Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds.

BACKGROUND: Local 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 Dreznica 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. RESULTS: Distinct genetic origin of the Dreznica 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 Dreznica 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 Dreznica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. CONCLUSIONS: Genetic diversity analyses revealed that the Slovenian Dreznica 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.

Payments for Conservation of Animal Genetic Resources in Agriculture: One Size Fits All?

Local livestock breeds in Slovenia have been eligible for financial incentives in the form of a fixed payment per livestock unit (LU) since 2002. The scheme has however not been successful in reversing the erosion of animal genetic resources (AnGR). This paper investigates an alternative, whereby incentive payments would better reflect breeders' actual opportunity costs. The paper contributes to the limited existing body of knowledge related to the use of tender mechanisms in the design of the payments for agrobiodiversity conservation schemes (PACS), particularly for AnGR. Empirical findings draw on the results of a stated preference survey involving 301 farmers in Slovenia, engaging, or being potentially able to engage, in the rearing of local pig, sheep and goat breeds. Interval and logistic regression model results suggest that willingness to accept (WTA) conservation support significantly differs from actual payment levels. The estimated WTA was found to be 27% lower for the local sheep and goat breeds and 5% higher for the local pig breed, suggesting that differentiated incentive payments would provide a more cost-effective alternative. Additional analysis of breeders' preferences and motives for engaging in local livestock breed production further informs understanding regarding AnGR conservation policy and the importance of accompanying actions to reverse negative population trends. These include reducing administrative barriers and enhancing the market valorisation of local breeds.