基于全基因组SNPs标记对河南斗鸡遗传多样性及选择信号分析

Analysis of the genetic diversity and selection signals of Henan Game chicken using genome-wide SNPs

【目的】对河南斗鸡品种的遗传多样性与全基因组选择信号进行分析,挖掘河南斗鸡品种重要的种质特性基因。【方法】使用AffymetrixAxiom 600K高密度鸡基因分型芯片对来自9个品种的173只鸡的群体(包括20只河南斗鸡及153只商品鸡)进行基因分型;计算各个品种的期望杂合度、观测杂合度、次等位基因频率及核苷酸多样性评估地方鸡群体的遗传多样性;通过构建系统发育树、主成分分析、祖先成分分析方法研究品种的群体结构;利用斗鸡与商品鸡的成对遗传分化指数值进行选择信号分析。【结果】河南斗鸡及各商品鸡群体的观测杂合度为0.153~0.311,期望杂合度为0.158~0.315,次等位基因频率为0.111~0.234,核苷酸多样性为9.77×10^(-5)~1.56×10^(-4),且斗鸡的遗传多样性低于商品肉鸡品种,高于商品蛋鸡品种。系统发育树、主成分分析及祖先成分分析表明品种间有明显的群体分化。河南斗鸡与商品鸡群的主成分分析发现,河南斗鸡与商品肉鸡品种的遗传距离相对较近;将河南斗鸡和商品鸡群进行遗传选择信号后分析发现,河南斗鸡在神经,骨骼肌肉发育,免疫等性状经过高度选择。【结论】本研究从全基因组水平探究了河南斗鸡的遗传多样性和群体结构,筛选出候选基因,为河南斗鸡遗传资源保护和利用提供参考。

【Objective】The aim of this study is to analyze the genetic diversity and whole-genome selection signals of Henan Game chicken breeds,and to identify important genetic traits of these breeds.【Method】Affymetrix Axiom 600K high-density chicken genotyping chips were used to genotype 173 chickens from 9 breeds(including 20 Henan Game chickens and 153 commercial chickens).The expected heterozygosity,observed heterozygosity,minor allele frequency,and nucleotide diversity were calculated to evaluate the genetic diversity of the local chicken populations.The population structure of the breeds was studied using methods such as phylogenetic trees,principal component analysis,and ancestry component analysis.Selection signals were analyzed using pairwise F ST values between Game chicken and commercial chicken breeds.【Result】The results showed that the observed heterozygosity of each population ranged from 0.153 to 0.311,the expected heterozygosity ranged from 0.158 to 0.315,the minor allele frequency ranged from 0.111 to 0.234,and the nucleotide diversity ranged from 9.77×10^(-5) to 1.56×10^(-4).The genetic diversity of Game chicken is lower than that of commercial broiler chicken breeds but higher than that of commercial egg-laying chicken breeds.Phylogenetic trees,principal component analysis,and ancestry component analysis showed significant population differentiation among the breeds.The PCA analysis of Henan Game chickens and commercial chickens populations revealed that the genetic distance between Henan Game chickens and commercial broiler chickens breeds was relatively close.After analyzing the genetic selection signals between Henan Game chickens and commercial chicken populations,it was found that Henan Game chickens had undergone strong selection for traits such as neural development,skeletal muscle development,and immunity.【Conclusion】These results suggest that Henan Game chickens have a high degree of inbreeding and have undergone inbreeding events,which is consistent with their morphological characteristics,behavior,and domestication history.The findings of this study provide a reference for the genetic resource protection,development,utilization,and evaluation of Henan Game chickens,and promote the development,utilization,and protection of genetic resources.