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.

S u m m a r yHoney bees defensin have a high level of polymorphism and exist as two peptides -defensin 1 and 2. Defensin 1 is synthesized in the salivary glands and is responsible for social immunity. Defensin 2 is synthesized by cells of the fat body and hemolymph is responsible for individual immunity. Defensins are inducible and controlled by the interaction of Toll and Imd signaling pathways and have a broad spectrum of antimicrobial action. The use of chitosan as an immunomodulator has been shown to lead to an increase in the expression levels of defensin and abaecin in the honey bee organism. Stimulation of the transcriptional activity of the defensin genes will allow for the control of a honey bee colony's immunity level, and reduce the using of antibiotics and other chemicals.

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