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Article

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

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Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy
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Libro Genealogico Cavallo Bardigiano, Associazione Regionale Allevatori dell’Emilia-Romagna, 43126 Parma, Italy
3
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden
*
Author to whom correspondence should be addressed.
Animals 2020, 10(6), 1005; https://doi.org/10.3390/ani10061005
Received: 14 May 2020 / Revised: 1 June 2020 / Accepted: 4 June 2020 / Published: 8 June 2020
(This article belongs to the Special Issue Horse Breeding and Genetics)
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 (Ne) 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. View Full-Text
Keywords: conservation; selection scan; autochthonous; genomics; coat color; LCORL; IBH; ROH; MC1R; horse conservation; selection scan; autochthonous; genomics; coat color; LCORL; IBH; ROH; MC1R; horse
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MDPI and ACS Style

Ablondi, M.; Dadousis, C.; Vasini, M.; Eriksson, S.; Mikko, S.; Sabbioni, A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals 2020, 10, 1005. https://doi.org/10.3390/ani10061005

AMA Style

Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals. 2020; 10(6):1005. https://doi.org/10.3390/ani10061005

Chicago/Turabian Style

Ablondi, Michela, Christos Dadousis, Matteo Vasini, Susanne Eriksson, Sofia Mikko, and Alberto Sabbioni. 2020. "Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data" Animals 10, no. 6: 1005. https://doi.org/10.3390/ani10061005

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