Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection

Haberland, A. M.; Borstel, Uta König von; Simianer, Henner; König, Sven

doi:10.1017/s1751731112000626

Cited by 30 publications

(14 citation statements)

References 28 publications

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“…However, given the specific nature and magnitude of the existing genetic relationships of morphology with each of the functional traits studied, it may be judicious to consider the possibility of developing and maintaining specialized lines within the Lusitano breeding program. The tremendous opportunities arising from the incorporation of genomic information in the selection program of Lusitano should also be investigated, as their contribution in reducing generation interval and enhancing selection accuracy could result in extraordinary benefits in terms of genetic progress (Haberland et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Selection for morphology, gaits and functional traits in Lusitano horses: I. Genetic parameter estimates

et al. 2014

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a b s t r a c tGenetic parameters were estimated for morphology, gaits and functional traits in Lusitano horses by uni-and multivariate animal models. Morphological traits considered in the analyses were partial scores attributed to up to 18,076 horses at the time of registration in the studbook and included head and neck, shoulder and withers, chest and thorax, back and loin, croup, legs and overall impression, plus a final score computed by summing the partial morphological scores and the gaits score. The functional traits considered were the scores obtained in the dressage and maneability trials of working equitation (WE, about 1500 records by 200 horses), and classical dressage (12,131 records by 759 horses). The heritability (h 2 ) estimates for all partial morphological scores ranged between 0.12 and 0.18, except for legs (0.07). The h 2 for final score, height at withers and gaits was 0.18, 0.61 and 0.17, respectively, while for WE dressage trial and classical dressage it was 0.32 and for WE maneability trial it was 0.18. The genetic correlations (r G ) of final score with the different partial scores were generally high (0.56-0.95), while among partial components of morphology they were positive but widely different (0.08-0.77). With the exception of legs, r G between morphology/gaits and functional traits were positive, with a stronger relationship between morphological traits and performance in WE dressage trial (r G between 0.36 and 0.56) when compared with performance in maneability trial or classical dressage. Height at withers had a r G of 0.40 with performance in classical dressage, but lower r G (0.06 and À 0.10) with WE trials. Final score and overall impression had moderate to strong genetic relationships with functional traits, especially with WE dressage trial, while gaits had a strong r G with performance in all the disciplines (0.60-0.72). Indirect selection for morphology/gaits to improve functionality was assessed, by selecting for final score or a combined index of partial scores. Compared to direct selection for functionality, selection for final score or an index combining partial morphological scores would be less effective, resulting in accuracies of, respectively, 0.28 and 0.37 for WE dressage trial, 0.14 and 0.38 for WE maneability trial and 0.22 and 0.39 for classical dressage. Thus, an index combining all partial morphological scores would be better than selection for overall final score, but its relative efficiency compared to direct selection would be about 0.7 in WE dressage trial and classical dressage, and 0.9 in WE maneability trial. Lusitano horses maintain considerable levels of genetic variability, and selection for both morphology and functionality should be effective. The favorable genetic relationships existing between morphology and performance indicate that morphology/gaits traits can play an important role in a two-stage selection program, contributing to enhance selection

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Section: Discussionmentioning

confidence: 99%

Selection for morphology, gaits and functional traits in Lusitano horses: I. Genetic parameter estimates

et al. 2014

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“…livsci.2014.03.017i (Vicente et al, 2012). The incorporation of genetic markers in selection of Lusitano is a possibility that should be kept in mind, as it is currently being used in selection of sport horses (Haberland et al, 2012;Hill et al, 2010) but, to our knowledge, genomic associations with morphological and beauty traits have not been studied so far.…”

Section: Tablementioning

confidence: 99%

Selection for morphology, gaits and functional traits in Lusitano horses: II. Fixed effects, genetic trends and selection in retrospect

et al. 2014

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a b s t r a c tMixed model procedures were used to analyze morphology and gaits records collected in about 18,000 Lusitano horses from 900 studs, over a period of 43 years, and functional records collected since 1998, to carry-out a critical assessment of the fixed effects and selection practices followed in this breed. Fixed effects considered in the analysis of morphology (head/ neck, shoulder/withers, chest/thorax, back/loin, croup, legs and overall impression), gaits and final score (computed by summing partial morphological and gaits scores) were stud, year, sex, inbreeding and age. Functional traits analyzed were the scores obtained in working equitation dressage (WEDT) and maneability (WEMT) trials and in classical dressage (CD), where fixed effects were event, level of competition, sex, inbreeding and age. Phenotypic trends were moderate over the period analyzed, with a slight increase in height at withers, and a decline in final score. Nevertheless, differences among years were mostly environmental. Males received lower scores for almost all morphological and gaits traits except croup, with a difference of about À 1.7 points for final score relative to females. Sex differences were small for functional traits, with general advantage of males in WEMT and CD, and a disadvantage in WEDT. Considerable differences were detected among studs, especially in their environmental effects but also in mean estimated breeding value (EBV), for morphology, gaits and functionality. The environmental effect of competition level in CD resulted in a progressively lower scoring as the competition became more difficult, while for WEMT the pattern was opposite and differences were minor for WEDT. Inbreeding depression was observed for all morphological and gait traits, but the magnitude of its impact was very small for all traits analyzed, never exceeding À 0.1% of the mean per 1% inbreeding. Still, for functional traits the effect of inbreeding was negligible. The EBV for morphology, gaits, WEMT and WEDT show considerable variability, indicating that selection can be effective. For CD, however, the distribution of EBV was narrower. The genetic trend was positive but moderate for all traits, and it was slightly higher for head and neck, overall impression, gaits and final score. As a percentage of the mean, these traits and working equitation trials showed the highest responses, which in the best cases did not exceed 0.2% of the mean per year. Genetic selection differentials and the corresponding selection intensities were very modest for all traits analyzed, with a slightly higher intensity in sires when compared to dams.& 2014 Elsevier B.V. All rights reserved.

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“…Incorporating genomic information is predicted to further improve selection for performance traits and was shown to be useful in a population of French Trotters (Haberland et al . ; Brard & Ricard ). The availability of parentage testing using SNPs could be an incentive to begin adding genotypes to current evaluations.…”

Section: Introductionmentioning

confidence: 98%

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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Integration of genomic information into sport horse breeding programs for optimization of accuracy of selection

Cited by 30 publications

References 28 publications

Selection for morphology, gaits and functional traits in Lusitano horses: I. Genetic parameter estimates

Selection for morphology, gaits and functional traits in Lusitano horses: I. Genetic parameter estimates

Selection for morphology, gaits and functional traits in Lusitano horses: II. Fixed effects, genetic trends and selection in retrospect

Single nucleotide polymorphisms for DNA typing in the domestic horse

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