Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd.
Abstract: Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and genomic relatedness and inbreeding measures in a herd of 36 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70 platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum number of markers sufficient for genomic inbreeding calculations. Pedigree inbreeding values were moderately correlated with genomic inbreeding values (r = 0.406), whereas genomic relationships and pedigree relationships have a high correlation (r = 0.77). Although first degree relationships were successfully reconstructed, more distant relationships were difficult to resolve. Multi-dimensional scaling and clustering analysis agreed with within-herd pedigree information. In comparing the herd to a reference sample of United States, Polish, and Egyptian Arabian horses, the herd's historically recorded Egyptian lineage was successfully recovered. We conclude that genomic estimates of inbreeding and relationships are superior to their pedigree counterparts. They can be thus utilized in conservation of valuable lines of livestock, and in breeds at risk for loss of genomic diversity. We also postulate a minimum of 2000 markers in linkage equilibrium to be used for inbreeding estimation.
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Publication Date: 2017-04-27 PubMed ID: 28444202DOI: 10.1093/jhered/esx025Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research project focuses on the comparison of pedigree and genomic methods for estimating inbreeding and population structure in a herd of Arabian horses, with the genomic method proving more reliable. The study also explores the minimum number of markers necessary for genomic inbreeding calculations.
Methods Utilized
- The researchers used genome-wide SNPs (Single Nucleotide Polymorphisms) as a quantitative tool to help in lineage assignments and calculations of genomic measures of relatedness. These are variations at a single position in a DNA sequence among individuals, which can help track inheritance patterns and reveal genetic diversity.
- In this research, a herd of 36 pedigreed Egyptian Arabian horses was genotyped using the Equine SNP70 platform by Geneseek, Inc.
Comparisons Made
- The study made comparisons between pedigree and genomic relatedness and inbreeding measures in the horse herd. Pedigree inbreeding values showed a moderate correlation with genomic inbreeding values, indicating that the genetic data provides a more accurate picture of relatedness and inbreeding than traditional pedigree data.
- The research also compared the horse herd to a reference sample of Arabian horses from the United States, Poland, and Egypt. The genomic data successfully recovered the herd’s historically recorded Egyptian lineage.
Findings
- The study concluded that genomic estimates of inbreeding and relationships are superior to their pedigree counterparts. This confirmation can greatly contribute to the conservation of livestock genetic diversity, especially in breeds at risk of genomic diversity loss.
- The research also proposed a minimum of 2,000 markers in linkage equilibrium—meaning they are inherited independently—for use in genomic inbreeding calculation.
Impact on Breeding Decisions
- Inaccurate pedigrees can lead breeders to make misguided breeding decisions, them mistakenly identifying false lineages or breed memberships. The use of genomic estimates, therefore, can be instrumental in achieving more accurate breeding decisions, which ultimately aids in limiting inbreeding.
- The genomic method’s efficiency in distinguishing first-degree relationships and tracking lineage supports its utilization over traditional pedigree-based methods, particularly when the objective is to limit inbreeding in selected livestock.
Cite This Article
APA
Al Abri MA, König von Borstel U, Strecker V, Brooks SA.
(2017).
Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd.
J Hered, 108(4), 361-368.
https://doi.org/10.1093/jhered/esx025 Publication
Researcher Affiliations
- From the Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman (Al Abri); Department of Animal Breeding and Genetics, University of Göttingen. Göttingen, Germany(von Borstel and Strecker); and Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks).
- From the Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman (Al Abri); Department of Animal Breeding and Genetics, University of Göttingen. Göttingen, Germany(von Borstel and Strecker); and Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks).
- From the Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman (Al Abri); Department of Animal Breeding and Genetics, University of Göttingen. Göttingen, Germany(von Borstel and Strecker); and Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks).
- From the Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman (Al Abri); Department of Animal Breeding and Genetics, University of Göttingen. Göttingen, Germany(von Borstel and Strecker); and Department of Animal Sciences, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks).
MeSH Terms
- Animals
- Breeding
- Cluster Analysis
- Female
- Genetics, Population
- Genomics
- Genotype
- Homozygote
- Horses / genetics
- Inbreeding
- Male
- Pedigree
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
Citations
This article has been cited 8 times.- Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022 Dec 2;13(12).
- Patterson Rosa L, Mallicote MF, Long MT, Brooks SA. Metabogenomics reveals four candidate regions involved in the pathophysiology of Equine Metabolic Syndrome. Mol Cell Probes 2020 Oct;53:101620.
- Cosgrove EJ, Sadeghi R, Schlamp F, Holl HM, Moradi-Shahrbabak M, Miraei-Ashtiani SR, Abdalla S, Shykind B, Troedsson M, Stefaniuk-Szmukier M, Prabhu A, Bucca S, Bugno-Poniewierska M, Wallner B, Malek J, Miller DC, Clark AG, Antczak DF, Brooks SA. Genome Diversity and the Origin of the Arabian Horse. Sci Rep 2020 Jun 16;10(1):9702.
- McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population. Sci Rep 2020 Jan 16;10(1):466.
- Kim D, Lee S, Oyungerel B, Cho G. Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds. Vet Sci 2025 Sep 15;12(9).
- Santiago E, Köpke C, Caballero A. Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods. Nat Commun 2025 Jul 1;16(1):6054.
- Al-Khaldi KO, Al-Ruzaiqi KH, Babji AS, Lim SJ, Sadiq MB, Yimer N. Safety and efficacy of oral edible bird's nest supplementation: Anti-inflammatory and immunomodulatory benefits for Arabian race stallions during exercise. Vet World 2025 Jan;18(1):178-188.
- Medeiros BB, Barcelos KMC, Andrade MO, Cristina da Paz Carvalho M, Miranda VR, de Oliveira Maia K, Reinhardt S, Patterson Rosa L. The Weight of Genetic Drift: A Pedigree-Based Evaluation of the Breton Horse Population in Brazil. Vet Med Int 2024;2024:4714077.
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