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.

the animal selection with favourable phenotypes of the past has been, currently, replaced by the genotype selection on quantitative traits, assisted by the expanding molecular techniques in the context of livestock improvement. in this study, the c.112t>c polymorphism in exon ii of β-lactoglobulin (β-LG) gene was investigated in karagouniko and chios sheep breeds by using polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP), and possible associations with milk traits were examined. in total, 125 blood dna samples were isolated for PCR-RFLP analysis and the respective 217 milk samples' composition profile was obtained. The goodness of fit test to Hardy-Weinberg equilibrium (HWE) for β-LG genotypes was estimated and associations found between β-LG genotypes and raw milk composition. two alleles and three genotypes were observed (AA, AB and BB) in both breeds, and Chios breed significantly deviated (P≤0.05) from Hardy-Weinberg equilibrium (HWE). Conclusively, linear mixed model analysis on samples, from both breeds collectively, showed significant effects of β-LG genotype on lactose percentage and somatic cell count (SCC), lactation stage on daily milk yield and protein, while the breed effect was significant only on daily milk yield.

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In this study, we analyzed microsatellite variation in DNA obtained from hair samples collected from 46 local Greek horse populations originating from the islands of Skyros (Skyros Small Horse; n=9), Rhodes (Rodos Small Horse; n=6), Lesvos (with the traditional miniature Midili Small Horse (n=2) and the larger Lesvos Gaiter (n=22)) and Crete (Messara) (n=7). We used 15 autosomal microsatellite markers (VHL20, HTG4, AHT4, HMS7, HTG6, AHT5, HMS6, ASB2, HTG10, HTG7, HMS3, HMS2, ASB17, ASB23 and LEX33) for the genetic characterization of the above populations and exploration of their genetic structure and diversity levels. A total of 120 alleles were detected across the 15 loci with a minimum of 4 alleles in HTG7 locus and a maximum of 13 alleles in ASB17 locus. Τhe total per population number of alleles was 42 (Skyros Small Horse), 20 (Rodos Small Horse), 71 (Lesvos Gaiter), 52 (Messara breed) and 21 (Midili Small Horse). The effective number of alleles (Ne) per locus ranged from 1.47±0.13 (Rodos Small Horse) to 4.67±0.31 (Lesvos Gaiter). The allelic richness (Ar) was between 1.50±0.12 (Rodos Small Horse) and 2.93±0.08 (Lesvos Gaiter) and the average Polymorphism Information Content (PIC) values varied from 0.200±0.035 (Rodos Small Horse) to 0.733±0.026 (Lesvos Gaiter). No significant deviations from H-W equilibrium were found except for three loci (ASB2, HTG10 and LEX33) in Messara and one locus (ASB23) in Lesvos Gaiter. Τhe inbreeding coefficient (Fis) ranged from -0.130 (Rodos Small Horse) to 0.042 (Lesvos Gaiter). The observed (Ho) and expected (He) multilocus heterozygosity mean estimations were highest in Lesvos Gaiter (0.764±0.027 and 0.783±0.024, respectively) and smallest in Rodos Small Horse (0.300±0.075 and 0.269±0.064, respectively). Across loci, the total genetic diversity HT was 0.741, the diversity among subpopulations HS was 0.621 and the multilocus genetic differentiation GST was 0.161, which was rather high. The population of Rodos Small Horse separated from the remaining horses as shown by factorial correspondence analysis, population assignment and metric multidimensional scaling diagrams. This study highlights the loss of genetic diversity in small isolated horse populations and the urgent need to take protective measures to preserve them.