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Home / Equine Research Bank / Genes (Basel) / Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Div...
Genes2023; 14(8); doi: 10.3390/genes14081623

Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds.

Abstract: The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP diversity and runs of homozygosity revealing the selection signature of breeds are still warranted. In our study, the identification of genes that play a vital role in muscle development is performed through SNP detection via the whole-genome sequencing approach. A total of 96 samples, categorized under seven breeds, and 620,721 SNPs were considered to ascertain the ROH patterns amongst all the seven breeds. Over 5444 ROH islands were mined, and the maximum number of ROHs was found to be present in Zanskari, while Thoroughbred was confined to the lowest number of ROHs. Gene enrichment of these ROH islands produced 6757 functional genes, with AGPAT1, CLEC4, and CFAP20 as important gene families. However, QTL annotation revealed that the maximum QTLs were associated with Wither's height trait ontology that falls under the growth trait in all seven breeds. An Equine SNP marker database (EqSNPDb) was developed to catalogue ROHs for all these equine breeds for the flexible and easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs. Such a study can reveal breed divergence in different climatic and ecological conditions.
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Publication Date: 2023-08-14 PubMed ID: 37628674PubMed Central: PMC10454598DOI: 10.3390/genes14081623Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article describes a genomic study that investigates the genetic diversity and selection signatures of seven key horse breeds. Using single-nucleotide polymorphism (SNP) detection from a whole-genome sequencing approach, important breed-specific genes relating to muscle development were identified, and an equine SNP marker database was created for cataloguing and retrieval of genomic information.

Objective and Methodology

  • The study aimed to understand the genetic diversity, phylogenetic relationship, and selection signatures of seven Indian horse breeds: Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred.
  • A total of 96 samples from these breeds were sequenced, unveiling 620,721 SNPs. The analysis focused on looking at runs of homozygosity (ROH) – stretching sequences of identical genomic blocks that shed light on the inheritance and selection patterns in the genomes.

Key Findings

  • Zanskari breed has the highest number of ROHs, while Thoroughbred has the lowest. This indicates a difference in the degree of selection and inbreeding these breeds have gone through, with Zanskari likely having a higher degree of selection or inbreeding.
  • A total of 5444 ROH islands were discovered across breeds, leading to the identification of 6757 functional genes. Among these genes, AGPAT1, CLEC4, and CFAP20 were noted as important gene families. These genes significantly contribute to the unique characteristics and capabilities of these horse breeds.
  • Wither’s height trait ontology, which falls under the growth trait, was revealed to be associated with the maximum Quantitative Trait Loci (QTLs) in all seven breeds. Quantitative Trait Loci are regions of the genome associated with particular phenotypic traits.

Equine SNP Marker Database (EqSNPDb)

  • The study also developed an Equine SNP marker database that catalogs ROHs for all the studied breeds. It allows easy chromosome-wise retrieval of ROH along with the genotype details of all the SNPs.
  • This tool will be instrumental in future studies of horse genetics, potentially aiding in breed development, conservation, and preservation of equine genetic diversity.

Conclusions and Implications

  • The study provides a deepened understanding of the genetic diversity and selection signatures across seven breed types of horses.
  • The unique features and capabilities of these breeds are primarily governed by their genetic composition and selective breeding, which has resulted in variations in terms of physical strength, endurance, and adaptability to agroclimatic conditions.
  • The findings could lead to improvements in breed conservation efforts, and could contribute to more precise genetic selection in breeding for desired traits in horses.

Cite This Article

APA
Bhardwaj A, Tandon G, Pal Y, Sharma NK, Nayan V, Soni S, Iquebal MA, Jaiswal S, Legha RA, Talluri TR, Bhattacharya TK, Kumar D, Rai A, Tripathi BN. (2023). Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds. Genes (Basel), 14(8). https://doi.org/10.3390/genes14081623

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 14
Issue: 8

Researcher Affiliations

Bhardwaj, Anuradha
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Tandon, Gitanjali
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Pal, Yash
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Sharma, Nitesh Kumar
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Nayan, Varij
  • ICAR-Central Institute for Research on Buffaloes, Hisar 125001, India.
Soni, Sonali
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Iquebal, Mir Asif
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Jaiswal, Sarika
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Legha, Ram Avatar
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Talluri, Thirumala Rao
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Bhattacharya, Tarun Kumar
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
Kumar, Dinesh
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Rai, Anil
  • Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India.
Tripathi, B N
  • ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India.
  • Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India.

MeSH Terms

  • Animals
  • Horses / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Phylogeny
  • Homozygote
  • Genotype
  • Genomics

Conflict of Interest Statement

The authors declare that there are no conflict of interest.

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