Abstract
BackgroundIn the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array.ResultsAfter quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding.ConclusionsThis study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.
Highlights
In the last 50 years, the diversity of cattle breeds has experienced a severe contraction
Genetic diversity indices Genetic diversity parameters are in Table 1. Ho and He ranged from 0.297 ± 0.194 (Pontremolese) to 0.358 ± 0.167 (Piedmontese) and from 0.267 ± 0.187 (Mucca Pisana) to 0.353 ± 0.137 (Sarda), respectively
The highest average FHOM were obtained for the Pontremolese (0.195 ± 0.101) and Mucca Pisana (0.183 ± 0.058) breeds, whereas the lowest FHOM was obtained for the Sarda breed (0.006 ± 0.063)
Summary
In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Local cattle breeds were used as triple purpose animals (work, milk, and meat); depending on the region, the animal characteristics, and the geographical boundaries, they began to diverge into the present-day breeds [7] Nowadays, most of these local breeds are fully adapted to a specific habitat or production system and represent a significant resource to satisfy present and future demands for sustainable farming in a changing environment [8].
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