Single nucleotide polymorphism and bioinformatics analysis of <i>DQA2</i> gene in yak

doi:10.3785/j.issn.1008-9209.2019.06.211

Journal of Zhejiang University (Agriculture and Life Sciences)

2020, Vol. 46

Issue (3): 376-382 DOI: 10.3785/j.issn.1008-9209.2019.06.211

Animal sciences & veterinary medicine

Single nucleotide polymorphism and bioinformatics analysis of DQA2 gene in yak

Zhuo LI(

),Lang CHEN,Tao JIANG,Lixia LIU,Li ZHANG,Rui WANG,Yaodong LI

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

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Abstract

Single nucleotide polymorphism (SNP) of DQA2 gene in yak was analyzed via genomic DNA pooled amplification and directly sequencing, and further the influence of SNP sites on the secondary structures of mRNA and protein of DQA2 gene were predicted and analyzed by bioinformatic software. The results showed that the polymorphism of DQA2 gene in yak was high, and 14 SNP sites were detected. Only one SNP site was located on the intron 1, while 13 SNP sites were located on exon regions. Nine SNP sites were missense mutations, which resulted in changes in corresponding amino acids. The results of secondary structure prediction showed that eight SNP sites increased the stability of secondary structure of mRNA, and four SNP sites reduced the stability of secondary structure of mRNA. The SNP sites of missense mutation changed the secondary structure of DQA2 protein in yak. The proportion of random coil was the highest, followed by extended strand, and β-turn was the lowest among components of protein secondary structure before and after mutation. The results can provide basic data for further research on yak major histocompatibility complex (MHC) gene and theoretical basis for screening the molecular markers of yak disease resistance.

Key words： yak DQA2 gene single nucleotide polymorphism site bioinformatics

Received: 21 June 2019 Published: 04 June 2020

CLC:

S 823.85

Corresponding Authors: Zhuo LI E-mail: smlz@xbmu.edu.cn

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	Zhuo LI
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	Lixia LIU
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	Rui WANG
	Yaodong LI

Cite this article:

Zhuo LI,Lang CHEN,Tao JIANG,Lixia LIU,Li ZHANG,Rui WANG,Yaodong LI. Single nucleotide polymorphism and bioinformatics analysis of DQA2 gene in yak. Journal of Zhejiang University (Agriculture and Life Sciences), 2020, 46(3): 376-382.

URL:

http://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2019.06.211 OR http://www.zjujournals.com/agr/Y2020/V46/I3/376

牦牛DQA2基因单核苷酸多态性及其生物信息学分析

利用基因组DNA混合池扩增产物直接测序的方法对55头牦牛DQA2基因的单核苷酸多态性（single nucleotide polymorphism, SNP）进行分析，并利用生物信息学软件预测分析了SNP位点对DQA2基因mRNA和蛋白质二级结构的影响。结果显示：牦牛DQA2基因多态性较高，共检测到14个SNP位点，仅有1个SNP位点位于内含子1上，其余13个均位于外显子区域，其中，9个SNP位点为错义突变，导致相应氨基酸发生改变。二级结构预测结果表明：8个SNP位点增大了mRNA二级结构的稳定性，4个位点降低了mRNA二级结构的稳定性。错义突变SNP位点均改变了牦牛DQA2蛋白质二级结构，突变前后二级结构各组分中无规则卷曲所占比例最高，其次为延伸链，β-转角的比例最低。研究结果为探究牦牛主要组织相容性复合体（major histocompatibility complex, MHC）基因的致病机制和免疫机制提供了有利条件，也为筛选牦牛抗病分子标记提供了理论基础。

关键词： 牦牛, DQA2基因, 单核苷酸多态性位点, 生物信息学

Table 1 Primer information of DQA2 gene

Fig. 1 Results of PCR amplification of DQA2 gene in yakM: 100 bp DNA marker; Lane 1-2: Amplification products of P1; Lane 3-4: Amplification products of P2; Lane 5-6: Amplification products of P3; Lane 7-8: Amplification products of P4.

Fig. 2 Sequencing peak diagrams of SNP sites for DQA2 gene in yak

Table 2 Mutation information and allele frequency of SNP sites for DQA2 gene in yak

Fig. 3 Secondary structure of mRNA of SNP sites before and after mutation in yak DQA2 gene

Table 3 Free energy of secondary structures of mRNA and secondary structure of protein of SNP sites before and after mutation in yak DQA2 gene


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