An Overview of Ten Italian Horse Breeds through Mitochondrial DNA

Abstract

Background: The climatic and cultural diversity of the Italian Peninsula triggered, over time, the development of a great variety of horse breeds, whose origin and history are still unclear. To clarify this issue, analyses on phenotypic traits and genealogical data were recently coupled with molecular screening.

Methodology: To provide a comprehensive overview of the horse genetic variability in Italy, we produced and phylogenetically analyzed 407 mitochondrial DNA (mtDNA) control-region sequences from ten of the most important Italian riding horse and pony breeds: Bardigiano, Esperia, Giara, Lipizzan, Maremmano, Monterufolino, Murgese, Sarcidano, Sardinian Anglo-Arab, and Tolfetano. A collection of 36 Arabian horses was also evaluated to assess the genetic consequences of their common use for the improvement of some local breeds.

Conclusions: In Italian horses, all previously described domestic mtDNA haplogroups were detected as well as a high haplotype diversity. These findings indicate that the ancestral local mares harbored an extensive genetic diversity. Moreover, the limited haplotype sharing (11%) with the Arabian horse reveals that its impact on the autochthonous mitochondrial gene pools during the final establishment of pure breeds was marginal, if any. The only significant signs of genetic structure and differentiation were detected in the geographically most isolated contexts (i.e. Monterufolino and Sardinian breeds). Such a geographic effect was also confirmed in a wider breed setting, where the Italian pool stands in an intermediate position together with most of the other Mediterranean stocks. However, some notable exceptions and peculiar genetic proximities lend genetic support to historical theories about the origin of specific Italian breeds.

Fig 1. Sampling locations and frequency distributions of mitochondrial haplogroups.

Breed code as in Table 2.

Fig 2. Median-Joining Network based on control-region sequences of ten Italian horse breeds.

The asterisk indicates the haplotype identical to ERS.

Fig 3. A two-dimensional breed-based bi-plot of mtDNA haplogroup profiles (S2 Table) from the eleven breeds analyzed in this study.

The rarest haplogroups (with overall frequencies ≤ 0.5%) H and K were phylogenetically grouped with the corresponding sister clades I and J, respectively. The geographic labels, indicated in bold, represent the centroids of breeds typical of Italy (in blue) and Sardinia (in green).

Fig 4. A two-dimensional region-based PCA plot obtained by including the available horse mtDNA data (S3 and S4 Tables).

The eleven breeds analyzed in this study (and corresponding macroareas) are highlighted. The macrogeographic labels, indicated in bold and underlined, represent the centroids of breeds from the area. Only those breeds with at least 15 different haplotypes were considered statistically significant and included in the final PC analysis. Below is the plot of the contribution of each haplogroup to the first and second PC (projections of the axes of the original variables).