Science

The iPLEX MassARRAY developed by Henriques et al. (2018) and our very own Dr Mark Barnett. This platform is typically used on DNA extracted from drones enabling the queen’s genotypes at these SNPs to be inferred. The platform is specifically designed to test for C lineage admixture levels in M lineage honey bees. We have compared admixture estimates for drones we have whole genome sequence (WGS) data for to estimates based on this array, and the results are very consistent.

The test analyses a small number of variants in the bees’ DNA (known as single nucleotide polymorphisms or ‘SNPs’). These particular variants have been shown to differentiate the 2 main honey bee lineages present in the UK: M – mellifera, or C – carnica/ligustica. This test allows to see how much hybridisation (admixture) is present in the bees, and is useful for projects focusing on breeding ‘native’ bees, selecting for M or C lineage. Traditionally native bees were identified based on physical characteristics such as wing venation and hair colour, however these will be under the genetic control of a very small number of the 10,000+ genes in the genome. Consequently, breeding on these characteristics alone will simply select for the handful of genes involved in their development. The SNPs on this however are distributed throughout the genome, providing a much more balanced and informed approach.

The Mitochondrial DNA assay uses PCR amplification and Sanger sequencing of tRNA-COII mitochondrial barcode using E2 and H2 primers designed by Garnery et al. (1992). This method will indicate maternal ancestry from the 16 kb mitochondrial genome only.

A Principal Components Analysis (PCA) reveals the same clusters in WGS and iPLEX data. B C-lineage ancestry estimates are highly correlated (r2 = 0.94) between WGS and iPLEX data. C Admixture (ALStructure) plots for WGS and iPLEX data assuming 2 genetic backgrounds.