bamei, Juema and Gansu Black pigs were screened via polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing analysis, and further secondary structure of mRNA, secondary and tertiary structures of DRA protein were predicted through the bioinformatics tools. The results showed that 6 SNP sites were detected, including A¹⁷⁷G, located in exon 1, A³⁰⁹³C, located in exon 2, A⁴¹⁶⁷G, A⁴²⁴⁶G, C⁴²⁸²T and G⁴²⁹³A, located in exon 4, and among these SNP sites, A³⁰⁹³C, A⁴¹⁶⁷G and G⁴²⁹³A were missense mutation, A³⁰⁹³C led to methionine (Met) into leucine (Leu), A⁴¹⁶⁷G led to glutamine (Gln) into arginine (Arg), and G⁴²⁹³A led to arginine (Arg) into histidine (His). Based on the 3 missense SNPs, 6 haplotypes were constructed, in which H1, H3 and H6 were the main haplotypes with frequencies 0.25, 0.21 and 0.21, respectively. The results of bioinformatics showed that secondary structure of mRNA, secondary and tertiary protein structures of DRA haplotypes in three pigs were different from those in wild type. The consequence would provide basis for study of breed conservation and molecular breeding in disease resistance for Bamei, Juema and Gansu Black pigs.

Key words: pig, SLA-DRA, SNP site, bioinformatics

中图分类号:

S852.4
Q751

刘丽霞, 张丽, 田晓静, 陈红, 寸海霞, 金丽, 谭小音, 谢德琼. 猪SLA-DRA基因SNP位点筛选及其生物信息学分析[J]. 浙江农业学报, 2017, 29(7): 1077-1085.

LIU Lixia, ZHANG Li, TIAN Xiaojing, CHEN Hong, CUN Haixia, JIN Li, TAN Xiaoyin, XIE Deqiong. SNP screening and bioinformatics analysis of SLA-DRA gene in pigs[J]. , 2017, 29(7): 1077-1085.

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猪SLA-DRA基因SNP位点筛选及其生物信息学分析

SNP screening and bioinformatics analysis of SLA-DRA gene in pigs

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