The American Quarter Horse: population structure and relationship to the thoroughbred.
Abstract: A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations.
Publication Date: PubMed ID: 24293614
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
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.
The study explores how selective breeding has affected the genetic diversity and structure of the American Quarter Horse (QH) breed across six performance groups. The study also observes the impact of Thoroughbred ancestry on QH diversity. It finds significant population structure differences among all QH performance groups, and highlights potential issues with inbreeding within performance groups, owing to the increased relatedness linked to the influence of popular sires.
Methodology
- The research employed pedigree analysis and genome-wide SNP (single nucleotide polymorphisms) data from horses in six performance groups: halter, western pleasure, reining, working cow, cutting, and racing.
- Genotype data (36,037 SNP) derived from 36 Thoroughbreds was analyzed in comparison with the data accumulated from 132 performing QHs. This approach was designed to evaluate the impact of Thoroughbred ancestry on QH genetic diversity.
Findings
- The study discovered significant population structure variations among all the QH performance groups studied. The only exception was the similarity between the cutting and working cow horses.
- The study observed the greatest divergence between the cutting and racing QHs, wherein the latter had a considerable influence of Thoroughbred ancestry.
- There are notable coancestry levels and potential for inbreeding within performance groups, particularly among the elite performers. This is a result of increased relatedness within groups following the input of popular sires contributing disproportionate levels of variation to each discipline.
- The QH breed can, in general, be broadly categorized into three groups: stock, racing, and pleasure/halter, per the expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses.
Implications of the Research
- While the QH breed overall contains significant genetic diversity, current breeding practices have caused this diversity to be divided into subpopulations.
- Understanding the effect of selective breeding on QH genetic diversity can influence future breeding practices to maintain and enhance genetic diversity within the breed.
Cite This Article
APA
().
The American Quarter Horse: population structure and relationship to the thoroughbred.
.
Publication
Researcher Affiliations
Citations
This article has been cited 11 times.- Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Seger G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF, Sadeghi R, Cothran G, Juras R, Khanshour AM, Rieder S, Penedo MC, Waiditschka G, Kalinkova L, Kalashnikov VV, Zaitsev AM, Almarzook S, Reißmann M, Brockmann GA, Brem G, Wallner B. Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses. Genes (Basel) 2022 Jan 26;13(2).
- Burattini B, Fenner K, Anzulewicz A, Romness N, McKenzie J, Wilson B, McGreevy P. Age-Related Changes in the Behaviour of Domestic Horses as Reported by Owners. Animals (Basel) 2020 Dec 7;10(12).
- Dell A, Curry M, Yarnell K, Starbuck G, Wilson PB. Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data. PLoS One 2020;15(10):e0240410.
- Todd ET, Thomson PC, Hamilton NA, Ang RA, Lindgren G, Viklund Å, Eriksson S, Mikko S, Strand E, Velie BD. A genome-wide scan for candidate lethal variants in Thoroughbred horses. Sci Rep 2020 Aug 4;10(1):13153.
- 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.
- Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019 Nov 27;10(12).
- Norton E, Schultz N, Geor R, McFarlane D, Mickelson J, McCue M. Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses. Genes (Basel) 2019 Nov 6;10(11).
- Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019 Dec;50(6):569-597.
- Gianino GM, Valberg SJ, Perumbakkam S, Henry ML, Gardner K, Penedo C, Finno CJ. Prevalence of the E321G MYH1 variant for immune-mediated myositis and nonexertional rhabdomyolysis in performance subgroups of American Quarter Horses. J Vet Intern Med 2019 Mar;33(2):897-901.
- Avila F, Mickelson JR, Schaefer RJ, McCue ME. Genome-Wide Signatures of Selection Reveal Genes Associated With Performance in American Quarter Horse Subpopulations. Front Genet 2018;9:249.
- Petersen JL, Valberg SJ, Mickelson JR, McCue ME. Haplotype diversity in the equine myostatin gene with focus on variants associated with race distance propensity and muscle fiber type proportions. Anim Genet 2014 Dec;45(6):827-35.
Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
