Abstract
The genetic differentiation of the current horse population was evolutionarily created by natural or artificial selection which shaped the genomes of individual breeds in several unique ways. The availability of high throughput genotyping methods created the opportunity to study this genetic variation on a genome-wide level allowing detection of genome regions divergently selected between separate breeds as well as among different horse types sharing similar phenotypic features. In this study, we used the population differentiation index (FST) that is generally used for measuring locus-specific allele frequencies variation between populations, to detect selection signatures among six horse breeds maintained in Poland. These breeds can be classified into three major categories, including light, draft and primitive horses, selected mainly in terms of type (utility), exterior, performance, size, coat color and appearance. The analysis of the most pronounced selection signals found in this study allowed us to detect several genomic regions and genes connected with processes potentially important for breed phenotypic differentiation and associated with energy homeostasis during physical effort, heart functioning, fertility, disease resistance and motor coordination. Our results also confirmed previously described association of loci on ECA3 (spanning LCORL and NCAPG genes) and ECA11 (spanning LASP1 gene) with the regulation of body size in our draft and primitive (small size) horses. The efficiency of the applied FST-based approach was also confirmed by the identification of a robust selection signal in the blue dun colored Polish Konik horses at the locus of TBX3 gene, which was previously shown to be responsible for dun coat color dilution in other horse breeds. FST-based method showed to be efficient in detection of diversifying selection signatures in the analyzed horse breeds. Especially pronounced signals were observed at the loci responsible for fixed breed-specific features. Several candidate genes under selection were proposed in this study for traits selected in separate breeds and horse types, however, further functional and comparative studies are needed to confirm and explain their effect on the observed genetic diversity of the horse breeds.
Highlights
The present horse population abounds in the variety of phenotypes resulting mainly from selective breeding directed at improvement of particular phenotypic features
These horse populations were mainly shaped by natural selection, selective breeding for breed standard and mating in closed populations makes their genetic characteristics largely similar to that found in other horse breeds
Five out of six breeds analyzed in this study are included in the conservation programs following FAO National Rare Livestock Breeds Preservation guidelines and according to our best knowledge, these native horse breeds were not studied before in terms of diversifying selection and this study provides new data on horse breeds genetic diversity and variation
Summary
The present horse population abounds in the variety of phenotypes resulting mainly from selective breeding directed at improvement of particular phenotypic features. Various selection criteria aimed towards the improvement of horse usability in transportation, agriculture or horsemanship have been applied [1,2]. This drove the specialization of particular populations in terms of utility and resulted in a creation of formal breeds constituting largely closed populations with high genetic uniformity of individuals within breeds [3]. Apart from the highly specialized breeds, there are horse populations which are valued for their primitive nature manifesting in their robust constitution for primitive living conditions [4] These horse populations were mainly shaped by natural selection, selective breeding for breed standard and mating in closed populations makes their genetic characteristics largely similar to that found in other horse breeds
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