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.

Keywords: Mediterranean; SNPs; domestication; mtDNA; sheep.

Figure 1

Neighbour-joining tree based on the 154 mtDNA haplotypes, showing differences among haplogroups and wild sheep (outgroup). Numbers indicate the percentage bootstrap support (10,000 resamplings).

Figure 2

Geographical distribution of haplogroups, circles are proportional to the number of samples. (green: haplogroup A; purple: haplogroup B; red: haplogroup C).

Figure 3

First (a) and second (b) components of eigenvectors spatial distribution calculated on mtDNA marker and first (c) and second (d) components calculated on SNPs markers. Background image is GTOPO30, a global digital elevation model (DEM) with a horizontal grid spacing of 30 arc seconds (approximately 1 kilometer) produced by the U.S. Geological Survey's Center for Earth Resources Observation and Science (EROS). The line in the map (c) shows the isoline for an eigenvalue of 0. It appears on panel C only because this is the only geographical configuration for which a limit is so obvious. The circle around the RUDA breed shows an isoline for the eigenvalue of 0.03.

Figure 4

PCA analysis of the breeds assessed by SNP markers. The first three axes, cumulatively explaining 48.87% of the total inertia, were considered.