Neža Pogorevc1, Mojca Simčič1, Negar Khayatzadeh2, Johann Sölkner2, Beate Berger3, Danijela Bojkovski1, Minja Zorc1, Peter Dovč1, Ivica Medugorac4, Simon Horvat5. 1. Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia. 2. Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna, Gregor Mendel Str. 33, A-1180, Vienna, Austria. 3. Department Animal Genetic Resources, AREC Raumberg-Gumpenstein, Institute of Organic Farming and Biodiversity of Farm Animals, 4601 Thalheim b., Wels, Austria. 4. Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Lena-Christ-Straβe 48, 8215, Martinsried/Planegg, Germany. 5. Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia. simon.horvat@bf.uni-lj.si.
Abstract
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 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. RESULTS: Distinct 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. CONCLUSIONS: 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. 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.
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 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. RESULTS: Distinct 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. CONCLUSIONS: 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. 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.
Authors: A Burren; M Neuditschko; H Signer-Hasler; M Frischknecht; I Reber; F Menzi; C Drögemüller; C Flury Journal: Anim Genet Date: 2016-07-20 Impact factor: 3.169
Authors: C Kumar; S Song; P Dewani; M Kumar; O Parkash; Y Ma; K K Malhi; N Yang; J M Mwacharo; X He; L Jiang Journal: Anim Genet Date: 2018-09-19 Impact factor: 3.169