David Neuman, Head of Agrigenomics Sales - Jul 08, 2024

Low-pass whole genome sequencing: A solution for traditional challenges in honey bee genotyping

In recent years, the scientific community has made remarkable strides in genomics, transforming our understanding of the genetic makeup of various organisms. Among these, honey bees (Apis mellifera) hold a special place due to their crucial role in agriculture. Despite this progress, decoding the genomic variation in honey bees presents unique challenges, with high recombination rates and large genomic variation.

The Importance of Honey Bee Genomics

Honey bees are not just producers of honey; they are vital pollinators in our ecosystems, contributing to the reproduction of many flowering plants, including numerous crops. Understanding their genetics is key to addressing issues such as colony collapse disorder, disease resistance, and enhancing traits like honey production and climate adaptability.

The sequencing of the honey bee genome in 2006 was a landmark achievement, revealing a relatively small yet complex genome of about 250 megabases. This genome is rich in adenine and thymine (AT-rich) and exhibits a bimodal GC distribution, making it challenging to sequence. Additionally, honey bees possess DNA methylation, a feature initially thought to be absent in insects. This discovery opened new avenues for exploring epigenetic regulation in bees.

Challenges in Honey Bee Genomics

One of the main challenges in honey bee genomics is the high recombination rate, which is significantly higher than in other organisms. This high recombination rate complicates the identification of genetic variants and the understanding of genetic linkages. Moreover, the genomic variation within honey bee populations is vast due to their diverse subspecies and the extensive movement of bee populations by humans over centuries.

Traditional sequencing methods are often cost-prohibitive for large-scale studies, which are necessary to capture the full extent of genetic diversity in honey bees. Low-pass whole genome sequencing, however, presents an opportunity for researchers to deepen their understanding of genetic variation in bees.

Gencove’s Role in Honey Bee Genomics

Gencove has pioneered low-pass whole genome sequencing as a cost-effective and high-throughput approach to obtaining genome-wide information across many different species. This method involves sequencing a genome at a lower coverage, typically below 1x, in the case of bees, however, closer to 4x. Proprietary imputation algorithms are then used to predict the full genome sequence. This approach significantly reduces costs while maintaining a high level of accuracy, and produces 43 million genome-wide SNPs and 8.2 million INDELs.

Dr. Brock Harper, an assistant professor of Entomology at Purdue University, has been leveraging Gencove’s technology to advance his research in honey bee genomics. By working with collaborators across the United States, Dr. Harper’s team has been able to sequence honey bee populations from various states, aiming to reach a goal of five million genotyped bees.

The Impact of Cost-Effective Sequencing

Gencove’s cost-effective sequencing has enabled researchers to undertake large-scale studies that were previously financially unfeasible. For instance, Dr. Harper’s lab has been using this technology to identify and track the spread of the so-called "killer" honey bees (Apis mellifera scutellata). These bees, known for their aggressive behavior, have been genetically traced back to their introduction in Brazil in the 1950s.

Additionally, the ability to sequence honey bees at a low cost allows for more extensive research into traits such as disease resistance, honey production, and environmental adaptability. This is crucial for developing strategies to support beekeepers and improve bee health and productivity.

Future Directions

The ongoing research facilitated by Gencove’s technology is poised to uncover even more about the genetic underpinnings of honey bee behavior and health. As sequencing costs continue to decrease, as seen in the last year, the potential for genomic studies expands, opening new frontiers in bee conservation and breeding programs.

Furthermore, the integration of genomic data with phenotypic traits holds promise for selective breeding programs. By identifying genetic markers associated with desirable traits, beekeepers can make informed decisions to enhance colony health and productivity.


The field of honey bee genomics is rapidly evolving, thanks in large part to innovative sequencing technologies like those developed by Gencove. These advancements are breaking down financial barriers, allowing researchers to understand more about honey bees' genetic diversity.

For a limited time Gencove is offering low-pass whole genome sequencing and imputation for honey bees starting at $30 USD per sample*. Get in touch today to get started with your next bee genotyping project.

Through collaborative efforts and cutting-edge technology, we are closer than ever to ensuring the sustainability and resilience of honey bee populations. Gencove’s contributions advance scientific knowledge and support the vital work of beekeepers worldwide.

*Offer available July 1st - September 30th, platform access fee not included and minimum sample volumes apply.