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

التفاصيل البيبلوغرافية
العنوان: Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds.
المؤلفون: Pogorevc N; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia., Simčič M; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia., Khayatzadeh N; 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., Sölkner J; 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., Berger B; Department Animal Genetic Resources, AREC Raumberg-Gumpenstein, Institute of Organic Farming and Biodiversity of Farm Animals, 4601 Thalheim b., Wels, Austria., Bojkovski D; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia., Zorc M; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia., Dovč P; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia., Medugorac I; Population Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Lena-Christ-Straβe 48, 8215, Martinsried/Planegg, Germany., Horvat S; Department of Animal science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia. simon.horvat@bf.uni-lj.si.
المصدر: BMC genomics [BMC Genomics] 2021 Jul 17; Vol. 22 (1), pp. 546. Date of Electronic Publication: 2021 Jul 17.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Goats*/genetics , Polymorphism, Single Nucleotide*, Animals ; Genetic Variation ; Genotype ; Italy ; Phylogeny
مستخلص: 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.
(© 2021. The Author(s).)
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معلومات مُعتمدة: P4-0220 Javna Agencija za Raziskovalno Dejavnost RS (SI); J4-1768 Javna Agencija za Raziskovalno Dejavnost RS; Young Researcher Award Javna Agencija za Raziskovalno Dejavnost RS
فهرسة مساهمة: Keywords: Admixture; Austrian goat breeds; Dataset optimization; Drežnica goat; Genetic diversity; Outlier test; Population structure; Slovenian goat breed
تواريخ الأحداث: Date Created: 20210718 Date Completed: 20210720 Latest Revision: 20210722
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8285797
DOI: 10.1186/s12864-021-07802-z
PMID: 34273960
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-021-07802-z