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Functional & integrative genomics2024; 24(6); 195; doi: 10.1007/s10142-024-01482-0

Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.

Abstract: The unique horse and pony breeds of India are declining at an alarming rate. These horses have been integral to the Indian culture and customs for centuries and represent a valuable genetic resource. It is imperative to harness the potential of this equine genetic resource that urgently needs conservation. The study highlights the design and development of a high density SNP array, the Axiom_Ashwa to aid in the genetic analysis and conservation efforts for Indian horse and pony breeds. With 613,950 SNPs, this chip offers extensive genome coverage having an average inter-marker distance of 4 kb. The Axiom_Ashwa has been validated on a larger set of diverse indigenous samples as well as Thoroughbreds, demonstrating a high call rate of 99.4% and robustness for genotyping indigenous breeds. Linkage disequilibrium (LD) analysis showed higher average LD in Indian breeds compared to exotic breeds, suggesting a limited effective population size and recent bottlenecks. Phylogenetic and population stratification analyses using PCA and DAPC clearly distinguished horses, ponies and Thoroughbreds, confirming the efficacy of the Axiom_Ashwa chip. These findings underscore the urgent need for conservation efforts for Indian horse breeds, which have experienced significant drop in population size. The Axiom_Ashwa SNP chip offers advantages such as cost-effectiveness and high throughput, providing a more accurate genetic representation of Indian horses.
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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Publication Date: 2024-10-23 PubMed ID: 39441226PubMed Central: 4367434DOI: 10.1007/s10142-024-01482-0Google Scholar: Lookup
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Summary

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This research undertakes the development of a high-density SNP chip, coined Axiom_Ashwa, to assist in genetic analysis and conservation of indigenous horse and pony breeds in India. These unique breeds are dwindling at an alarming rate despite their cultural significance and genetic value.

Study Purpose and Approach

  • The purpose of the study was to create a platform for understanding the genetic makeup of the Indian horse and pony breeds and to aid in conservation efforts.
  • The approach used involved designing a high-density SNP (Single Nucleotide Polymorphisms) array known as the Axiom_Ashwa chip, which was used to profile these genetic markers within the breeds’ genomes.

SNP Chip Exhibit and Validation

  • This SNP chip contains 613,950 SNPs and delivers comprehensive genome coverage with an average inter-marker distance of 4kb.
  • Validation was achieved through trials on a diverse grouping of indigenous samples as well as Thoroughbreds.
  • The Axiom_Ashwa chip demonstrated a strong performance with a high call rate of 99.4% and proved robust for genotyping local breeds.

Linkage Disequilibrium Analysis

  • Analysis of linkage disequilibrium (LD), the non-random association of alleles at different loci, showed a higher average LD in Indian breeds compared to exotic breeds.
  • This indicates a limited effective population size and recent bottleneck events, where a significant percentage of the population has been wiped out.

Phylogenetic and Population Stratification Analyses

  • Phylogenetic and population stratification analyses were conducted using PCA (Principal Component Analysis) and DAPC (Discriminant Analysis of Principal Components).
  • The results clearly differentiated horses, ponies and Thoroughbreds, which confirm the efficacy of the Axiom_Ashwa chip in genetic analysis.

Significance of the Study

  • The study emphasizes the need for urgent conservation efforts for Indian horse breeds, considering their declining population size.
  • It introduces a cost-effective and high throughput Axiom_Ashwa SNP chip that provides a more accurate genetic representation of Indian horses.
  • This tool can be instrumental in guiding breeding programs aimed at preserving the genetic diversity of Indian horse and pony populations.

Cite This Article

APA
Ahlawat S, Niranjan SK, Arora R, Vijh RK, Kumar A, Sharma U, Raheja M, Popli K, Yadav S, Mehta SC. (2024). Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies. Funct Integr Genomics, 24(6), 195. https://doi.org/10.1007/s10142-024-01482-0

Publication

Functional & integrative genomics
ISSN: 1438-7948
NlmUniqueID: 100939343
Country: Germany
Language: English
Volume: 24
Issue: 6
Pages: 195

Researcher Affiliations

Ahlawat, Sonika
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Niranjan, Saket Kumar
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Arora, Reena
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India. rejagati@gmail.com.
Vijh, Ramesh Kumar
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Kumar, Amod
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Sharma, Upasna
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Raheja, Meenal
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Popli, Kanika
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Yadav, Seema
  • ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Mehta, Sharat Chandra
  • Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner, Rajasthan, 334 001, India.

MeSH Terms

  • Animals
  • Horses / genetics
  • Polymorphism, Single Nucleotide
  • Linkage Disequilibrium
  • Genomics / methods
  • India
  • Oligonucleotide Array Sequence Analysis
  • Phylogeny
  • Breeding

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Citations

This article has been cited 3 times.
  1. Sharma M, Singh A, Kumar V, Olla N, Arora R, Sharma R, Mohan NH, Ahlawat S. Advances in Equine Genomics: Decoding the Genetic Architecture of Morphology, Performance, Behavior, and Adaptation. Mol Biotechnol 2025 Dec 19;.
    doi: 10.1007/s12033-025-01544-zpubmed: 41417456google scholar: lookup
  2. Song X, Zhang J, Song Y, Raza SHA, Pant SD, Zan L, Zhang G, Wei D. Multi-Omics analysis unveils the regulatory mechanism of ZNF423 in bovine intramuscular fat formation. Funct Integr Genomics 2025 Oct 13;25(1):213.
    doi: 10.1007/s10142-025-01723-wpubmed: 41081960google scholar: lookup
  3. Ahlawat S, Sharma U, Niranjan SK, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK, Mehta SC. Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis. Mamm Genome 2025 Mar;36(1):118-128.
    doi: 10.1007/s00335-024-10089-6pubmed: 39630294google scholar: lookup
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