Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Jun 28;10(7):491.
doi: 10.3390/genes10070491.

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

Gertrud Grilz-Seger  1 , Markus Neuditschko  2 , Anne Ricard  3 , Brandon Velie  4   5 , Gabriella Lindgren  6   7 , Matjaz Mesarič  8 , Marko Cotman  9 , Michaela Horna  10 , Max Dobretsberger  11 , Gottfried Brem  12 , Thomas Druml  13
Affiliations

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

Gertrud Grilz-Seger et al. Genes (Basel). .

Abstract

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/OPCML) 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).

Keywords: ROH island; altitude adaptation; autophagy; body size; coat color; embryonic morphogenesis; selection signature.

PubMed Disclaimer

Conflict of interest statement

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.

Figures

Figure 1
Figure 1
Geographic origin of twelve investigated European and Near Eastern horse breeds (Graphics Thomas Druml).
Figure 2
Figure 2
Principal component analysis (PCA) scatterplot illustrating the population stratification of 1,476 horses originating from 12 breeds. On the left visualization of PC1 versus PC2, together explaining 39% of genetic variance, and on the right visualization of PC1 versus PC3 together explaining 37% of variation, are presented. (AKT = Akhal Teke, BMH = Bosnian Mountain Horse, EXP = Exmoor Pony, FT = French Trotter, GID = Gidran, HAF = Haflinger, LIP = Lipizzan, NOR = Noriker, POS = Posavina, PAR = Purebred Arabian, SF = Selle Francais and SHA = Shagya Arabian).
Figure 3
Figure 3
ROH islands on ECA11 between 19.5 Mb and 37.5 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
Figure 4
Figure 4
ROH islands on ECA3 between 26 Mb and 122 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
Figure 5
Figure 5
ROH islands on ECA7 between 36 Mb and 54 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
Figure 6
Figure 6
ROH islands on ECA22 between 14 Mb and 50 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
Figure 7
Figure 7
ROH islands on ECA6 between 26 Mb and 80 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
Figure 8
Figure 8
ROH islands on ECA18 between 1 Mb and 81 Mb. Location and length of ROH islands (shared by more than 50% of individuals per breed) per breed are illustrated as horizontal boxes, location of genes of specific interest are indicated as vertical lines.
See this image and copyright information in PMC

References

    1. Gu J., Orr N., Park S.D., Katz L.M., Sulimova G., MacHugh D.E., Hill E.W. A genome scan for positive selection in thoroughbred horses. PLoS ONE. 2009;4:e5767. doi: 10.1371/journal.pone.0005767. - DOI - PMC - PubMed
    1. Petersen J.L., Mickelson J.R., Cothran E.G., Andersson L.S., Axelsson J., Bailey E., da Câmara Machado A. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS ONE. 2013;8:e54997. doi: 10.1371/journal.pone.0054997. - DOI - PMC - PubMed
    1. Schaefer R.J., Schubert M., Bailey E., Bannasch D.L., Barrey E., Bar-Gal G.K., Brem G., Brooks S.A., Distl O., Fries R. Developing a 670k genotyping array to tag ~2 M SNPs across 24 horse breeds. BMC Genom. 2017;18:565–583. doi: 10.1186/s12864-017-3943-8. - DOI - PMC - PubMed
    1. McCue M.E., Bannasch D.L., Petersen J.L., Gurr J., Bailey E., Binns M.M., Leeb T. A high density SNP array for the domestic horse and extant Perissodactyla: Utility for association mapping; genetic diversity; and phylogeny studies. PLoS Genet. 2012;8:e1002451. doi: 10.1371/journal.pgen.1002451. - DOI - PMC - PubMed
    1. Petersen J.L., Mickelson J.R., Rendahl A.K., Valberg S.J., Andersson L.S., Axelson J., Bailey E., Bannesch D., Binns M.M., Borges A.S. Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS ONE. 2013;9:e10003211. doi: 10.1371/journal.pgen.1003211. - DOI - PMC - PubMed

Publication types

MeSH terms

Substances