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Using Whole-Genome Sequencing Data Reveals the Population Structure and Selection Signatures for Reproduction Traits
Keyao Wang1, Qianjun Li1, Zhigang Niu2
1State Key Laboratory of Animal Biotech Breeding/National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Animals : an Open Access Journal From MDPI
|December 11, 2025
Summary
This study reveals the genetic population structure and reproductive traits of Duolang sheep using whole-genome sequencing. Key genes influencing domestication, growth, and reproduction were identified, providing insights into their adaptive traits.
Area of Science:
- Animal Genomics
- Population Genetics
- Reproductive Biology
Background:
- Duolang sheep, a Xinjiang indigenous breed, are valued for prolificacy and early sexual maturity.
- Limited research exists on their population structure and trait inheritance.
Purpose of the Study:
- To analyze the genetic population structure of Duolang sheep.
- To identify genes associated with reproductive traits in this breed.
- To provide a comprehensive genomic landscape for Duolang sheep.
Main Methods:
- Whole-genome resequencing of 60 Duolang sheep.
- Single Nucleotide Polymorphism (SNP) calling and quality control.
- Population structure analysis using Principal Component Analysis (PCA) and linkage disequilibrium (LD) decay.
- Selection signature detection using Tajima's D, iHS, XP-CLR, FST, and XP-EHH.
- Functional enrichment analysis of candidate genes.
Main Results:
- Over 31 million SNPs were identified, with 4.4 million high-quality SNPs retained.
- PCA revealed 14 kinship outliers, and LD decay indicated low selection pressure.
- Multiple methods identified numerous candidate SNPs under selection, with significant overlap.
- Functional analysis highlighted genes related to domestication, growth, and reproduction (e.g., ESRRA, OXT, FSHR).
Conclusions:
- This study presents the first comprehensive genomic landscape of Duolang sheep.
- Genetic signatures of adaptive traits, particularly in reproduction, were elucidated.
- Findings provide a foundation for future genetic improvement and conservation efforts for Duolang sheep.
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