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Inbreeding depression and the probability of racing in the Thoroughbred horse.

ABSTRACT: Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding (F_ROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of F_ROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.

SUBMITTER: Hill EW

PROVIDER: S-EPMC9240673 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Inbreeding depression and the probability of racing in the Thoroughbred horse.

Hill Emmeline W EW Stoffel Martin A MA McGivney Beatrice A BA MacHugh David E DE Pemberton Josephine M JM

Proceedings. Biological sciences 20220629 1977

Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increas ...[more]

PMID: 35765835

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Project description:The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2 = 0.942, P = 2.19 × 10-13; FROH R2 = 0.88, P = 1.81 × 10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Project description:Reasons for performing studyPalmar/plantar osteochondral disease (POD) is a common, debilitating condition in Thoroughbred racehorses; however, training- and racing-related factors associated with this disease are unknown.ObjectivesTo determine horse-, racing- and training-related risk factors for POD. The general hypotheses were that early training and racing, and increased intensity of racing and training, lead to increased severity of POD.MethodsThe metacarpo/metatarsophalangeal joints of 164 Thoroughbred racehorses were examined at post mortem and graded for third metacarpal and metatarsal POD. The relationships between training- and racing-related factors and grade of POD in each condyle were determined using multilevel, multivariable, ordinal logistic regression models.ResultsA total of 1288 condyles were graded. Factors associated with higher grades of POD were the total lifetime number of races, an increase in gallop sessions in the previous season, racing before import to Hong Kong and an increase in the number of short (8-16 weeks) between-race intervals per season. Horses in their first racing season were more likely to have lower POD grades, while horses that had a long between-race interval (greater than 16 weeks) in the season prior to euthanasia were also more likely to have lower POD grades. Lower POD grades were significantly more likely as days since last race increased up to 400 days. Age at first race was not significantly associated with grade of POD.Conclusions and potential relevanceCumulative racing exposure and training intensity in the previous season were associated with higher grades of POD, supporting the hypothesis that the disease is due to repetitive loading. Longer between-race intervals and increased time since racing were associated with lower POD grades, which may indicate that lesions heal. Further work is required to enable optimisation of racing and training programmes to reduce the frequency and severity of this disease.

Project description:This article reports on the results of a survey of racehorse trainers (n = 112) outlining the reasons for tongue-tie (TT) and noseband (NB) use by Thoroughbred trainers (TBTs) (n = 72) and Standardbred trainers (SBTs) (n = 40). The study also investigated the reported effectiveness of TTs and possible complications arising from their use. Tongue-tie use was reported by 62.5% (n = 70) of racehorse trainers. The reasons for TT use varied between TBTs and SBTs. For TBTs, the most common reason for TT use was to prevent or reduce airway obstruction (72.3%, n = 34), followed closely by to prevent or reduce airway noise (55.3%, n = 16). Standardbred trainers assigned equal importance for TT use [to prevent or reduce airway obstruction (69.6%, n = 16) and to prevent the horse from moving its tongue over the bit (69.6%, n = 16)]. Tongue-ties were considered significantly less effective at improving performance than at reducing airway obstruction and preventing the tongue from moving over the bit (t = -2.700, p = 0.0007). For respondents who used both TTs and NBs, there was a mild to moderate positive association between the reasons for using TTs and NBs. Of the 70 TT-using respondents, 51.4% (n = 36) recorded having encountered either a physical or behavioural complication due to TT use, with redness/bruising of the tongue (20.0%, n = 14) being the most common physical complication reported. Duration of use influenced the risk of observing complications. The likelihood of a respondent reporting a behavioural complication due to TT use increased with every minute of reported application and a nine-minute increment in application period doubled the odds of a respondent reporting a complication. Tightness was a risk factor for physical complications: Checking TT tightness by noting the tongue as not moving was associated with increased reporting of physical complications (OR = 6.59; CI 1.1-67.5). This pilot study provides some insight into how and why TTs are applied by some racehorse trainers, and the potential risks associated with their use. A further study of a larger cohort is recommended because these results are valid for only the 112 trainers who responded and cannot be generalized to the equine industry.

Project description:BackgroundInbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological traits and two morphology defects in the Pura Raza Española (PRE) horse breed.ResultsThe regression coefficients that were calculated between trait performances and inbreeding coefficients demonstrated the existence of inbreeding depression. In total, 58,772,533 partial inbreeding coefficients (Fij) were estimated for the whole PRE population (328,706 horses). We selected the descendants of horses with a Fij ≥ 6.25% that contributed to at least four offspring and for which morphological traits were measured for the subsequent analysis of inbreeding depression load (639 horses). A pedigree was generated with the last five generations (5026 animals) used as the reference population (average inbreeding coefficient of 8.39% and average relatedness coefficient of 10.76%). Heritability estimates ranged from 0.08 (cresty neck) to 0.80 (height at withers), whereas inbreeding depression load ratios ranged from 0.01 (knock knee) to 0.40 (length of shoulder), for an inbreeding coefficient of 10%. Most of the correlations between additive and inbreeding depression load genetic values and correlations between inbreeding depression load genetic values for the different traits were positive or near 0.ConclusionsAlthough the average inbreeding depression loads presented negative values, a certain percentage of the animals showed neutral or even positive values. Thus, high levels of inbreeding do not always lead to a decrease in mean phenotypic value or an increase in morphological defects. Hence, individual inbreeding depression loads could be used as a tool to select the most appropriate breeding animals. The possibility of selecting horses that have a high genetic value and are more resistant to the deleterious effects of inbreeding should help improve selection outcomes.

Dataset Information

Inbreeding depression and the probability of racing in the Thoroughbred horse.

Publications

Inbreeding depression and the probability of racing in the Thoroughbred horse.

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