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Open AccessArticle

The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands

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Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
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Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
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Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007 Uppsala, Sweden
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Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112-114, 3584 CM Utrecht, The Netherlands
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Department of Surgery and Anaesthesiology of Domestic Animals, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
*
Author to whom correspondence should be addressed.
Genes 2019, 10(6), 480; https://doi.org/10.3390/genes10060480
Received: 15 May 2019 / Revised: 11 June 2019 / Accepted: 22 June 2019 / Published: 25 June 2019
(This article belongs to the Special Issue Equine Genetics)
The spectrum of modern horse populations encompasses populations with a long history of development in isolation and relatively recently formed types. To increase our understanding of the evolutionary history and provide information on how to optimally conserve or improve these populations with varying development and background for the future, we analyzed genotype data of 184 horses from 9 Dutch or common horse populations in the Netherlands: The Belgian draft horse, Friesian horse, Shetland pony, Icelandic horse, Gelder horse, Groninger horse, harness horse, KWPN sport horse and the Lipizzaner horse population. Various parameters were estimated (e.g., runs of homozygosity and FST values) to gain insight into genetic diversity and relationships within and among these populations. The identified genomic makeup and quantified relationships did mostly conform to the development of these populations as well as past and current breeding practices. In general, populations that allow gene-flow showed less inbreeding and homozygosity. Also, recent bottlenecks (e.g., related to high selective pressure) caused a larger contribution of long ROHs to inbreeding. Maintaining genetic diversity through tailor-made breeding practices is crucial for a healthy continuation of the investigated, mostly inbred and (effectively) small sized horse populations, of which several already experience inbreeding related issues. View Full-Text
Keywords: genetic diversity; horses; inbreeding; population structure; relatedness; runs of homozygosity genetic diversity; horses; inbreeding; population structure; relatedness; runs of homozygosity
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Schurink, A.; Shrestha, M.; Eriksson, S.; Bosse, M.; Bovenhuis, H.; Back, W.; Johansson, A.M.; Ducro, B.J. The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands. Genes 2019, 10, 480.

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