Genetic Diversity of Sheep Breeds from Albania, Greece, and Italy Assessed by Mitochondrial DNA and Nuclear Polymorphisms (SNPs)

Abstract

We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries.

Landscape Genomics in Livestock

“…This can be explained by the easiness of transportation of sheep compared to cattle. Anyway, using a different dataset, Pariset et al (2011) show a good correspondence of breeds to geographical locations.…”

“…From domestication centres, livestock followed human migrations by demic expansion (Cavalli Sforza, 1966) or by active trade (Ajmone-Marsan et al, 2010). For the reconstruction of migration routes landscape genetics has been extensively used to infer also possible alternative routes through land or sea (Pariset et al, 2011). Since molecular markers include sex specific ones, like Y chromosome and mtDNA markers, geographic maps of genetic diversity can be constructed for inferring male or female mediated gene flow .…”

“…By adding or removing neutral markers from datasets it could be possible to individuate the effects of the forces acting on a population (Pariset et al, 2009a(Pariset et al, , 2011). This will work in an efficient way if the number of markers is high, as in the case of landscape genomics.…”

“…Berthouly et al (2009) reported the effects of gene flow due to the spatial distribution of ethnic groups, farmer ethnicity and husbandry practices on goat spatial pattern. Good examples of application of spatial genomics to sheep and goats was performed by the Econogene project (http://www.econogene.eu) (Pariset et al 2006;Bertaglia et al, 2007;Peter et al, 2007;Cañon et al, 2007;Pariset et al, 2011). Within the same project Joost et al (2007) analysed European sheep breeds and found 40 alleles significantly associated with at least one environmental parameter; Pariset et al (2009b) using different landscape genomics approaches identified adaptive variation in goat, which is characterized by a large range of climatic conditions in the rearing areas and by a history of intense trade.…”

“…The nature of the markers used for the analysis can affect the detection of geographical structuring of populations, as suggested by Naderi et al (2007). The simultaneous use of both nuclear and single parent transmitted markers (mitochondrial and Y chromosome) is likely to provide more significant results respect to the use of either marker alone (Hewitt, 2004;Gonçalves et al, 2010;Wang et al, 2011;Pariset et al, 2011).…”