宁蒗高原鸡全基因组选择信号分析

doi:10.16431/j.cnki.1671-7236.2025.05.001

摘要/Abstract

摘要： 【目的】检测宁蒗高原鸡(Gallus gallus domesticus)的基因组选择信号，挖掘宁蒗高原鸡有价值的种质特性基因。【方法】本研究对57只宁蒗高原鸡和10只红原鸡(Gallus gallus)的全基因组重测序数据进行比对分析，利用GATK软件检测两个群体中常染色体的单核苷酸多态性(single nucleotide polymorphism，SNP)，使用Annovar软件对检测的SNP进行注释，使用主成分分析(principal components analysis,PCA)和系统发育树分析群体遗传结构，利用群体遗传分化指数(fixation index,Fst)和群体核苷酸多态性(pairwise nucleotide variation,θ_π)两种方法检测宁蒗高原鸡基因组上受选择的信号区域，取Top 5%的Fst和θ_π交集以确定基因组受选择区域，并对提取到的候选基因进行GO功能和KEGG通路富集分析。【结果】宁蒗高原鸡全基因组共注释到10 666 468个SNPs。PCA和系统发育树结果显示，宁蒗高原鸡和红原鸡被聚为两个不同的类群，两群体的遗传背景差异较大。对Fst和θ_π共同检测到的284个基因进行GO功能富集分析，结果显示，284个候选基因显著富集于354个GO条目，包括236个生物过程、78个分子功能、40个细胞组分；KEGG通路主要富集的有破骨细胞分化、心肌收缩、矿物质吸收、HIF-1信号通路等24条通路，这些通路主要与环境适应和生长发育相关。共筛选到13个功能基因：SEMA3C、MAPK1、EGFR、RYR2、CACNA2D3、CACNA2D1、PLCE1、FGFR2、ZFYVE9、PIK3C2G、MMP16、HESX1和COL6A1，主要与生长发育、海拔适应性和抗病性等相关。【结论】宁蒗高原鸡与红原鸡之间存在明显的群体分化，与红原鸡相比较，宁蒗高原鸡生长发育、环境适应和免疫性状相关基因受到一定程度的选择作用。研究结果为挖掘宁蒗高原鸡种质特性基因提供参考。

关键词: 宁蒗高原鸡; 全基因组重测序; 单核苷酸多态性; 选择信号

Abstract: 【Objective】 This study was aimed to identify selection signals in the genome of the Ninglang Plateau chickens (Gallus gallus domesticus) and to identify valuable germplasm trait genes.【Method】 The study was based on whole-genome resequencing data from 57 Ninglang Plateau chickens and 10 Gallus gallus.Single nucleotide polymorphism (SNP) in the autosomes were identified using GATK software,and these SNPs were annotated using Annovar software.Principal components analysis (PCA) and phylogenetic tree analysis were performed to explore the population genetic structure.Two methods-fixation index (Fst) and pairwise nucleotide variation (θ_π),were employed to detect the selection signal regions in the genome of Ninglang Plateau chickens.The intersection of the top 5% Fst and θ_π values was used to identify the selected genomic regions.The extracted candidate genes were subjected to GO functional and KEGG pathway enrichment analyses.【Result】 A total of 10 666 468 SNPs were annotated in the whole genome of Ninglang Plateau chickens.The results of PCA and phylogenetic tree analyses indicated that the Ninglang Plateau chickens and Gallus gallus were clustered into two distinct groups,showing significant differences in their genetic backgrounds.GO enrichment analysis of the 284 candidate genes detected by both Fst and θ_π showed significant enrichment in 354 GO terms,including 236 biological processes,78 molecular functions,and 40 cellular components.KEGG pathway analysis showed that the candidate genes were mainly enriched in 24 pathways,including osteoclast differentiation,cardiac muscle contraction,mineral absorption,and the HIF-1 signaling pathway,which were primarily associated with environmental adaptation,growth,and development.Thirteen functional genes,including SEMA3C,MAPK1,EGFR,RYR2,CACNA2D3,CACNA2D1,PLCE1,FGFR2,ZFYVE9,PIK3C2G,MMP16,HESX1,and COL6A1,were identified and were mainly related to growth and development,altitude adaptation and disease resistance.【Conclusion】 There was significant population differentiation between Ninglang Plateau chickens and Gallus gallus.Compared with Gallus gallus,the selected genes in Ninglang Plateau chickens were mainly associated with growth and development,environmental adaptation,and immune traits.These findings provided valuable insights into the genetic traits of Ninglang Plateau chickens.

Key words: Ninglang Plateau chickens; whole-genome resequencing; SNP; selection signals

中图分类号:

S831.2

徐扩卫, 冷堂健, 熊宝, 李金燕, 郭盘江, 吴培福, 陈粉粉, 周杰珑. 宁蒗高原鸡全基因组选择信号分析[J]. 中国畜牧兽医, 2025, 52(5): 1941-1954.

XU Kuowei, LENG Tangjian, XIONG Bao, LI Jinyan, GUO Panjiang, WU Peifu, CHEN Fenfen, ZHOU Jielong. Whole-genome Selection Signal Analysis of Ninglang Plateau Chickens[J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(5): 1941-1954.

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