A genome-wide association study of osteochondritis dissecans in the Thoroughbred

Corbin, Laura J; Blott, Sarah; Swinburne, June; Sibbons, Charlene; Fox-Clipsham, Laura; Helwegen, Maud; Parkin, T. D. H.; Newton, J. R.; Bramlage, L. R.; McIlwraith, C. Wayne; Bishop, Stephen; Woolliams, John; Vaudin, Mark D.

doi:10.1007/s00335-011-9363-1

Cited by 37 publications

(50 citation statements)

References 49 publications

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“…ECA1, ECA15, ECA16 and ECA18 were selected as related to OCD in Hanoverian horses (Lampe et al 2010), ECA15 was identified in French trotters (Corbin et al 2012), ECA10 in the Dutch horse population (Orr et al 2013) and ECA28 in Norwegian Standardbred trotters (Lykkjen et al 2010). Polish Warmblood horses are closely related to Hanoverian and Dutch Warmblood horses.…”

Section: Resultsmentioning

confidence: 99%

“…A French study identified osteochondrosis associated SNP on ECA03, ECA13, ECA14, ECA15 for the Standardbred Trotter (Teyssèdre et al 2010), whereas a Norwegian study found corresponding SNP on ECA05, ECA10, ECA27, and ECA28 (Lykkjen et al 2010). Breeds may differ in the linkage disequilibrium (Corbin et al 2012), but it is expected that breed-specific results will be more compatible.…”

Section: Introductionmentioning

confidence: 99%

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Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training

et al. 2017

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Abstract. The genetic background of osteochondrosis dissecans (OCD) has been studied for years, but the compatibility of the position of markers has not been reached between results, probably because of unknown additional effects that may influence the results, such as definition of the trait, gene-environmental interactions and the dynamics of trait development. The aim of the study was to identify single nucleotide polymorphisms (SNP) associated with the occurrence of OCD in Polish Warmblood sport breed horses in two different stages of training. Warmblood horses (87 stallions and 114 mares) were phenotyped and genotyped. Horses were X-rayed twice, at the beginning and at the end of the tests (100 days for stallions and 60 days for mares). Ten images per horse were collected using digital equipment for the fetlocks, stifles and hocks. The DNA was genotyped using the Illumina Neogen Equine Array. Statistical analysis included the Cochran-Armitage test and logistic regression assuming an additive model of inheritance. The Monte Carlo Markov Chain method was also applied to determine heritability coefficients. Nineteen and twenty SNP were identified that were significantly associated with OCD using logistic regression at the first and second stage of training, respectively. Four SNP were significant for both stages of training. The estimation of the heritability of a horse's OCD status does not achieve the same level at different stages of training. The study on the genetic background of horse OCD should include as much detailed information on their training as possible.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training

et al. 2017

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“…However, until now, there have been no studies associate the traits of Jeju horse with epigenetic patterns. With the advent of next-generation sequencing (NGS) and genome-wide association studies, some studies were performed using NGS and microarray technology in thoroughbred horses [35, 40, 41]. These studies concentrated only on gene expression and genetic markers of athletic ability during and after exercise.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of DNA methylation patterns in horse

et al. 2014

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BackgroundDNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.ResultsWe report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.ConclusionsWe provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-598) contains supplementary material, which is available to authorized users.

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“…In addition to simple monogenic traits, GWA studies using the equine SNP chips have identified quantitative trait loci for further investigation in osteochondritis dissecans (Corbin et al, 2012), recurrent laryngeal neuropathy (Dupuis et al, 2011), body size (Makvandi-Nejad et al, 2012) guttural pouch tympany (Metzger et al, 2012), equine uveitis (Kulbrock et al, 2013) and insect bite hypersensitivity (Schurink et al, 2012). Despite the apparent success in mapping more complex traits and diseases, underlying genetic mutations have not been uncovered for many of these traits.…”

Section: Discussionmentioning

confidence: 99%

“…This array was used to identify chromosomal regions, leading to mutation discovery, for various monogenic traits in the horse using relatively small sample sizes (Brooks et al, 2010; Fox-Clipsham et al, 2011; Andersson et al, 2012). In addition to simple monogenic traits, GWA studies using the equine SNP chips have identified quantitative trait loci for more complex traits (Dupuis et al, 2011; Corbin et al, 2012; Kulbrock et al, 2013). Despite the apparent success in mapping more complex traits and diseases, underlying genetic mutations have not been uncovered for many of these traits.…”

Section: Introductionmentioning

confidence: 99%

Risk of false positive genetic associations in complex traits with underlying population structure: A case study

Finno¹,

Aleman²,

Higgins³

et al. 2014

The Veterinary Journal

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Genome-wide association (GWA) studies are widely used to investigate the genetic etiology of diseases in domestic animals. In the horse, GWA studies using 40–50,000 single nucleotide polymorphisms (SNPs) in sample sizes of 30–40 individuals, consisting of only 6–14 affected horses, have led to the discovery of genetic mutations for simple monogenic traits. Equine neuroaxonal dystrophy is a common inherited neurological disorder characterized by symmetric ataxia. A case-control GWA study was performed using genotypes from 42,819 SNP marker loci distributed across the genome in 99 clinically phenotyped Quarter horses (37 affected, 62 unaffected). A significant GWA was not achieved although a suggestive association was uncovered when only the most stringently phenotyped NAD-affected horses (n = 10) were included (chromosome 8:62130605 and 62134644 [log(1/P) = 5.56]). Candidate genes (PIK3C3, RIT2, and SYT4) within the associated region were excluded through sequencing, association testing of uncovered variants and quantitative RT-PCR. It was concluded that variants in PIK3C3, RIT2, and SYT4 are not responsible for equine neuroaxonal dystrophy. This study demonstrates the risk of false positive associations when performing GWA studies on complex traits and underlying population structure when using 40–50,000 SNP markers and small sample size.

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A genome-wide association study of osteochondritis dissecans in the Thoroughbred

Cited by 37 publications

References 49 publications

Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training

Single nucleotide polymorphisms associated with osteochondrosis dissecans in Warmblood horses at different stages of training

Genome-wide analysis of DNA methylation patterns in horse

Risk of false positive genetic associations in complex traits with underlying population structure: A case study

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