3个贵州地方鸡种NKX2-5基因多态性及生物信息学分析

Polymerphism Detection and Bioinformatics Analysis of NKX2-5 Gene of Three Local Chicken Breeds in Guizhou

以高脚鸡、威宁鸡、乌蒙乌骨鸡(含白壳蛋鸡和绿壳蛋鸡)3个贵州地方鸡种为研究对象,构建品种DNA池,扩增NKX2-5基因第1外显子全部序列及第2内含子部分序列,采用直接测序法对3个品种(4个群体)的NKX2-5基因进行单核苷酸多态性检测,利用生物信息学软件预测不同多态性位点对NKX2-5基因mRNA二级结构、蛋白质二级结构的影响。结果表明,在3个品种(4个群体)中共检测到G108A、T288C、C400T、T420G和G429A5个SNPs位点,其中,G108A位于非编码区;T288C、C400T位于第1外显子区;T420G和G429A位于内含子区。T288C和C400T均为错义突变,T288C突变导致丝氨酸(Ser)变为脯氨酸(Pro)、C400T突变导致丙氨酸(Ala)变为缬氨酸(Val),SNPs位点对于NKX2-5基因mRNA二级结构、蛋白质二级结构有一定影响。

In this study,Gaojiao chickens,Weining chickens,Wumeng black-bone chickens(including blue-shell chickens and white-shell chickens)from three local breeds of Guizhou were selected for research subjects.By constructing DNA pools to amplify the all sequences of extron 1and the segmental sequences of intron 2on NKX2-5gene.Taking direct sequencing method to detect the single nucleotide polymorphisms on NKX2-5gene of three varieties(four groups).By bioinformatics software to predict the effects of different polymorphism loci on mRNA,protein secondary structure of NKX2-5gene.The results showed that 5SNPs including G108 A,T288C,C400 T,T420Gand G429 A were discovered.And among these SNPs,G108 A was located in non-coding regions,T288 Cand C400T were located in extron 1,T420 Gand G429A were located in intron region.T288 Cand C400Twere missense mutations,T288 Cmutation leaded to serine(Ser)into proline(Pro),C400 Tmutation leaded to alanine(Ala)into valine(Val),and SNPs sites had some effects on mRNA secondary structure,protein secondary structure of NKX2-5gene.