Non-Destructive Genotyping of Honeybee Queens to Support Selection and Breeding

Abstract

In traditional bee breeding, the honeybee queen is chosen for breeding based on the performance of the colony produced by its mother. However, we cannot be entirely certain that a specific queen will produce offspring with desirable traits until we observe the young queen’s new colony. Collecting the queen’s genetic material enables quick and reliable determination of the relevant information. We sampled exuviae, feces, and wingtips for DNA extraction to avoid fatally injuring the queen when using tissue samples. Quantity and purity of extracted DNA were measured. Two mitochondrial markers were used to determine the lineage affiliation and exclude possible contamination of DNA extracts with non-honeybee DNA. dCAPS (derived Cleaved Amplified Polymorphic Sequences) markers allowed detection of single nucleotide polymorphisms (SNPs) in nuclear DNA regions presumably associated with Varroa sensitive hygiene and set the example of successful development of genotyping protocol from non-destructive DNA sources. One of the logical future steps in honeybee breeding is introducing genomic selection and non-destructive sampling methods of genetic material may be the prerequisite for successful genotyping. Our results demonstrate that the extraction of DNA from feces and exuviae can be introduced into practice. The advantage of these two sources over wingtips is reducing the time window for processing the samples, thus enabling genotyping directly after the queen’s emergence.

Reconstructing queen genotypes by pool sequencing colonies in eusocial insects: Statistical Methods and their application to honeybee

“…Contrary to large animal species, sampling the queen for genotyping without threatening its integrity is risky. Non-destructive methods to genotype the honeybee queen have been proposed by Gregory and Rinderer (2004), Su et al (2007) or Bubniĉ et al (2020) but can rarely be performed in routine beekeeping practices. Another possible approach is to perform individual or pool genotyping of a set of males (Petersen et al, 2020), gametes of the queen, and reconstruct its genotypes.…”

Cutting corners: The impact of storage and DNA extraction on quality and quantity of DNA in honeybee (Apis mellifera) spermatheca

“…Different tissue types yield different amount and quality of extracted DNA (Lopez Vaamonde et al, 2012;Bubnič et al, 2020). In our work, the median quantities of DNA were between 0.21 and 4.56 ng/μL.…”

“…The paternity of the queen's offspring is usually determined from known sources through an analysis in which worker brood is sampled (Jensen et al, 2005). Such indirect sampling combined with non-lethal indirect genotyping of the queen may serve in future breeding programs as a genomic information and can provide reliable relationship in the selection process (Châline et al, 2004;Gregory and Rinderer, 2004;Bubnič et al, 2020;Eynard et al, 2022). The drawback of such sampling is that it is costly and time consuming.…”

Identification of runs of homozygosity in Western honey bees (Apis mellifera) using whole‐genome sequencing data

“…Another disadvantage of honey bee drones is that they only explain part of the genetic diversity, as multiple paternal origins are involved in the formation of honey bee colonies (Estoup et al, 1994;Neumann et al, 1999;Tarpy et al, 2004). However, genotyping of honey bee queens for the evaluation of admixture and genomic inbreeding without harming them remains difficult (Bubnič et al, 2020;Madella et al, 2020).…”