河南农业大学学报2024，Vol.58Issue(3)：394-402,9.DOI:10.16445/j.cnki.1000-2340.20240328.002
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
摘要
Abstract
[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 FST 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.关键词
河南斗鸡/遗传多样性/群体结构/选择信号/全基因组/单核苷酸多态性Key words
Henan Game chicken/genetic diversity/population structure/selection signals/genome-wide/single nucleotide polymorphism(SNP)分类
农业科技引用本文复制引用
胡晓玉,肖成朋,高超群,张晨曦,史浚来,贾鑫涛,王克君,李文婷..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[J].河南农业大学学报,2024,58(3):394-402,9.基金项目
神农种业实验室一流课题(SN01-2022-05) （SN01-2022-05）
河南省优秀青年科学基金项目(232300421034) （232300421034）
