Abstract
The autochthonous cattle population of Greece is like that bred throughout the Balkan Peninsula and they consist of the Brachyceros (“Shorthorn”) and the Podolian or Steppe type. In the middle of the 20th century, eight indigenous breeds of cattle were reported in Greece. Today, four of them are considered officially extinct (Tinos, Andros, Chios, Corfu), three as threatened (Brachykeros, Katerini, and Sykia), and one (Kea) as a rare breed. During the introduction of domesticated cattle to Europe, the east Mediterranean coast and the southern Balkans played a decisive role. Greek cattle breeds originate from a geographical area near the center of domestication with a Mediterranean climate. The breeding of these breeds is characterized by the absence of performance records and thus low use of artificial selection, also by poor feeding and housing conditions as well as by the rare veterinary service. Most of these populations come from the last remains of formerly large populations and a ...
The autochthonous cattle population of Greece is like that bred throughout the Balkan Peninsula and they consist of the Brachyceros (“Shorthorn”) and the Podolian or Steppe type. In the middle of the 20th century, eight indigenous breeds of cattle were reported in Greece. Today, four of them are considered officially extinct (Tinos, Andros, Chios, Corfu), three as threatened (Brachykeros, Katerini, and Sykia), and one (Kea) as a rare breed. During the introduction of domesticated cattle to Europe, the east Mediterranean coast and the southern Balkans played a decisive role. Greek cattle breeds originate from a geographical area near the center of domestication with a Mediterranean climate. The breeding of these breeds is characterized by the absence of performance records and thus low use of artificial selection, also by poor feeding and housing conditions as well as by the rare veterinary service. Most of these populations come from the last remains of formerly large populations and are bred mainly in mountainous areas and/or islands with poor infrastructure. Finally, these populations are reproductively isolated due to geographic distances and physical barriers without the use of artificial insemination. The Greek local cattle breeds have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 11 indigenous cattle populations from continental Greece, Greek islands and Cyprus and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). The following local breeds from Greece and Cyprus were sampled in our analysis: (i) from mainland Greece: Greek Brachyceros breed (n = 97), Katerini breed (n = 20), Prespa cattle (n = 10), Rodope cattle (n = 12), Sykia breed (n = 16), (ii) from the islands: Kea breed (n = 97), Agathonisi cattle (n = 6), Crete cattle (n = 11), Kastelorizo cattle (n = 4), Nisyros cattle (n = 7) and (iii) Cyprus cattle (n = 5).Several parameters of genetic diversity (e.g., heterozygosity and allelic diversity) were estimated and indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. Greek Brachyceros breed present high level in almost all parameters similar with Buša and Anatolian Breeds. This high inbreeding status also resulted in higher genetic differentiation between island and mainland Greek breeds compared to the breeds from the remaining geographic groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding shared ancestry with breeds of Anatolian or Balkan origin. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Cyprus, Kastelorizo, and Agathonisi cattle populations showed a higher indicine ancestry compared to other populations from Greece and the Balkans. All investigated Cyprus and Greek breeds present complex mosaic genomes, as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.
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