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Animal genetics2020; 51(5); 716-721; doi: 10.1111/age.12976

Exome analysis and functional classification of identified variants in racing Quarter Horses.

Abstract: The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted  < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.
© 2020 Stichting International Foundation for Animal Genetics.
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Publication Date: 2020-07-21 PubMed ID: 32696541DOI: 10.1111/age.12976Google Scholar: Lookup
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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.

This study’s goal was to identify and classify changes in the genetic codes of sprinting Quarter Horses, including both known and newly discovered variants. Two genes were particularly significant in relation to racing performance.

Overview

In this research, the authors aimed to identify and classify variations in the genetic codes of Quarter Horses specifically bred for speed (racing line). The variance was searched in the form of SNPs and indels by sequencing the exome regions (coding sections of the DNA).

Methods

  • The researchers began by working with a group of 349 racing Quarter Horses and determining each animal’s estimated genetic value in terms of maximum speed.
  • From this larger group, they then identified and separated the top 20 high-speed and 19 low-speed horses for a more detailed examination. This division was based on the derived genetic speed indices.
  • They then sequenced the parts of these horses’ DNA that create proteins (exons) and control regions (UTRs).

Results

  • The team discovered 105,182 variations in the DNA of the horses in the study. These variations occur in regions of the genome associated with gene expression (making proteins).
  • A subset of these, 72,166 variants, were already known, while 33,016 were newly discovered during the study and documented in a database for further use.
  • Only a small subset of these variants showed a significant correlation (p<0.05) with the high speed or low-speed groups of horses, suggesting possible influence on racing performance.
  • Particularly, two genes stood out as candidate genes potentially related to racing performance: SLC3A1 (located on chromosome 15, denoted as ECA15) and CCN6 (on chromosome 10, or ECA10).

Conclusions

  • The research identified a host of variants in the exome of Quarter Horses. Some of these variations seem to be related to the animals’ racing ability.
  • The findings provide a resource for future studies on the genetics of racing performance in horses. They also highlighted possible candidate genes SLC3A1 and CCN6 for further exploration in the context of racing.

Cite This Article

APA
Curi RA, Pereira GL, Alvarez MVN, Baldassini WA, Machado Neto OR, Chardulo LAL. (2020). Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim Genet, 51(5), 716-721. https://doi.org/10.1111/age.12976

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 51
Issue: 5
Pages: 716-721

Researcher Affiliations

Curi, R A
  • Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Pereira, G L
  • Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Alvarez, M V N
  • Department of Parasitology, Institute of Biosciences, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Baldassini, W A
  • Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Machado Neto, O R
  • Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Chardulo, L A L
  • Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.

MeSH Terms

  • Animals
  • Breeding
  • Exome / genetics
  • Horses / genetics
  • Horses / physiology
  • INDEL Mutation / genetics
  • Physical Conditioning, Animal
  • Polymorphism, Single Nucleotide

Grant Funding

  • 2014/20207-1 / Fundação de Amparo à Pesquisa do Estado de São Paulo

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