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Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data

Ablondi, Michela and Dadousis, Christos and Vasini, Matteo and Eriksson, Susanne and Mikko, Sofia and Sabbioni, Alberto (2020). Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals. 10 , 1005 , 1-15
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Abstract

Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed's genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (N-e) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were <= 2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.

Authors/Creators:Ablondi, Michela and Dadousis, Christos and Vasini, Matteo and Eriksson, Susanne and Mikko, Sofia and Sabbioni, Alberto
Title:Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data
Year of publishing :2020
Volume:10
Article number:1005
Number of Pages:15
Publisher:MDPI
ISSN:2076-2615
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Keywords:conservation, selection scan, autochthonous, genomics, coat color, LCORL, IBH, ROH, MC1R, horse
URN:NBN:urn:nbn:se:slu:epsilon-p-107204
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-107204
Additional ID:
Type of IDID
DOI10.3390/ani10061005
Web of Science (WoS)000554610400001
ID Code:17452
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:14 Sep 2020 11:14
Metadata Last Modified:14 Sep 2020 11:14

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