| 海南黄牛IGF2R基因单核苷酸多态性及其生物信息学分析 |
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| 引用本文： | 杨伟杰,满初日嘎,吴慧,张振兴,何美荣,蒋俊明,陈巧玲,高宏岩,王凤阳,陈思.海南黄牛IGF2R基因单核苷酸多态性及其生物信息学分析[J].南方农业学报,2022,53(12):3520-3528. |
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| 作者姓名： | 杨伟杰 满初日嘎 吴慧 张振兴 何美荣 蒋俊明 陈巧玲 高宏岩 王凤阳 陈思 |
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| 作者单位： | 海南大学动物科技学院/海南省热带动物繁育与疫病研究重点实验室/海口市动物基因工程重点实验室, 海南海口 570228 |
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| 基金项目： | 海南省院士创新平台科研项目（YSPTZX202153）；中央引导地方科技发展资金项目（ZY2022HN09） |
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| 摘 要： | 【目的】明确海南黄牛胰岛素样生长因子2受体基因（IGF2R）遗传多态性及其在海南黄牛群体中的遗传分布情况，为进一步揭示IGF2R基因对海南黄牛生长性状的调控机理提供理论依据，也为分子标记辅助选择提供新的候选位点。【方法】构建海南黄牛DNA混池，通过PCR扩增和测序技术对海南黄牛IGF2R基因编码区（CDS）进行基因多态性分析，并以Chromas序列比对筛选出错义突变SNP位点；应用PCR-RFLP对202头海南黄牛个体进行基因型鉴定，同时对筛选到的SNP位点进行连锁不平衡及单倍型分析，评估海南黄牛群体中各单倍型的分布情况；通过生物信息学方法分析各单倍型和SNP位点对海南黄牛IGF2R基因CDS区mRNA二级结构、蛋白理化性质及蛋白二级结构的影响。【结果】在海南黄牛IGF2R基因CDS区共检测到4个错义突变SNPs位点，分别为SNP1（g.63977A>G）、SNP2（g.63999T>C）、SNP3（g.69772G>A）和SNP4（g.94987A>C），其中SNP1、SNP2和SNP3位点间呈强连锁不平衡状态。4个SNPs位点在海南黄牛群体中均表现为中度多态性，且处于Hardy-Weinberg平衡状态（P>0.05）。海南黄牛群体中存在4种单倍型（F>0.01），分别是H1（ATG）、H2（GCA）、H3（ACA）和H4（GCG）；各单倍型及SNP4突变型对海南黄牛IGF2R基因CDS区mRNA二级结构及其最小自由能均有影响。海南黄牛IGF2R蛋白为亲水蛋白，存在跨膜结构和信号肽，其二级结构主要由无规则卷曲和延伸链构成，α-螺旋和β-转角的占比较小。【结论】在海南黄牛IGF2R基因CDS区共检测到4个错义突变SNPs位点，在海南黄牛群体中均表现为中度多态性，且处于Hardy-Weinberg平衡状态。海南黄牛IGF2R基因SNP位点突变对其mRNA二级结构及稳定性均会造成影响，致使IGF2R蛋白二级结构肽链构象发生改变，进而对海南黄牛生长性状的调控造成影响。
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| 关 键 词： | 海南黄牛 IGF2R基因 SNP位点 生物信息学 生长性状 |
| 收稿时间： | 2022-09-12 |
Single nucleotide polymorphism and bioinformatics analysis of IGF2R gene in Hainan cattle |
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| YANG Wei-jie,MANCHU Ri-ga,WU Hui,ZHANG Zhen-xing,HE Mei-rong,JIANG Jun-ming,CHEN Qiao-ling,GAO Hong-yan,WANG Feng-yang,CHEN Si.Single nucleotide polymorphism and bioinformatics analysis of IGF2R gene in Hainan cattle[J].Journal of Southern Agriculture,2022,53(12):3520-3528. |
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| Authors: | YANG Wei-jie MANCHU Ri-ga WU Hui ZHANG Zhen-xing HE Mei-rong JIANG Jun-ming CHEN Qiao-ling GAO Hong-yan WANG Feng-yang CHEN Si |
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| Affiliation: | School of Animal Science and Technology/Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research of Hainan Province/Key Laboratory of Animal Genetic Engineering of Haikou, Hainan University, Haikou, Hainan 570228, China |
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| Abstract: | 【Objective】 To explore genetic polymorphism of the insulin-like growth factor 2 receptor gene(IGF2R) in Hainan cattle and its genetic distribution in Hainan cattle population, and to provide theoretical basis for revealing regulatory mechanism of gene IGF2R to growth traits of Hainan cattle and sites for molecular marker-assisted selection.【Method】 A DNA pool was constructed, and polymorphism analysis of gene coding regions(CDS) of Hainan cattle IGF2R gene was operated through PCR amplification and sequencing technology. The single nucleotide polymorphism (SNP) sites of missense mutation were screened with Chromas sequence alignment;a total of 202 individuals of Hainan cattle were genotyped by PCR-RFLP and the selected SNP sites were used for linkage disequilibrium and haplotype analysis to evaluate haplotype distribution in Hainan cattle population;effects of haplotypes and SNP sites on mRNA secondary structure, protein physicochemical properties and protein secondary structure of CDS of Hainan cattle IGF2R gene were analyzed by bioinformatics methods.【Result】 Four SNP sites of missense mutation in Hainan cattle IGF2R gene CDS region were detected, including SNP1(g.63977 A>G), SNP2(g.63999 T>C), SNP3(g.69772 G>A), and SNP4 (g.94987 A>C), and a strong linkage disequilibrium between SNP1, SNP2 and SNP3. Four SNP sites showed mediumly polymorphism in the population, and they were in Hardy-Weinberg disequilibrium(P>0.05). Four haplotypes were in Hainan cattle population(F>0.01), namely H1(ATG), H2(GCA), H3(ACA), and H4(GCG);each haplotype and mutated SNP4 influenced secondary structure and minimum free energy of mRNA in the CDS of Hainan cattle IGF2R gene. IGF2R protein was hydrophilic, which had transmembrane structure and a signal peptide and its secondary structure was mainly composed of irregular curls and extended strand, followed by α-helix and β-turn.【Conclusion】 Four missense mutation SNP sites in CDS regions of IGF2R gene in Hainan cattle are detected, and medium polymorphism is detected in Hainan cattle population and are in Hardy-Weinberg disequilibrium. Mutation of SNP sites of IGF2R gene in Hainan cattle may affect mRNA secondary structure and stability, leading to changes of peptide chain conformation of IGF2R protein secondary structure, thus influencing regulation of growth traits in Hainan cattle. |
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