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

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 (F) 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 structure and admixture in sheep from terminal breeds in the United States

“…In addition, the observed heterozygosity was consistent with other US sheep including Suffolk, Rambouillet, Columbia, Polypay and Targhee (Zhang et al 2013). However, the breeds in this study had lower observed heterozygosity when compared with Boutsko, Karagouniko and Chios breeds from Greece (Michailidou et al 2018).…”

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

“…Especially for Spanish breeds [22], this has been stimulated by seasonal transhumant migrations [23]. Current patterns of genetic diversity have been interpreted in historic and environmental terms, for example in Switzerland [24], mainland Italy [25,26], Sicily [27], Belgium [28], France [19], the Pyrenean region [29], Spain [30], Greece [31], Wales [32], Russia [33], Nepal [34], China [35,36], Iran [37], north Africa [38,39], South Africa [40], Ethiopia [41,42], New-Zealand [43] and the Carribean region [44] and Merino sheep generally [20]. Recurring observations and themes are the contrast between sheep with fat and normal tails [26,33,35,41,42], the influence of Merino sheep [19,20,33,39] or other breeds [25,44], the level of breed separation [27,30,32,38,39,43] and the adaptation to the environment [34,36,…”

Genetic improvement of indigenous Greek sheep and goat breeds

“…GELASAKIS, G. BANOS, G. ARSENOS sity within and between breeds is an important step towards revealing the genetic architecture of animal traits. Studies aiming to characterize indigenous Greek sheep breeds and assess genetic distances between them have been based on polymorphisms of blood proteins (Rogdakis et al, 1995;Koutsouli and Rogdakis, 2002) and different types of markers such as microsatellite loci (Bizelis et al, 2007;Koutsouli et al, 2007;Ligda et al, 2009;Mastranestasis et al, 2015;Loukovitis et al, 2016), Random Amplified Polymorphic DNA (RAPD) (Mastranestasis et al, 2011) and SNPs (Pariset et al, 2011;Kominakis et al, 2017a;Michailidou et al, 2018). Respective studies on indigenous Greek goats are limited and used either microsatellite markers (Cañon et al, 2006) or SNPs (Pariset et al, 2009).…”