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

Animals : an Open Access Journal From MDPI
Michela AblondiAlberto Sabbioni

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 (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 ≤ 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. Th...Continue Reading

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Citations

Aug 6, 2020·Animals : an Open Access Journal From MDPI·Enrico MancinCristina Sartori
Nov 24, 2020·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Laura KvistJouni Aspi
Aug 8, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Julia Poyato-BonillaMercedes Valera

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Methods Mentioned

BETA
genotyping

Software Mentioned

Biomart
DetectRUNS
UCSC genome browser
Ensembl
PLINK
R
SNeP

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