Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

Abstract

Background: The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socioeconomic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results: We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that 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. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed 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 crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. 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. Conclusions: 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 still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.

Genomic Characterization of a Set of Iberian Peninsula Bovine Local Breeds at Risk of Extinction: Morenas Gallegas

“…The results have evidenced the own genetic signatures of the Limiá, Frieiresa, Vianea, and Caldelá breeds, as revealed by the PCA and Reynolds genetic distance dendrograms which clearly separate them with respect to the Iberian Peninsula, Italian, and French bovine breeds analyzed that are grouped in different clusters in agreement with previous results [23,24]. The Morenas Gallegas bovine breeds are mainly located in mountainous rural areas that prevented their spread to other areas.…”

“…In addition, the adaptation of rare breeds to local environmental can represent a valuable source of genes [22]. Recently, several authors have successfully analyzed a set of local breeds in an European context [23,24].…”

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

“…Recently, various studies have successfully shed light on the patterns of genetic diversity and the relatedness of cattle populations in Europe and worldwide [ 21 – 24 ]. However, the knowledge on the genetic constitution of red cattle breeds from Northern Europe is still limited.…”

Μελέτη Των Χαρακτηριστικών Ποιότητας Των Παραγόμενων Σφάγιων Και Του Βόειου Κρέατος Στην Ελλάδα

“…Σύμφωνα με τη διεθνή βιβλιογραφία, οι εποχιακές αλλαγές στη θερμοκρασία επηρεάζουν το επίπεδο του γλυκογόνου πριν τη σφαγή και συνεπώς το τελικό pH και την ποιότητα του κρέατος (Kadim et al, 2004, Florek et al, 2009 (Papachristou et al, 2020). Η ποιότητα του κρέατος της φυλής Κατερίνης αναφέρεται ως μέτρια λόγω της σκληρότητας των μυών, που οφείλεται στο ότι εκτρέφονται εκτατικά σε ιδιαίτερα σκληρές περιβαλλοντικές συνθήκες (Ligda, 2009, Karatosidi et al, 2013, Papachristou et al, 2020. Η ίδια διαδικασία ακολουθήθηκε και για τα δείγματα από την 13 η θωρακική πλευρά μετά από την 7 η ημέρα της σφαγής.…”

“…Σύμφωνα με τον Κατσαούνη (2000), τα γηγενή βοοειδή της Ελλάδας κατατάσσονται σε δύο φυλές, εκείνα του υποείδους Bos taurus europeus (Ελληνική Βραχυκερατική και Ελληνική Στεππική) και σε μία αυτά του είδους Buballus Bubalis (Ελληνικός Βούβαλος). Οι φυλές Κατερίνης και Συκιάς ανήκουν στην αυτόχθονη φυλή βοοειδών της Στεππικής φυλής, που προέρχεται από τον Bos primigenius(Ligda, 2009, Papachristou et al, 2020. Οι εκπρόσωποι της φυλής αυτής χαρακτηρίζονται από μικρού μεγέθους ζώα με χαμηλή παραγωγή σε γάλα και κρέας ενώ, στο παρελθόν, χρησιμοποιούνταν ευρέως και ως ζώα εργασίας.…”