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Molecular approach to preservation of animal genetic resources

DAGENE workshop, Bled, September 03, 2004. Molecular approach to preservation of animal genetic resources. University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Groblje 3, 1230 Domzale, Slovenia. Peter DOVC. Population reduction whirl. Small population. Inbreeding.

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Molecular approach to preservation of animal genetic resources

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  1. DAGENE workshop, Bled, September 03, 2004 Molecular approach to preservation of animal genetic resources University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Groblje 3, 1230 Domzale, Slovenia Peter DOVC

  2. Population reduction whirl Small population Inbreeding Genetic drift Reduction of individual fitness and adaptation ability Loss of genetic variation Reduced reproduction efficacy Increased mortality Smaller population

  3. Domesticated animals Short time intervals Ex situ conservation Genetic variation controlled by man Conservation of animal genetic resources • Free living animals • Open end • In situ only • Natural selection, genetic variability limited within their genetic system

  4. Parts of population held in captivity Frozen repositories Molecular markers for resolving taxonomic uncertainties addressing inbreeding (Florida panther) loss of genetic diversity in wild populations Establishment of genetic resources Advance in genomic research Genetic management of rare populations

  5. Breeds involved in the formation of the Lipizzan breed Berber Iberian horse Arabs Italian horses Andalusians Karst horse Neapolitans Lipizzan Nuerenberg, 1998

  6. Population structure of the Lipizzan horse (random sample of 30 horses, 20 markers, no missing data, genotypic data for individuals) NJ-Tree (Shared Allele Distance) Principal Component Analysis

  7. founder mare Impact of pedigree errors on haplotype distribution error error • 56 maternal family lines • 40 single haplotyp • 11 two haplotypes • 5 three haplotypes analysed samples

  8. A23 A21 A U A22 Gratiosa Strana V A08 N A07 A06 A01 Gaetana K M Z A05 L J I A04 A27 A24 Thais A16 Betalka Monteaura A13 O Wera A03 A14 Q Allegra A15 P Batosta H A26 Slavina A02 Dubovina A11 X A25 Capriola A12 B C E D A10 A09 0.01 NJ tree identical haplotypes A28 A17 1 nucleotide difference Trompeta A20 G A19 2 nucleotides difference F T S R

  9. 650 604 585 811 585 672 596 777 498 597 534 55 726 667 809 811 root 644 595 667 Kavar et al., 2002

  10. Two forms of Marble trout Predelica form Idrijca form

  11. Distribution of trout populations in Slovenia

  12. mtDNA: results Polymorphic sites and different genotypes C

  13. Primer designation Number of fragments UBC-509 9 UBC-516 12 UBC-566 7 UBC-571 13 UBC-744 9 UBC-759 15 RAPD study Agilent 2100 Bioanalyzer

  14. Ribnica Zadlaščica Soča Povodje Tolminka Sovpot Studenec Krka Mahnečica Obrh The Correspondence analysis

  15. Pronounced phenotypic variation among grayling populations has been observed Constant decline of the population size during the last two decades threatened the existence of grayling in some regions, therefore Grayling… stocking is an inevitable conservation action

  16. The Adriatic populations of grayling could be, according to evolutionary or phylogenetic species concept,potentially a distinct species According to the mtDNA and MS data the Adriatic pop. of grayling forman evolutionary significant unit (ESU)which is a formal unit for conservation actions Proposed name: Adriatic grayling Conservation of the “Adriatic grayling”

  17. MOLECULAR PHYLOGENY OF ARCHAIC TROUTS AND THEIR TAXONOMIC CLASSIFICATION SALMONIDAE FAMILY (common characteristics) • Native to Northern hemisphere • Characteristically coldwater fishes • Many are anadromous • Adipose fin present • Predators

  18. SALMONID CLASSIFICATION(three subfamilies) outgroup • Coregoninae • Thymallinae • Salmoninae

  19. Acantholingua (belvica) Brachymystax (lenok) Hucho Oncorhynchus (pacific salmon) Salmo Salmothymus (soft muzzle trout) Salvelinus SALMONINAE CLASSIFICATION (seven genera) • S. salar • S. marmoratus • S. trutta • Atlantic • Danubian • Adriatic • Mediterranean

  20. THE ARCHAIC TROUTS… Brachymystax lenok • …exhibit several plesiomorphies • Short, broad maxillae • Short dentaries • Small teeth • Obligatory freshwater • etc… Salmothymus obtusirostris Acantholingua ohridana

  21. RECLASSIFICATION BASED ON MOLECULAR DATA(mtDNA, GH2C, ITS1) Thymallus Salmothymus Hucho Brachymystax Salvelinus Acantholingua Salmo Oncorhynchus Thymallus Brachymystax Acantholingua Salmothymus Hucho Salvelinus Salmo Oncorhynchus

  22. NATURAL HABITATS OF Salmothymus S. o. krkensis S. o. oxyrhynchus S. o. salonitana S. o. zetensis J. Prosek

  23. INTERGENERIC TREE based on mtDNA control region and cyt b gene Coregonus lavaretus Coregonus albula Thymallus thymallus Thymallus arcticus Salvelinus alpinus Brachymystax lenok Salvelinus fontinalis Oncorhynchus keta Salmo trutta Acantholingua ohridana Salmo salar Salmothymus obtusirostris Oncorhynchus mykiss 0.1

  24. Credits: Department of Animal Science, BF, University of Ljubljana Tatjana Kavar Franc Habe Simona Susnik Tamara Jug Enver Melkic Ales Snoj Andrej Razpet Ludwig-Bolzmann Institut, VU Wien: Roland Achmann Franz Zohmann Gottfried Brem BOKU, Wien Peter Zechner Hans Sölkner Faculty of Veterinary Science, University of Bern Eliane Marti Faculty of Veterinary Science, University of Budapest Imre Bodo University Montpellier, CNRS Patrick Berrebi Tour du Valat Alain Criveli

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