Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays
- 321 Downloads
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.
KeywordsGenetic 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
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.
- Barbato M, Orozco-TerWengel P, Tapio M, Bruford MW (2015) SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontiers in Genetics 6Google Scholar
- Buchmann R, Hazelhurst S (2015) The ‘genesis’ manual. University of the Witwatersrand, JohannesburgGoogle Scholar
- Ciani E, Crepaldi P, Nicoloso L, Lasagna E, Sarti FM, Moioli B, Napolitano F, Carta A, Usai G, D’Andrea M, Marletta D, Ciampolini R, Riggio V, Occidente M, Matassino D, Kompan D, Modesto P, Macciotta N, Ajmone-Marsan P, Pilla F (2014) Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds. Anim Genet 45:256–266CrossRefPubMedGoogle Scholar
- FAO (1998) Secondary guidelines for development of national farm animal genetic resources management plans. Management of Small Populations at Risk, RomeGoogle Scholar
- FAOSTAT (2016) Food and Agriculture Organization of the United Nations. FAOSTAT Database. Rome, Italy: FAO. Retrieved November 18, 2016 from http://www.fao.org/faostat/en/#data/QL
- Fernandez ME, Goszczynski DE, Liron JP, Villegas-Castagnasso EE, Carino MH, Ripoli MV, Rogberg-Munoz A, Posik DM, Peral-Garcia P, Giovambattista G (2013) Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genet Mol Biol 36:185–191CrossRefPubMedPubMedCentralGoogle Scholar
- Hatziminaoglou I (2006a) Sheep and goats in Greece and in the world. Ed. Jahoudi, Thessaloniki Greece. 2nd ednGoogle Scholar
- Hatziminaoglou I (2006b) Sheep and goats in Greece and worldwide. Yahoudi-Yapouli Press, ThessalonikiGoogle Scholar
- Hatziminaoglou I, Liamadis D, Avdi M (2006) Introduction to animal production. Yahoudi-Yapouli Press, ThessalonikiGoogle Scholar
- Hatziminaoglu J, Zervas NP, Boyazoglu J (1990) Prolific dairy sheep breeds in Greece. In: Bougler J (ed.), Tisserand J-L (eds). Les petits ruminants et leurs productions laitières dans la region méditerranéenne.. Montpellier: CIHEAM. pp 25–30 (Options Méditerranéennes: Série A.Séminaires Méditerranéens; n. 12)Google Scholar
- Heaton MP, Leymaster KA, Kalbfleisch TS, Kijas JW, Clarke SM, McEwan J, Maddox JF, Basnayake V, Petrik DT, Simpson B, Smith TPL, Chitko-McKown CG, Consortium ISG (2014) SNPs for parentage testing and traceability in globally diverse breeds of sheep. Plos One 9Google Scholar
- Kijas JW, Lenstra JA, Hayes B, Boitard S, Neto LRP, San Cristobal M, Servin B, McCulloch R, Whan V, Gietzen K, Paiva S, Barendse W, Ciani E, Raadsma H, McEwan J, Dalrymple B, Consortium ISG (2012) Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. Plos Biol 10:e1001258CrossRefPubMedPubMedCentralGoogle Scholar
- Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, Taberlet P, Nicolazzi EL, Solkner J, Simianer H, Ciani E, Garcia JF, Bruford MW, Ajmone-Marsan P, Weigend S (2012) Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 43:483–502CrossRefPubMedGoogle Scholar
- McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, MacLeod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF (2008) Runs of homozygosity in European populations. Am J Hum Genet 83:359–372CrossRefPubMedPubMedCentralGoogle Scholar
- Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A (2015) SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC Genom 16:283CrossRefGoogle Scholar
- R Development Core Team (2010) R: a language and environment for statistical computing. In. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
- Warnes GR, Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B (2011) gplots: various R programming tools for plotting data. R Foundation for Statistical Computing, Vienna. http://CRAN.R-project.org/package=gplot
- Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simao FA, Ioannidis P, Seppey M, Loetscher A, Kriventseva EV (2017) OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. Nucleic Acids Res 45:D744-D749CrossRefPubMedGoogle Scholar