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Animals : an open access journal from MDPI2020; 10(6); 1005; doi: 10.3390/ani10061005

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

Abstract: 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) 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 ≤ 2Mbp 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.
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Publication Date: 2020-06-08 PubMed ID: 32521830PubMed Central: PMC7341496DOI: 10.3390/ani10061005Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research investigated the loss of genetic variability and potential sections of genome under selective pressure in the Bardigiano breed of horses, using the GGP Equine70k SNP dataset. This was the first such comprehensive study of its kind for an Italian native horse breed.

Research Goals and Methods

  • The primary aim of this study was to evaluate the genetic diversity of the Bardigiano horse breed, an Italian native breed, and to identify genomic regions that might be under selective pressure.
  • To accomplish this, the researchers utilized the GGP Equine70k SNP dataset. SNP stands for Single Nucleotide Polymorphism, a type of genetic variation among individuals. This dataset is often used in genetic studies of horses.
  • In addition, the researchers calculated the effective population size (N) of the breed based on Linkage Disequilibrium, a measure of the non-random association of alleles at different loci. They also calculated the average inbreeding based on runs of homozygosity (ROH), which refers to a contiguous sequence of identical genetic markers that are inherited from both parents.

Key Findings

  • The effective population size was found to be 39 horses, indicating a significant decline over time. This small size could lead to a loss of genetic diversity, which can negatively impact individual fitness and the breed’s long-term survival.
  • The average inbreeding was reported to be 0.17 (with a standard deviation of 0.03). High inbreeding can also be harmful as it can increase the chances of offspring being affected by deleterious or recessive traits.
  • Most of the ROH identified were relatively short (91% were less than or equal to 2Mbp long), suggesting a history of older inbreeding rather than recent. Shorter ROH tend to be the result of older, distant inbreeding events, whereas longer ROH suggest more recent inbreeding.
  • Researchers identified eight shared ROH islands (contiguous areas of homozygosity), four of which corresponded to known regions related to morphological traits (like body size and coat color) and susceptibility to diseases. This suggests that these traits have been under selective pressure in the Bardigiano breed.

Contribution to the Field

  • This investigation represents the first genome-wide scan of genetic diversity and selection pressures in the Bardigiano breed, or indeed any Italian native breed of horse.
  • The findings can aid in conservation strategies for the breed by identifying areas where selective breeding has potentially diminished genetic diversity. Also, the identification of traits under selective pressure might assist in making breeding decisions aimed at maintaining breed characteristics while reducing inbreeding.

Cite This Article

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

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 10
Issue: 6
PII: 1005

Researcher Affiliations

Ablondi, Michela
  • Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy.
Dadousis, Christos
  • Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy.
Vasini, Matteo
  • Libro Genealogico Cavallo Bardigiano, Associazione Regionale Allevatori dell'Emilia-Romagna, 43126 Parma, Italy.
Eriksson, Susanne
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden.
Mikko, Sofia
  • Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden.
Sabbioni, Alberto
  • Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy.

Conflict of Interest Statement

The authors declare no conflict of interest.

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