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

Abstract

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

CLC Number:

S831.2

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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Whole-genome Selection Signal Analysis of Ninglang Plateau Chickens

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