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

S Michailidou, G Tsangaris, GC Fthenakis, A Tzora, I Skoufos, SC Karkabounas, G Banos, A Argiriou, G Arsenos

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Abstract

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.
Original languageEnglish
Pages (from-to)753 - 768
Number of pages16
JournalMolecular Genetics and Genomics
Volume293
Issue number3
Early online date25 Jan 2018
DOIs
Publication statusFirst published - 25 Jan 2018

Bibliographical note

1031406

Keywords

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

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    Michailidou, S., Tsangaris, G., Fthenakis, GC., Tzora, A., Skoufos, I., Karkabounas, SC., Banos, G., Argiriou, A., & Arsenos, G. (2018). Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays. Molecular Genetics and Genomics, 293(3), 753 - 768. https://doi.org/10.1007/s00438-018-1421-x