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. 2024 Aug 21:15:1432105.
doi: 10.3389/fgene.2024.1432105. eCollection 2024.

Genetic structure and selective sweeps in Kirghiz sheep using SNP50K bead chip

Xiaopeng Li #  1   2 , Lijun Zhu #  1   2 , Cheng-Long Zhang  1   2 , Xueyan Wang  1   2 , Yanhao Li  1   2 , Wen Zhou  1   2 , Zhipeng Han  1   2 , Ruizhi Yang  1   2 , Yuwei Peng  1   2 , Yahui Han  1   2 , Lulu Zhang  1   2 , Langman Zheng  1   2 , Shudong Liu  1   2
Affiliations

Genetic structure and selective sweeps in Kirghiz sheep using SNP50K bead chip

Xiaopeng Li et al. Front Genet. .

Abstract

The objective of this study is to analyze environmental genetic selection signals in large-scale sheep populations with conflicting environmental adaptations, aiming to identify and isolate genes associated with environmental adaptations in sheep populations. Kirghiz sheep, which inhabit high-altitude environments year-round, demonstrate the ability to adapt to extreme conditions. In this study, 42 Kirghiz sheep, 24 Tien-Shan in Kyrgyzstan sheep, 189 Qira black sheep, and 160 Chinese Merino sheep were genotyped using Illumina Ovine SNP50K chip. Regions exhibiting a selection signal threshold of 5%, as well as PI analysis and haplotype statistical scanning gene data were annotated, and intersecting genes were identified as candidate genes. Through Fst and haplotype statistical analysis revealed the key gene PDGFD and its vicinity's impact on fat deposition in sheep tails. Additionally, Fst and PI analysis uncovered genes related to high-altitude adaptation as well as those linked to animal growth and reproduction.Further GO and KEGG enrichment pathway analyses unveiled pathways associated with high-altitude adaptation such as negative regulation of peptidyl-tyrosine phosphorylation and xenobiotic metabolism processes.This investigation into the adaptability of Kirghiz sheep provides theoretical support and practical guidance for the conservation and genetic enhancement of Kirghiz sheep germplasm resources.

Keywords: GO enrichment analysis; Kirghiz sheep; genetic patterns; selection signature; selective sweeps.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
(A) NJ evolutionary tree. (B) Principal Component Analysis of Four Sheep Breeds (X-axis represents PC1, Y-axis represents PC2, Z-axis represents PC3. (C) sNMF Ancestral Proportion Estimation (minimized CV_error when K = 5).
FIGURE 2
FIGURE 2
(A) Fst results of KE and TNSH, the red line in the figure represents the 0.05 threshold (B) Haplotype analysis of the region near PDGFD (chr15:3800010-4200000) based on the genehap R package. (C, D) Phenotypic correlation analyses of the fat tail of Kirghiz sheep with the thin tail of TNSH).
FIGURE 3
FIGURE 3
(A) Plot of Fst and PI results for KE vs. QR and CM,with different colored dots representing whether the locus is under selection, using a significance threshold of 0.05. (B) Intersection of genes annotated from nucleotide diversity in KE and the top 5% Fst loci from KE. QR and CM comparisons).
FIGURE 4
FIGURE 4
significance threshold of the top twenty key genes for the interaction of enrichment pathway.
See this image and copyright information in PMC

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