Abstract
BackgroundLocal breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.ResultsDistinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.ConclusionsGenetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.
Highlights
Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change
Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds
We focused on methodology and investigated how different post-genotyping approaches to dataset formation can affect the genetic diversity and population structure parameters
Summary
Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Local breeds are being recognized as an important way forward to economically, environmentally, and socially sustainable animal production in both developed and developing countries. Likewise, they provide a basis for future studies on diversity, domestication and positional cloning of interesting genes and traits segregating in the breeds. They provide a basis for future studies on diversity, domestication and positional cloning of interesting genes and traits segregating in the breeds Such rare local breeds demonstrate phenotypes implying that they retained adaptive and selected alleles to thrive in alpine environments with harsh climate conditions that will likely become more widespread as global temperatures continue to rise. Decreasing population size and loss of genetic diversity in rare breeds presents a general problem
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