Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds.

Autor:	Grilz-Seger G; Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. gertrud.grilz@vetmeduni.ac.at., Neuditschko M; Agroscope, Swiss National Stud Farm, Les Longs Prés, CH-1580 Avenches, Switzerland. markus.neuditschko@agroscope.admin.ch., Ricard A; UMR 1313 Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, Domaine de Vilvert, Bat 211, 78352 Jouy-en-Josas, France. anne.ricard@inra.fr., Velie B; Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden. brandon.velie@sydney.edu.au.; School of Life and Environmental Sciences, University of Sydney, Eastern Ave, 2006 NSW Sydney, Australia. brandon.velie@sydney.edu.au., Lindgren G; Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Ulls väg 26, 750 07 Uppsala, Sweden. gabriella.lindgren@slu.se.; Livestock Genetics, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium. gabriella.lindgren@slu.se., Mesarič M; Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary, Faculty, Cesta v Mestni log 47, 1000 Ljubljana, Slovenia. Matjaz.Mesaric@vf.uni-lj.si., Cotman M; Institute for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Gerbičeva 60, 1000 Ljubljana, Slovenia. marko.cotman@vf.uni-lj.si., Horna M; Department of Animal Husbandry, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia. michaela.horna@post.sk., Dobretsberger M; Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. maximilian.dobretsberger@vetmeduni.ac.at., Brem G; Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. gottfried.brem@vetmeduni.ac.at., Druml T; Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, 1210 Vienna, Austria. thomas.druml@vetmeduni.ac.at.
Jazyk:	angličtina
Zdroj:	Genes [Genes (Basel)] 2019 Jun 28; Vol. 10 (7). Date of Electronic Publication: 2019 Jun 28.
DOI:	10.3390/genes10070491
Abstrakt:	Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color ( MC1R , STX17 , ASIP ), body size ( LCORL/NCAPG , ZFAT , LASP1 , HMGA2 ), racing ability ( PPARGC1A ), behavioral traits ( GRIN2B , NTM/OP C ML ) and gait patterns ( DMRT3 ), several putative target genes related to embryonic morphogenesis ( HOXB ), energy metabolism ( IGFBP - 1 , IGFBP - 3 ), hair follicle morphogenesis ( KRT25 , KRT27 , INTU ) and autophagy ( RALB ) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats ( UVSSA , STXBP4 , COX11 , HLF , MMD ). Competing Interests: Data Availability: The primary data of this study are owned by different research groups. Primary data of the breeds Lipizzan, Noriker, Haflinger, Akhal Teke, Shagya Arabian, Gidran, Bosnian Mountain Horse and Posavina are available from project consortium FFG project number 843464, Veterinary University Vienna, Xenogenetik, five European state stud farms and the Austrian and Slovenian Horse breeders Association, but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of project consortium, FFG project number 843464, Veterinary University Vienna, Xenogenetik and partners. Genotype data for the Exmoor Pony breed will be provided by contacting authors Lindgren/Velie or for a larger data set via the following reference: Velie, B.D.; Shrestha, M.; Franҫois, L.; Schurink, A.; Tesfayonas, Y.G.; Stinckens, A.; Blott, S.; Ducro, B.J.; Mikko, S.; Thomas, R.; Swinburne, J.E.; Sundqvist, M.; Eriksson, S.; Buys, N.; Lindgren, G. Using an inbred horse breed in a high density genome-wide scan for genetic risk factors of insect bite hypersensitivity (IBH). PLoS One. 2016, 11, e0152966.
Databáze:	MEDLINE
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