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Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie2023; doi: 10.1111/jbg.12812

Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line.

Abstract: With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (F ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, and to map selection signatures in relevant chromosomal regions in the Quarter Horse racing line. A total of 336 animals registered with the Brazilian Association of Quarter Horse Breeders (ABQM) were genotyped. One hundred and twelve animals were genotyped using the Equine SNP50 BeadChip (Illumina, USA), with 54,602 single nucleotide polymorphisms (SNPs; 54K). The remaining 224 samples were genotyped using the Equine SNP70 BeadChip (Illumina, USA) with 65,157 SNPs (65K). To ensure data quality, we excluded animals with a call rate below 0.9. We also excluded SNPs located on non-autosomal chromosomes, as well as those with a call rate below 0.9 or a p-value below 1 × 10 for Hardy-Weinberg equilibrium. The results indicate moderate to high genomic inbreeding, with 46,594 ROH and 16,101 ROHet detected. In total, 30 and 14 candidate genes overlap with ROH and ROHet regions, respectively. The ROH islands showed genes linked to crucial biological processes, such as cell differentiation (CTBP1, WNT5B, and TMEM120B), regulation of glucose metabolic process (MAEA and NKX1-1), heme transport (PGRMC2), and negative regulation of calcium ion import (VDAC1). In ROHet, the islands showed genes related to respiratory capacity (OR7D19, OR7D4G, OR7D4E, and OR7D4J) and muscle repair (EGFR and BCL9). These findings could aid in selecting animals with greater regenerative capacity and developing treatments for muscle disorders in the QH breed. This study serves as a foundation for future research on equine breeds. It can contribute to developing reproductive strategies in animal breeding programs to improve and preserve the Quarter Horse breed.
© 2023 John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.
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Publication Date: 2023-06-06 PubMed ID: 37282810DOI: 10.1111/jbg.12812Google 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 explores the genetic attributes of the Quarter Horse racing line using genomics to work towards improving and preserving the breed. Researchers conducted a detailed scan of the genome of these horses to estimate genomic inbreeding coefficients, identify runs of homozygosity and heterozygosity, and map selection signatures on chromosomes.

Overview of the Study

  • The main goal of this research was to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (ROH), identify and outline the nature (length and distribution) of ROH and heterozygosity (ROHet), and map selection patterns in the Quarter Horse racing line’s relevant chromosomal regions.
  • The researchers analyzed the genomes of 336 animals registered with the Brazilian Association of Quarter Horse Breeders.
  • Two types of SNP BeadChips (Genotyping panels) were used, one with 54,602 single nucleotide polymorphisms (SNPs) for 112 animals and another with 65,157 SNPs for the remaining 224 samples. This was done to extract high quality, comprehensive genomic data.

Quality Assurance

  • Only animals with a high-quality call rate (above 0.9) were included in the study.
  • SNPs located on non-autosomal chromosomes were excluded, along with those with a low call rate or unsatisfactory Hardy-Weinberg equilibrium p-value.

Findings

  • The study identified a moderate to high level of genomic inbreeding, along with 46,594 runs of homozygosity and 16,101 runs of heterozygosity.
  • In total, 30 and 14 candidate genes overlapped with the respective ROH and ROHet regions.
  • The ROH islands demonstrated genes linked to crucial biological processes such as glucose metabolic regulation, cell differentiation, heme transport, and the negative regulation of calcium ion import.
  • The ROHet islands showed genes linked to respiratory capacity and muscle repair, indicating potential areas of focus for improving regenerative capacity in these horses and developing treatments for muscle disorders in the Quarter Horse breed.

Implications

  • This study has implications for the development of reproductive strategies in animal breeding programs aimed at improving and preserving the Quarter Horse breed.
  • It lays a foundation for more comprehensive future research on equine breeds and their genetics.

Cite This Article

APA
Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA. (2023). Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. J Anim Breed Genet. https://doi.org/10.1111/jbg.12812

Publication

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
ISSN: 1439-0388
NlmUniqueID: 100955807
Country: Germany
Language: English

Researcher Affiliations

Santos, Wellington B
  • Department of Animal Science, São Paulo State University, Jaboticabal, Brazil.
Pereira, Camila B
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.
Maiorano, Amanda M
  • Department of Animal Science, Federal University of Uberlândia, Uberlândia, Brazil.
Arce, Cherlynn D Silva
  • Department of Animal Science, São Paulo State University, Jaboticabal, Brazil.
Baldassini, Welder A
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.
Pereira, Guilherme L
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.
Chardulo, Luis Artur L
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.
Neto, Otávio R M
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.
Oliveira, Henrique N
  • Department of Animal Science, São Paulo State University, Jaboticabal, Brazil.
Curi, Rogério A
  • Department of Breeding and Animal Nutrition, São Paulo State University, Botucatu, Brazil.

Grant Funding

  • 2014/20207-1 / Fundau00e7u00e3o de Amparo u00e0 Pesquisa do Estado de Su00e3o Paulo - FAPESP
  • Conselho Nacional de Desenvolvimento Cientu00edfico e Tecnolu00f3gico (CNPq)

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