Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits
Understanding the genetic characteristics of indigenous goat breeds is vital for their conservation and breeding. Haimen goats, native to China’s Yangtze River Delta, possess distinctive traits such as white hair, moderate growth rate, high-quality meat, and small body size. However, knowledge regar...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/14/1/40 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832589028927471616 |
|---|---|
| author | Zhen Zhang Jiafeng Lu Yifei Wang Zhipeng Liu Dongxu Li Kaiping Deng Guomin Zhang Bingru Zhao Peihua You Yixuan Fan Feng Wang Ziyu Wang |
| author_facet | Zhen Zhang Jiafeng Lu Yifei Wang Zhipeng Liu Dongxu Li Kaiping Deng Guomin Zhang Bingru Zhao Peihua You Yixuan Fan Feng Wang Ziyu Wang |
| author_sort | Zhen Zhang |
| collection | DOAJ |
| description | Understanding the genetic characteristics of indigenous goat breeds is vital for their conservation and breeding. Haimen goats, native to China’s Yangtze River Delta, possess distinctive traits such as white hair, moderate growth rate, high-quality meat, and small body size. However, knowledge regarding the genetic structure and germplasm characteristics of Haimen goats remains limited. In this study, we performed 20× whole-genome resequencing of 90 goats (60 Haimen goats and 30 Boer goats) to identify single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) associated with growth traits. Here, we analyzed population genetic structure and genome-wide selection signatures between the Haimen and Boer goats based on whole-genome resequencing data. The principal component analysis (PCA) and neighbor-joining (N-J) tree results demonstrated significant genetic differentiation between the Haimen and Boer goats. The nucleotide diversity (Pi) and linkage disequilibrium (LD) decay results indicated higher genomic diversity in the Haimen goat population. Furthermore, selective sweep analysis identified candidate genes associated with growth traits. These genes exhibited strong selection signatures and were related to body size (DONSON, BMPR1B, and EPHA5), muscle development (GART, VGLL3, MYH15), and fat metabolism (ADAMTS5, LRP6, XDH, CPT1A, and GPD1). We also identified growth-related candidate genes (NCOR1, DPP6, NOTCH2, and FGGY) specific to Haimen goats. Among these genes, pancreatic lipase-related protein 1 (PNLIPRP1) emerged as the primary candidate gene influencing growth phenotypes. Further analysis revealed that a 26 bp Indel in PNLIPRP1 increased its gene expression, suggesting that this Indel could serve as a molecular marker for early marker-assisted selection, potentially enhancing early growth in goats. These findings provide valuable molecular markers and candidate genes for improving growth traits in Haimen goat breeding. |
| format | Article |
| id | doaj-art-1ed547a92470400e974825c3cac28b0b |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj-art-1ed547a92470400e974825c3cac28b0b2025-01-24T13:23:24ZengMDPI AGBiology2079-77372025-01-011414010.3390/biology14010040Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth TraitsZhen Zhang0Jiafeng Lu1Yifei Wang2Zhipeng Liu3Dongxu Li4Kaiping Deng5Guomin Zhang6Bingru Zhao7Peihua You8Yixuan Fan9Feng Wang10Ziyu Wang11Sanya Research Institute, Nanjing Agricultural University, Sanya 572025, ChinaJiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaSanya Research Institute, Nanjing Agricultural University, Sanya 572025, ChinaJiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, ChinaPortal Agri-Industries Co., Ltd., Xingdian Street, Pikou District, Nanjing 210095, ChinaJiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, ChinaSanya Research Institute, Nanjing Agricultural University, Sanya 572025, ChinaSanya Research Institute, Nanjing Agricultural University, Sanya 572025, ChinaUnderstanding the genetic characteristics of indigenous goat breeds is vital for their conservation and breeding. Haimen goats, native to China’s Yangtze River Delta, possess distinctive traits such as white hair, moderate growth rate, high-quality meat, and small body size. However, knowledge regarding the genetic structure and germplasm characteristics of Haimen goats remains limited. In this study, we performed 20× whole-genome resequencing of 90 goats (60 Haimen goats and 30 Boer goats) to identify single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) associated with growth traits. Here, we analyzed population genetic structure and genome-wide selection signatures between the Haimen and Boer goats based on whole-genome resequencing data. The principal component analysis (PCA) and neighbor-joining (N-J) tree results demonstrated significant genetic differentiation between the Haimen and Boer goats. The nucleotide diversity (Pi) and linkage disequilibrium (LD) decay results indicated higher genomic diversity in the Haimen goat population. Furthermore, selective sweep analysis identified candidate genes associated with growth traits. These genes exhibited strong selection signatures and were related to body size (DONSON, BMPR1B, and EPHA5), muscle development (GART, VGLL3, MYH15), and fat metabolism (ADAMTS5, LRP6, XDH, CPT1A, and GPD1). We also identified growth-related candidate genes (NCOR1, DPP6, NOTCH2, and FGGY) specific to Haimen goats. Among these genes, pancreatic lipase-related protein 1 (PNLIPRP1) emerged as the primary candidate gene influencing growth phenotypes. Further analysis revealed that a 26 bp Indel in PNLIPRP1 increased its gene expression, suggesting that this Indel could serve as a molecular marker for early marker-assisted selection, potentially enhancing early growth in goats. These findings provide valuable molecular markers and candidate genes for improving growth traits in Haimen goat breeding.https://www.mdpi.com/2079-7737/14/1/40whole-genome sequencinggoatgrowth traitsPNLIPRP1Indel |
| spellingShingle | Zhen Zhang Jiafeng Lu Yifei Wang Zhipeng Liu Dongxu Li Kaiping Deng Guomin Zhang Bingru Zhao Peihua You Yixuan Fan Feng Wang Ziyu Wang Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits Biology whole-genome sequencing goat growth traits PNLIPRP1 Indel |
| title | Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits |
| title_full | Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits |
| title_fullStr | Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits |
| title_full_unstemmed | Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits |
| title_short | Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits |
| title_sort | genome wide scans for selection signatures in haimen goats reveal candidate genes associated with growth traits |
| topic | whole-genome sequencing goat growth traits PNLIPRP1 Indel |
| url | https://www.mdpi.com/2079-7737/14/1/40 |
| work_keys_str_mv | AT zhenzhang genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT jiafenglu genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT yifeiwang genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT zhipengliu genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT dongxuli genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT kaipingdeng genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT guominzhang genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT bingruzhao genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT peihuayou genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT yixuanfan genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT fengwang genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits AT ziyuwang genomewidescansforselectionsignaturesinhaimengoatsrevealcandidategenesassociatedwithgrowthtraits |