Genomics and genetics: A daily double for the horse industry

Rothschild, Max F.

doi:10.1111/evj.12668

Cited by 3 publications

(1 citation statement)

References 11 publications

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“…). Genomic selection, on the other hand, is not commonly utilized (Rothschild ). However, genetic evaluations using pedigrees and performance data are performed in a variety of European breeds (Stock & Distl ; Viklund et al .…”

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphisms for DNA typing in the domestic horse

et al. 2017

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Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA typing suitability. The overall minor allele frequency of the panel was 0.376 (range 0.304-0.419), with per breed probability of identities ranging from 5.6 × 10 to 1.86 × 10 . When one parent was available, exclusion probabilities ranged from 0.9998 to 0.999996, although when both parents were available, all breeds had exclusion probabilities greater than 0.9999999. A set of 388 horses from 35 breeds was genotyped to evaluate marker performance on known families. The set included 107 parent-offspring pairs and 101 full trios. No horses shared identical genotypes across all markers, indicating that the selected set was sufficient for individual identification. All pairwise comparisons were classified using ISAG rules, with one or two excluding markers considered an accepted parent-offspring pair, two or three excluding markers considered doubtful and four or more excluding markers rejecting parentage. The panel had an overall accuracy of 99.9% for identifying true parent-offspring pairs. Our developed marker set is both present on current generation SNP chips and can be highly multiplexed in standalone panels and thus is a promising resource for SNP-based DNA typing.

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Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphisms for DNA typing in the domestic horse

et al. 2017

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Variation in the SLC16A1 and the ACOX1 Genes Is Associated with Gallop Racing Performance in Arabian Horses

Fontanel

Todd

Drabbe

et al. 2020

Journal of Equine Veterinary Science

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Genomic-Inbreeding Landscape and Selection Signatures in the Polo Argentino Horse Breed

Azcona,

Molina,

Demyda-Peyrás

2024

IJMS

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Analyzing genetic variability and inbreeding trends is essential for effective breed management in animal populations. To this, the characterization of runs of homozygosity (ROH) provides a good genomic approach to study the phenomena. The Polo Argentino (PA) breed, globally recognized as the best adapted to playing polo, is known for its strong influence of Thoroughbreds, intense selective breeding, and extensive use of reproductive biotechnologies. This study investigates the PA’s genomic variability, by characterizing the ROH landscape and identifying ROH islands (ROHi) as potential genomic footprints for the breed. PA horses (n = 506) were genotyped using EquineGGP™ array v5 (70 k). We calculated the inbreeding coefficient based on ROH (FROH—ancestral and recent) using a chromosomal approach. Finally, we identified genomic regions with increased ROH frequency (ROHi) and their associated genes. An average of 79.5 ROH per horse was detected, with a mean length of 4.6 Mb. The average FROH was 0.151, but most of them (54%) corresponded to ancestral inbreeding (ROH < 5.5 Mb). However, 4 ROHi were identified in ECA 1, 3, 7 and 17, containing 67 genes, some of which were related to behavior, neurodevelopment, and metabolic functions. This genomic analysis determined, for the first time, the length and location of homozygosity segments in the PA breed and identified ROHi associated with potential genomic regions and genes for positive selection in the breed.

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Genomics and genetics: A daily double for the horse industry

Cited by 3 publications

References 11 publications

Single nucleotide polymorphisms for DNA typing in the domestic horse

Single nucleotide polymorphisms for DNA typing in the domestic horse

Variation in the SLC16A1 and the ACOX1 Genes Is Associated with Gallop Racing Performance in Arabian Horses

Genomic-Inbreeding Landscape and Selection Signatures in the Polo Argentino Horse Breed

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