藏羊VEGF-A基因编码区多态性及生物信息学分析

doi:10.7668/hbnxb.2013.06.009

摘要/Abstract

摘要： 为研究藏羊VEGF-A基因编码区多态性与藏羊耐高寒、缺氧环境的相关性,以藏羊的血样为材料,运用DNA池测序和直接测序法检测VEGF-A基因的序列变异,比较其基因型频率和等位基因频率的差异,并对不同的多态位点间进行连锁不平衡和单倍型分析。然后预测蛋白质序列的改变,并用生物信息学软件对蛋白质序列的结构及性质进行分析。结果表明,在藏羊VEGF-A的编码区中有3个多态性位点,SNP2(g.15020T/A)碱基的突变导致了半胱氨酸变为丝氨酸。此氨基酸的变化并没有引起基因所编码蛋白的二级结构的变化。二级结构主要以无规则卷曲和α螺旋为主。SNP1(g.15005T/A)的基因型频率和等位基因频率在藏羊群体中和湖羊群体中差异不显著(P>0.05),而SNP2(g.15020T/A)、SNP3(g.15020T/A)的基因型频率和等位基因频率在藏羊群体和湖羊群体中差异显著(P<0.05),SNP2(g.15020T/A)、SNP3(g.15020T/A)的等位基因A是藏羊群体中的优势等位基因,SNP2和SNP3处于紧密连锁不平衡状态(D'>0.75,r2>0.33)。在单倍型分析中发现6种单倍型,其中TTT是藏羊群体中的主要单倍型。这可能与藏羊耐高寒、缺氧环境有关,可以尝试作为藏羊低氧适应性的候选分子标记,为藏羊遗传资源的保护、开发与新品种的选育提供科学依据。

关键词: 藏羊, VEGF-A基因, 多态性, 生物信息学分析

Abstract: To detect the polymorphisms of VEGF-A gene CDS ( Coding domain sequence ) with the correlation of cold resistant, anoxic environment in Tibetan sheep.The sample material is Tibetan sheep blood.The polymor-phisms of VEGF-A gene CDS were identificated by DNA pools and direct sequencing in Tibetan sheep.The change of VEGF-A protein was predicted, then the structure and characteristics around mutation change of VEGF-A protein sequences were analyzed by bioinformatics software.To campare the differences of genotype and allele frequencies.Then to analysis the different single nudeotide polymorphisms of linkage disequilibrium and haplotype.Three SNPs were discovered in VEGF-A gene CDS ( Coding domain sequence ) in Tibetan sheep.SNP2 in Tibetan sheep was ca-pable of cysteine to serine.This amino acid changes did not cause the protein encoded changes in secondary struc -ture.The secondary structures are mainly composed of Helix and Coli.The genotype and allele frequencies of SNP 1 in the Tibetan sheep breeds and Hu sheep breeeds was not significant (P>0.05),the genotype and allele frequen-cies of SNP2,SNP3 in Tibetan sheep breeds and Hu sheep breeds were significant (P<0.05).Allele A of SNP2 (g.15020T/A)、SNP3(g.15020T/A) is the advantage alleles within Tibetan sheep breeds.SNP2 and SNP3 were in close linkage disequilibrium (D'>0.75,r2 >0.33).We found six haplotypes in haplotype analysis, TTT is the main haplotype in Tibetan sheep population.This may be related to resistant to cold, lack of oxygen to the environ-ment in Tibetan sheep.We can try as hypoxic adaptation candidate molecular markers for the Tibetan sheep and for Tibetan sheep genetic resources protection, development and breeding of new varieties to provide a scientific basis.

Key words: Tibetan sheep, VEGF-A gene, PolymoRphisms, BioinfoRmatics analysis

中图分类号:

S826

王朝风, 岳耀敬, 张勇, 刘建斌, 韩吉龙, 赵兴绪, 杨博辉. 藏羊VEGF-A基因编码区多态性及生物信息学分析[J]. 华北农学报, 2013, 28(6): 53-58. doi: 10.7668/hbnxb.2013.06.009.

WANG Chao-feng, YUE Yao-jing, ZHANG Yong, LIU Jian-bin, HAN Ji-long, ZHAO Xing-xu, YANG Bo-hui. PolymoRphisms Detection and BioinfoRmatics Analysis of Coding Domain Sequence of VEGF-A Gene in Tibetan Sheep[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2013, 28(6): 53-58. doi: 10.7668/hbnxb.2013.06.009.

http://www.hbnxb.net/CN/Y2013/V28/I6/53

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