A genome-wide scan for diversifying selection signatures in selected horse breeds

Artur Gurgul , Igor Jasielczuk , Ewelina Semik-Gurgul , Klaudia Pawlina-Tyszko , Monika Stefaniuk-Szmukier , Tomasz Szmatoła , Polak Grażyna , Iwona Tomczyk-Wrona , Monika Bugno-Poniewierska

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.
Author Artur Gurgul
Artur Gurgul,,
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, Igor Jasielczuk
Igor Jasielczuk,,
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, Ewelina Semik-Gurgul
Ewelina Semik-Gurgul,,
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, Klaudia Pawlina-Tyszko
Klaudia Pawlina-Tyszko,,
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, Monika Stefaniuk-Szmukier (FoAS / IoAS)
Monika Stefaniuk-Szmukier,,
- Institute of Animal Science
, Tomasz Szmatoła
Tomasz Szmatoła,,
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, Polak Grażyna
Polak Grażyna,,
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, Iwona Tomczyk-Wrona
Iwona Tomczyk-Wrona,,
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, Monika Bugno-Poniewierska (FoAS / IoVS)
Monika Bugno-Poniewierska,,
- Institute of Veterinary Sciences
Journal seriesPLoS ONE, ISSN 1932-6203, (N/A 100 pkt)
Issue year2019
Vol14
No1
Pages1-14
Publication size in sheets0.65
Article numbere0210751
ASJC Classification2700 General Medicine; 1100 General Agricultural and Biological Sciences; 1300 General Biochemistry, Genetics and Molecular Biology
DOIDOI:10.1371/journal.pone.0210751
URL https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210751
Internal identifierWHiBZ/2019/35
Languageen angielski
Score (nominal)100
Score sourcejournalList
Publication indicators WoS Citations = 4; Scopus SNIP (Source Normalised Impact per Paper): 2017 = 1.111; WoS Impact Factor: 2018 = 2.776 (2) - 2018=3.337 (5)
Citation count*
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Finansowanie The study was financed from funds of the project: “Directions for use and conservation of livestock genetic resources in sustainable development" co-financed by the National Research and Development Center (Poland) under the Strategic Research and Development Program: "Environment, Agriculture and Forestry" – BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016.
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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