鸡Lpin1基因3′-UTR遗传变异及其对miRNA结合位点的潜在效应

Genetic Variation Analysis of 3′-UTR Region of Chicken Lpin1 Gene and the Potential Effect on miRNA Binding Sites

【目的】研究鸡Lpin1基因3′-UTR遗传变异/单倍型及其在品种间的分布,并预测这些变异对miRNA结合位点的潜在效应。【方法】根据鸡Lpin1基因组序列(GenBank登录号:NC_006090)设计一对特异性引物,采用PCR直接测序结合克隆测序的方法,进行鸡Lpin1基因3′-UTR及其邻近外显子在品种间的遗传变异/单倍型分析【。结果】①从6个品种中发现了8个变异位点,包含两个插入/缺失变异。这些变异均位于鸡Lpin1基因的3′-UTR,3′-UTR的变异频率为17SNPs/kb;②在鸡Lpin1基因3′-UTR区域,从固始鸡、卢氏绿壳蛋鸡中分别检测到7个变异位点,未检测到河南斗鸡品种内的变异;③用次要等位基因频率≥5%的6个变异位点(g.11A>T,g.77C>G,g.108_109delinsG,g.110_111delinsG,g.270A>G和g.348G>T)进行单倍型的构建和分析,从6个品种鸡中共检测到6种单倍型,其中P1和P4单倍型是群体的优势单倍型,频率均大于30%,河南斗鸡仅包含一种单倍型;④g.77C>G变异可引起多个miRNA结合位点的增加/丢失。【结论】鸡Lpin1基因3′-UTR具有丰富的变异,3′-UTR变异位点/单倍型在品种间的分布存在明显的差异。

【Objective】 This experiment was conducted to study the genetic variation/haplotype of the 3′-UTR of chicken Lpin1 gene and their distributions among breeds,and their potential effects on miRNA binding sites were predicted.【Method】 According to the chicken Lpin1 genome sequence（GenBank accession： NC_006090）,a pair of specific primers was designed to conduct the genetic variation/haplotype analysis in the 3′-UTR of chicken Lpin1 gene in different breeds of chickens through direct PCR sequence combined with clone sequencing.【Result】Eight variable sites were uncovered,these variation sites were all located at the 3′-UTR of chicken Lpin1 gene.Analysis showed the no variation sites were detected from Henan Game chicken in this region,however,six variation sites were detected from Gushi and Lushi chickens.Six variable sites（g.11〉A T,g.77C〉 G,g.108_109delinsG,g.110_111delinsG,g.270A〉G and g.348G〉T） with minor allele frequency ≥5% were selected for haplotype reconstruction,and six haplotypes were detected from six chicken breeds.P1 and P4 were the predominant haplotypes with frequencies 〉30%,respectively,only one haplotype was detected from Henan game chicken.Software prediction showed that g.77CG variant could cause the increase/loss of several miRNA binding sites.【Conclusion】 The results showed that the 3′-UTR of chicken Lpin1 gene was highly polymorphic,the distribution of variable sites and haplotypes in different breeds of chickens had clear difference.