Molecular Genetics and Genomics

, Volume 293, Issue 3, pp 753–768 | Cite as

Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays

  • S. Michailidou
  • G. Tsangaris
  • G. C. Fthenakis
  • A. Tzora
  • I. Skoufos
  • S. C. Karkabounas
  • G. Banos
  • A. Argiriou
  • G. Arsenos
Original Article


In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina’s OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (FGRM) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.


Genetic diversity Population structure OvineSNP50K beadchip Ovis aries Breed identification Conservation Breeding programs 



This work was partially supported by the program ‘GOSHOMICS’ under the action COOPERATION 2009 (SYNERGASIA 2009), financed by the European Regional Development Fund and national resources, project code: 09SYN-23-990.

Compliance with ethical standards

Ethical approval

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

438_2018_1421_MOESM1_ESM.pdf (500 kb)
Supplementary material 1 (PDF 500 KB)
438_2018_1421_MOESM2_ESM.pdf (683 kb)
Supplementary material 2 (PDF 683 KB)
438_2018_1421_MOESM3_ESM.docx (16 kb)
Supplementary material 3 (DOCX 16 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • S. Michailidou
    • 1
    • 2
  • G. Tsangaris
    • 3
  • G. C. Fthenakis
    • 4
  • A. Tzora
    • 5
  • I. Skoufos
    • 5
  • S. C. Karkabounas
    • 6
  • G. Banos
    • 1
    • 7
  • A. Argiriou
    • 2
  • G. Arsenos
    • 1
  1. 1.Laboratory of Animal Husbandry, School of Veterinary Medicine, Department of Animal Production, Ichthyology, Ecology and Environmental ProtectionAristotle University of ThessalonikiThessalonikiGreece
  2. 2.Institute of Applied BiosciencesCenter for Research and Technology HellasThermiGreece
  3. 3.Proteomics Research Unit, Center of Basic Research IIBiomedical Research Foundation of the Academy of AthensAthensGreece
  4. 4.Veterinary FacultyUniversity of ThessalyKarditsaGreece
  5. 5.Department of Animal ProductionTechnological Educational Institute of EpirusArtaGreece
  6. 6.Cell and Molecular Physiology Unit, Laboratory of Experimental Physiology, Medical SchoolUniversity of IoanninaIoanninaGreece
  7. 7.Scotland’s Rural College and The Roslin Institute University of EdinburghScotlandUK

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