Development and application of genomic approaches to identify Apis mellifera subspecies

A growing concern across Europe is emerging to preserve the genetic integrity of Apis mellifera populations and subspecies that might be adapted to local environmental conditions and climates. Subspecies integrity is also important for the beekeeping sector i) that in many countries or regions requires certified queens of authorized subspecies, according to local regulations, or ii) that needs different genetic resources to design selection and crossbreeding programs. In this study we developed and applied DNA based approaches to identify the honey bee subspecies, combining information at the mitochondrial DNA and nuclear genome levels. These methods were applied both indirectly, using environmental DNA (eDNA) present in the honey, and directly, using DNA extracted from honey bee workers of different colonies to obtain genetic information on the A. mellifera populations of the whole Italian peninsula, Sardinia and Sicily. In addition, results obtained with the traditional morphometric method, usually applied to identify honey bee subspecies, have been compared with results obtained from genomic analyses. Genomic data revealed a broad genetic diversity in the Italian honey bee populations. Genomic approaches resulted much more informative than morphometric analyses. We also demonstrated that eDNA from honey can be exploited to design a cost-effective population genetic study in honey bees. The obtained results can be useful to design conservation strategies of A. mellifera genetic resources in Italy.