Distribution of the Main Apis mellifera Mitochondrial DNA Lineages in Italy Assessed Using an Environmental DNA Approach

Abstract

Growing interest has been emerging on the need to monitor the genetic integrity of the European Apis mellifera subspecies that could be threatened by the human-mediated dispersion of non-native populations and lines. Mitochondrial DNA (mtDNA) lineages can provide useful information for this purpose. In this study, we took advantage of the environmental DNA (eDNA) contained in the honey, which can be analyzed to detect the main groups of mitotypes of the honey bees that produced it. In this study, we applied this eDNA to produce a distribution map all over the Italian peninsula and the two major islands (Sicily and Sardinia) of the following three honey bee mtDNA lineages: A, C and M. A total of 607 georeferenced honey samples, produced in all Italian regions, was analyzed to detect these lineages. The A lineage was widespread in Sicily, as expected, considering that A. m. siciliana carries the African lineage. Surprisingly, this lineage was also reported in about 14% of all other samples produced in almost all continental regions, and in Sardinia. The applied method obtained an updated distribution map of honey bee mtDNA lineages that could be useful to design policies for the conservation of Italian honey bee genetic resources.

Application of Next Generation Semiconductor-Based Sequencing for the Identification of Apis mellifera Complementary Sex Determiner (csd) Alleles from Honey DNA

“…The reasons for this difference could be attributed (i) to the lower number of large alleles that we could amplify/sequence from the degraded honey DNA (as discussed above, a potential bias in our study) than what could be obtained directly from the drone DNA in [23]; (ii) to a higher level of functional inbreeding in the Italian population analyzed in our study (from a limited number of colonies) than in the Polish populations that were also investigated from a larger number of colonies [23]; and/or (iii) to different levels of subspecies introgression (which usually increases variability) between the Italian and the Polish honey bee populations. This latter aspect could be hypothesized considering the high rate of hybridization of the original dark bee in Poland, as demonstrated by the mitochondrial and nuclear DNA markers [50], and the relatively lower level of hybridization that might have experienced the A. m. ligustica, particularly in the Italian region from which the analyzed samples originated (Emilia-Romagna), as could be inferred from our recent mtDNA investigation [34]. Other studies are needed to better address these questions.…”

“…Honey is a unique source of environmental DNA (eDNA) as it contains traces of all the organisms that directly or indirectly contributed to produce it or were part of the hive environment where it was produced [30][31][32][33][34][35][36][37][38]. Therefore, honey also contains the DNA of the honey bees that produced it [33].…”

“…Therefore, honey also contains the DNA of the honey bees that produced it [33]. We recently analyzed honey bee mitochondrial DNA (mtDNA) variability using honey as a source of DNA [33] and produced a distribution map of the main A. mellifera mtDNA lineages in Italy [34]. We also applied whole DNA shotgun sequencing approaches using next generation sequencing platforms for metagenomic analyses of honey DNA, and established a method to identify the A. mellifera subspecies using variants sequenced and retrieved from this matrix [31,32].…”

“…We also applied whole DNA shotgun sequencing approaches using next generation sequencing platforms for metagenomic analyses of honey DNA, and established a method to identify the A. mellifera subspecies using variants sequenced and retrieved from this matrix [31,32]. The method offers the possibility of analyzing more than one colony and many queen lineages at the same time, considering that honey (as it is usually prepared by the beekeepers) is derived from several families or even more than one apiary [33,34,37,38]. Therefore, honey can be used to obtain a quite extensive population-wide picture of the presence of honey bee genetic features including information on variability at the csd gene.…”

Honey Environmental DNA Can Be Used to Detect and Monitor Honey Bee Pests: Development of Methods Useful to Identify Aethina tumida and Galleria mellonella Infestations

“…Honey is a unique collector of eDNA that can be exploited for several applications that may benefit the beekeeping sector [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. Environmental DNA in the honey derives from all organisms that directly and indirectly have been involved in its production process and that have been part of the hive ecosystem where it comes from [ 10 , 11 ].…”