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

doi:10.3969/j.issn.1004-1524.2017.07.04

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

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S852.4
Q751

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

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