Skip to main content
SLU publication database (SLUpub)

Research article2019Peer reviewedOpen access

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

Grilz-Seger, Gertrud; Neuditschko, Markus; Ricard, Anne; Velie, Brandon; Lindgren, Gabriella; Mesaric, Matjaz; Cotman, Marko; Horna, Michaela; Dobretsberger, Max; Brem, Gottfried; Druml, Thomas

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; selection signature; body size; coat color; autophagy; altitude adaptation; embryonic morphogenesis

Published in

Genes
2019, Volume: 10, number: 7, article number: 491
Publisher: MDPI

      SLU Authors

      • Sustainable Development Goals

      End hunger, achieve food security and improved nutrition and promote sustainable agriculture

      UKÄ Subject classification

      Animal and Dairy Science

      Publication identifier

      DOI: https://doi.org/10.3390/genes10070491

      Permanent link to this page (URI)

      https://res.slu.se/id/publ/101272