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

Grilz-Seger Grilz-Seger,Lindgren Lindgren,Brem Brem,Dobretsberger Dobretsberger,Druml Druml,Horna Horna,Neuditschko Neuditschko,Velie Velie,Cotman Cotman,Mesarič Mesarič,Ricard Ricard

doi:10.3390/genes10070491

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).

Highlights

The scientific interest in the identification of selection signatures in horses successively rose withThe scientific interest in the identification of selection signatures in horses successively rose the enhancement of whole-genome sequencing and analysis methods
Visualization of principal component 1 (PC1) versus PC3 illustrated the genetic relationship between the breeds and highlighted that the draught horse breeds gradually overlap along PC1 in direction from heavy to lighter type and geographically from North to South (Noriker, Haflinger, Posavina), whilst the Bosnian
ECA3 and ECA11 were common runs of homozygosity (ROH) island hotspots in most breeds of our dataset, except for French Trotter and Selle Francais, harboring genes involved in coat color (ECA3: MC1R), size (ECA3: LCORL/NCAPG, ECA11: LASP1), nucleotide excision repair (NER) pathway (ECA3: UVSSA), embryonic skeletal morphogenesis (ECA11: HOXB-cluster) and coat texture (ECA11: KRT-complex)

Summary

Introduction

The scientific interest in the identification of selection signatures in horses successively rose the enhancement of whole-genome sequencing and analysis methods. A milestone in equine is the population study of Gu et al [1] that concentrated on the identification of selection targets in genetics is the population study of Gu et al [1] that concentrated on the identification of selection thoroughbreds using microsatellite markers. With the availability of cost extensive high throughput targets in thoroughbreds using microsatellite markers. Several studies were conducted to scan the genome throughput singlepolymorphism nucleotide polymorphism data, several studies were conducted to scan the of numerous populations for genetic diversity [2,3], and for selection [4,5,6,7]. Genome ofhorse numerous horse populations for genetic diversity [2,3], and forsignatures selection signatures [4,5,6,7]

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Discussion

Conclusion