Background With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. Results Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. Conclusions The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.

One indigenous water buffalo population to Anatolia was characterised with 11 cattle autosomal microsatellite loci. A set of 4 cattle microsatellite loci was found to be polymorphic in the Anatolian buffalo genome. Genotyping of these polymorphic microsatellite loci revealed alleles ranging from 3 to 9. The observed heterozygosity ranged from 0.550 to 0.775 and the expected heterozygosity ranged from 0.494 to 0.815. The FIS value within each locus, changed from –0.101 to 0.205. Total FIS was 0.043 indicating that Anatolian water buffalo population samples seemed to be in Hardy- Weinberg expectation

ABSTRACT:In Turkey most farmers keep 1-2 buffaloes for family consumption and this system is very widespread in villages while farms with around 100 heads are located near to the big cities. These two most common housing systems were used to contribute to the somatic characterization of Anatolian buffalo in the context of a wide typification programme of this buffalo aimed to improve its productive and reproductive potentiality in agreement with a sustainable development. 76 males and 127 females of the Istanbul district and 32 males and 70 females raised in Danamandra vıllage of Silivri district were measured. On each buffalo, withers height, rump height, body length, chest depth and chest width were determined. The results showed a significant difference between males and females starting from 12 months in buffaloes of Danamandra village and from 3 years of age in animals of Istanbul district.

Italian Maremmana, Turkish Grey and Hungarian Grey breeds belong to the same Podolic group of cattle, have a similar conformation and recently experienced a similar demographic reduction. The aim of this study was to assess the relationship among the analysed Podolic breeds and to verify whether their genetic state reflects their history. To do so, approximately 100 single nucleotide polymorphisms (SNPs) were genotyped on individuals belonging to these breeds and compared to genotypes of individuals of two Italian beef breeds, Marchigiana and Piemontese, which underwent different selection and migration histories. Population genetic parameters such as allelic frequencies and heterozygosity values were assessed, genetic distances calculated and assignment test performed to evaluate the possibility of recent admixture between the populations. The data show that the physical similarity among the Podolic breeds examined, and particularly between Hungarian Grey and Maremmana cattle that experienced admixture in the recent past, is mainly morphological. The assignment of individuals from genotype data was achieved using Bayesian inference, confirming that the set of chosen SNPs is able to distinguish among the breeds and that the breeds are genetically distinct. Individuals of Turkish Grey breed were clearly assigned to their breed of origin for all clustering alternatives, showing that this breed can be differentiated from the others on the basis of the allelic frequencies. Remarkably, in the Turkish Grey there were differences observed between the population of Enez district, where in situ conservation studies are practised, and that of Bandirma district of Balikesir, where ex situ conservation studies are practised out of the original raising area. In conclusion, this study demonstrates that molecular data could be used to reveal an unbiased view of past events and provide the basis for a rational exploitation of livestock, suggesting appropriate cross-breeding plans based on genetic distance or breeding strategies that include the population structure.

The genetic variation and relationships among six Turkish water buffalo populations, typical of different regions, were assessed using a set of 26 heterologous (bovine) microsatellite markers. Between seven and 17 different alleles were identified per microsatellite in a total of 254 alleles. The average number of alleles across all loci in all the analysed populations was found to be 12.57. The expected mean heterozygosity (H(e)) per population ranged between 0.5 and 0.58. Significant departures from Hardy-Weinberg equilibrium were observed for 44 locus-population combinations. Population differentiation was analysed by estimation of the F(st) index (values ranging from 0.053 to 0.123) among populations. A principal component analysis of variation revealed the Merzifon population to show the highest differentiation compared with the others. In addition, some individuals of the Danamandira population appeared clearly separated, while the Afyon, Coskun, Pazar and Thural populations represented a single cluster. The assignment of individuals to their source populations, performed using the Bayesian clustering approach implemented in the structure 2.2 software, supports a high differentiation of Merzifon and Danamandira populations. The results of this study are useful for the development of conservation strategies for the Turkish buffalo.