贵州地方猪味觉受体TAS1R3基因SNP位点筛选及其与生长性状的关联分析

Screening of SNP loci of the taste receptor TAS1R3 gene in Guizhou local pigs and their association analysis with growth traits

  • 摘要:目的】筛选贵州地方猪味觉受体TAS1R3基因单核苷酸多态性(SNP)位点,解析群体遗传特征和TAS1R3基因与体尺性状的关联,为贵州地方猪种质资源的遗传改良提供候选分子标记。【方法】以242头贵州地方猪(从江香猪、黔东花猪、江口萝卜猪、关岭猪和白洗猪)为研究对象,针对TAS1R3基因的全部外显子设计9对特异性引物进行PCR扩增与测序。筛选TAS1R3基因SNP位点,并进行SNP位点的遗传学分析、连锁不平衡分析、单倍型和双倍型分析、关联分析及TAS1R3基因mRNA二级结构预测。【结果】在从江香猪、黔东花猪、江口萝卜猪和关岭猪4个贵州地方猪中共鉴定出4个错义突变SNP位点:g.63613635T>C、g.63614535G>A、g.63616733T>C和g.63617113G>A。遗传学分析结果显示,黔东花猪和关岭猪中g.63613635T>C和g.63616733T>C处于中度多态水平。卡方χ2检验结果显示,4个SNP位点的基因型分布均未显著偏离哈迪—温伯格平衡(P>0.05)。连锁不平衡分析结果显示,江口萝卜猪g.63613635T>C和g.63614535G>A、g.63614535G>A和g.63616733T>C、g.63613635T>C和g.63616733T>C及关岭猪g.63613635T>C和g.63616733T>C、g.63613635T>C和g.63617113G>A、g.63616733T>C和g.63617113G>A间存在强连锁不平衡效应。关联分析结果显示,从江香猪g.63613635T>C TC基因型个体的体长和胸围均显著高于TT基因型个体(P<0.05,下同),g.63616733T>C TC基因型个体的胸围指数、体长和胸围均显著高于TT基因型个体。【结论】4个贵州地方猪TAS1R3基因中鉴定出4个错义突变SNP位点,g.63613635T>C和g.63616733T>C在黔东花猪和关岭猪中处于中度多态水平。在江口萝卜猪和关岭猪中存在强连锁不平衡效应。从江香猪TAS1R3基因SNP位点H1H3双倍型个体与更优的体尺性状相关。TAS1R3基因具有影响贵州地方猪生长性状的遗传潜能。g.63613635T>C和g.63616733T>C及其双倍型H1H3可作为后续分子标记辅助选择的参考。

     

    Abstract:Objective】This study aimed to screen the single nucleotide polymorphism (SNP) loci of taste receptor TAS1R3 gene in Guizhou local pigs, investigate associations between population genetic characteristics and TAS1R3 gene, as well as body size traits, to provide candidate molecular markers for genetic improvement of germplasm resources of Guizhou local pigs.【Method】A total of 242 pigs of Guizhou local breeds (Congjiang Xiang pig, Qiandonghua pig, Jiangkou Radish pig, Guanling pig, and Baixi pig) were used as research objects. Nine pairs of specific primers were designed for all exons of the TAS1R3 gene for PCR amplification and sequencing. SNP loci of the TAS1R3 gene were screened to perform genetic analysis, linkage disequilibrium analysis, haplotype and diplotype analysis, association analysis, and prediction of the secondary structure of TAS1R3 gene mRNA for the screened SNP locus.【Result】Four missense mutation loci, g.63613635T>C, g.63614535G>A, g.63616733T>C, and g.63617113G>A, were found in Cong-jiang Xiang pig, Qiandonghua pig, Jiangkou Radish pig, and Guanling pig. Genetic analysis showed that the g.63613635T>C and g.63616733T>C were moderately polymorphic in Qiandonghua pig and Guanling pig. Chi-square (χ2) test showed that the genotype distributions of all four SNP loci did not deviate significantly from Hardy-Weinberg equilibrium (P>0.05). Linkage disequilibrium analysis revealed strong linkage disequilibrium effects between the follo-wing SNP pairs: g.63613635T>C and g.63614535G>A, g.63614535G>A and g.63616733T>C, and g.63613635T>C and g.63616733T>C in Jiangkou Radish pigs; g.63613635T>C and g.63616733T>C, g.63613635T>C and g.63617113G>A, and g.63616733T>C and g.63617113G>A in Guanling pig. Association analysis indicated that in Congiang Xiang pigs, individuals with the TC genotype at locus g.63613635T>C had significantly greater body length and chest circumference than those with the TT genotype (P<0.05, the same below); while individuals with the TC genotype at locus g.63616733T>C exhibited significantly higher chest circumference index, body length, and c compared to TT genotype individuals.【Conclusion】Four missense mutation loci are identified from four breeds of Guizhou local pigs. The loci g.63613635T>C and g.63616733T>C are moderately polymorphic in Qiandonghua pig and Guanling pig. Strong linkage disequilibrium effects are found in Jiangkou Radish pig and Guanling pig. Individuals carrying the diplotype H1H3 in SNP locus of TAS1R3 gene in Congjiang Xiang pigs are associated with superior body size traits. TAS1R3 gene has the genetic potential to influence growth traits in Guizhou local pig breeds. g.63613635T>C and g.63616733T>C, as well as their diplotype H1H3, can serve as references for subsequent marker-assisted selection.

     

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