Conservation Genetics

, Volume 18, Issue 4, pp 893–910 | Cite as

Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives

  • Veronika Kukučková
  • Nina Moravčíková
  • Maja Ferenčaković
  • Mojca Simčič
  • Gábor Mészáros
  • Johann Sölkner
  • Anna Trakovická
  • Ondrej Kadlečík
  • Ino Curik
  • Radovan Kasarda
Research Article


A genome-wide scan of Slovak Pinzgau cattle was prepared for the first time in order to estimate their genetic diversity at a more detailed level compared to previously published studies. The aim of this study was to describe the genetic diversity based on the runs of homozygosity (ROHs), linkage disequilibrium (LD) and effective population size (NeLD) using genome-wide data. Moreover, Bayesian clustering algorithms and multivariate methods were used to detect the population structure, potential admixture level and relationship between Austrian and Slovak Pinzgau cattle with respect to a large meta-population consisting of 15 European cattle breeds. The proportion of ROH segments ranged from 0.43 to 1.91% in Slovak Pinzgau, depending on the minimum size of an ROH. The genomic inbreeding coefficients were higher than the pedigree ones possibly due to the limited number of available generations in pedigree data. The observed NeLD was close to the limit value characterizing the endangerment status, based both on genomic and pedigree data. Population structure within analyzed breeds based on the Wright’s FST index, Nei’s genetic distances, and unsupervised as well as supervised analysis has been established. Overall, these analyses clearly distinguished populations based on their origin. A detailed analysis of the introgression of each breed into the Pinzgau breeds prepared using a Bayesian approach showed that the contribution of Holstein cattle in Austrian as well as Slovak Pinzgau was larger than contribution of beef breeds. A possible reason is the recent usage of Holstein sires to increase milk production. There are considerable differences between well-defined regions that clearly distinguish Austrian and Slovak Pinzgau, despite their close common history. Generally, the breeding program of Austrian Pinzgau is more focused on meat production than Slovak Pinzgau, which was clearly reflected in the obtained autozygosity islands. Considering the genetic establishment of Slovak Pinzgau population the genetic potential of the breed is insufficiently used. On a long term, more global breeding program including very close populations will be more efficient providing higher genetic progress and diversity. Established methodology how to distinguish genealogically close populations on high-throughput molecular information based of Slovak and Austrian Pinzgau can be proposed as general for analysis of differences in all highly related breeds.


Autozygosity BovineSNP50 BeadChip Genetic distance Linkage disequilibrium Effective population size 



Thanks to anonymous reviewers that constructively improved final version of this manuscript.


This study was supported by the Slovak Research and Development Agency under the Contract no. APVV-0636-11 and APVV-14-0054.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material (967 kb)
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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Veronika Kukučková
    • 1
  • Nina Moravčíková
    • 1
  • Maja Ferenčaković
    • 2
  • Mojca Simčič
    • 3
  • Gábor Mészáros
    • 4
  • Johann Sölkner
    • 4
  • Anna Trakovická
    • 1
  • Ondrej Kadlečík
    • 1
  • Ino Curik
    • 2
  • Radovan Kasarda
    • 1
  1. 1.Department of Animal Genetics and Breeding BiologySlovak University of Agriculture in NitraNitraSlovakia
  2. 2.Department of Animal ScienceUniversity of ZagrebZagrebCroatia
  3. 3.Department of Animal Science, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
  4. 4.Division of Livestock SciencesUniversity of Natural Sciences and Life SciencesViennaAustria

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