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Home / Equine Research Bank / J Anim Breed Genet / Fine-scale estimation of inbreeding rates, runs of homozygos...
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie2020; 138(2); 161-173; doi: 10.1111/jbg.12508

Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed.

Abstract: With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (F ) = 0.16; pedigree-based (F ) = 0.008; and a method based on excess homozygosity (F ) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0-2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0-2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg /Mn dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.
© 2020 Wiley-VCH GmbH.
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Publication Date: 2020-09-19 PubMed ID: 32949478DOI: 10.1111/jbg.12508Google 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 research used new genomic technologies to examine inbreeding and genetic variation in the Mangalarga Marchador horse breed. The study aimed to measure inbreeding levels and identify genome-wide patterns of homozygosity and heterozygosity, providing more detailed information than traditional methods.

Study Methodology

  • The study genotyped 192 Mangalarga Marchador horses using high-density SNP panels, specifically the Axiom® Equine Genotyping Array-670k SNP developed by Thermo Fisher.
  • The purpose was to estimate inbreeding levels using different coefficients, and to characterize homozygous and heterozygous runs in the horse population.

Findings on Inbreeding

  • The analysis of the genomic data provided different inbreeding estimates. Genomic coefficient-based inbreeding was estimated at 0.16, while pedigree-based inbreeding was estimated to be much lower, at 0.008.
  • An alternate method of estimating inbreeding based on an excess of homozygosity yielded an inbreeding estimate of 0.010.
  • The correlations between the different inbreeding coefficients were rated low to moderate, with some comparisons yielding virtually no correlation.

Analysis of Homozygosity and Heterozygosity

  • A total of 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized across the 31 horse autosomal chromosomes.
  • The category with the majority of homozygosity runs was identified within 0-2 Mbps, making up about 92.78% of the observations. However, in the heterozygosity analysis, only observations in the 0-2 Mbps category were represented.

Highlighted Genomic Variability

  • Among the regions with higher genetic variability, chromosome 11 stood out. This suggests that recent selection pressure and important changes in the development and performance of the Mangalarga Marchador breed may have contributed to this variability.
  • In the regions showing higher heterozygosity (ROHet), three genes were discovered with known functions. These are the tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg/Mn dependent 1E (PPM1E), and carbonic anhydrase 10 (CA10) genes.
  • From their findings, researchers inferred moderate inbreeding which might be due to breed formation, but they found virtually no recent inbreeding.

These findings offer significant insights into the genetic health and diversity of the Mangalarga Marchador horse breed and demonstrate the value of high-density SNP panels for in-depth genomic research.

Cite This Article

APA
Bizarria Dos Santos W, Pimenta Schettini G, Fonseca MG, Pereira GL, Loyola Chardulo LA, Rodrigues Machado Neto O, Baldassini WA, Nunes de Oliveira H, Abdallah Curi R. (2020). Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed. J Anim Breed Genet, 138(2), 161-173. https://doi.org/10.1111/jbg.12508

Publication

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
ISSN: 1439-0388
NlmUniqueID: 100955807
Country: Germany
Language: English
Volume: 138
Issue: 2
Pages: 161-173

Researcher Affiliations

Bizarria Dos Santos, Wellington
  • School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal, Brazil.
Pimenta Schettini, Gustavo
  • School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal, Brazil.
Fonseca, Mayara Gonçalves
  • Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil.
Pereira, Guilherme Luis
  • School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil.
Loyola Chardulo, Luis Artur
  • School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil.
Rodrigues Machado Neto, Otávio
  • School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil.
Baldassini, Welder Angelo
  • School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil.
Nunes de Oliveira, Henrique
  • School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (Unesp), Jaboticabal, Brazil.
Abdallah Curi, Rogério
  • School of Veterinary Medicine and Animal Science (FMVZ), São Paulo State University (Unesp), Botucatu, Brazil.

MeSH Terms

  • Animals
  • Genome
  • Genotype
  • Homozygote
  • Horses
  • Inbreeding
  • Polymorphism, Single Nucleotide

Grant Funding

  • 001 / Coordenau00e7u00e3o de Aperfeiu00e7oamento de Pessoal de Nu00edvel Superior
  • 2016/19081-9 / Fundau00e7u00e3o de Amparo u00e0 Pesquisa do Estado de Su00e3o Paulo

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Citations

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