Dr Mark Barnett on the genetics of bees
The creation of the campus apiary and how whole genome sequencing, bioinformatics and breeding could help honey bee health.
In this interview, Maggie Szymanska talked with Dr Mark Barnett about how he and his colleague Dr Tim Regan have used whole genome sequencing to identify organisms living inside honey bees, and how they use that knowledge to help to improve bee health and to identify honey bees native to the UK. Mark coordinates the bee apiary on our campus.
Could you tell me about your work in a nutshell?
I work in the laboratory of Tom Freeman. The laboratory combines lab and computational methods to examine complex biological systems with particular interest in data visualisation, together with experimental studies, to create and test models of biological pathways. A biological pathway is a series of actions between molecules that results in a particular product or change in the cell eg genes can be turned on or off.
In the past few years we have started doing research on honey bees and it is my aim to develop that further. We have several ongoing projects and we are currently tracking funding to cement this work.
We built an apiary here at the Institute a few years ago to primarily support honey bee research, however things quickly developed beyond this and the campus apiary now makes it possible for all staff and students to experience beekeeping and help manage the bees.
We have run three beekeeping courses on campus that equip people with all they need to know to help in the apiary. The apiary also helps to promote sustainability by enhancing pollination on campus and also contributes towards the well-being of staff and students as beekeeping is a fun and relaxing activity. There is a definite tendency not to think about anything else whilst you examine a hive of 40,000 bees.
So I now have a team of people helping me out there, which will help in continuing research in this field.
What are the challenges you experience?
My biggest challenge is probably that my background is in developmental biology and neuroscience, not insects. However, having become an enthusiastic beekeeper in 2010, I was very happy for this to come into my work life.
For example, at the moment, I’m trying to dissociate honey bee pupae for single cell sequencing, so that we can create an expression atlas of the developing worker bee (a database of the genes expressed in each cell of the bee). This is very different from my previous research.
I suppose the other big challenge I face is that I am traditionally a lab-based scientist. However, right now there is so much data being generated that computer science and bioinformatics are becoming more and more important. It has become a necessity for lab-based scientists to understand and use those techniques. Learning to align sequencing reads to the honey bee genome and then to use programmes to identify all the genetic variation was a big challenge for me, as there are no graphical user interfaces for this. It’s all done on the command line, so you need to learn to write scripts. But I really wanted to understand it and not be put off from the data. I didn’t want to just do my bit and look at the result at the end, I wanted to understand it.
How do you use computer science and bioinformatics?
For example, we did whole genome sequencing of honey bees as a pilot to look at genetic diversity in the UK population. The reasoning behind this study was to figure out what depth of whole genome sequencing we would need to do if we were going to sample the UK population and find all of the variation in that population.
My colleague Tim Regan then used the data collected to look at everything else in the bee, as when you sequence a bee you also get information about the microbiome, bacteria and pathogens. This is really interesting, as using whole genome sequencing data to look at diseases can work as a potential health screen, especially as it is becoming cheaper and cheaper.
Why are bees so important?
Bees are responsible for pollination. Honey bees pollinate plants in the environment. This makes bees a very important animal for agriculture. If you have a crop that you want to pollinate, you will usually use honey bees. This can be seen in the United States with almonds and in the UK with apple, pear and plum orchards.
With bees being so important, you can take the whole genome sequencing we’ve done, identify all the genetic variation in the population and start breeding bees to hold that variation. You can also start trying to link parts of DNA to various traits you want to breed into your bees. This is important to make sure we have strong bees that can adapt to diverse conditions.
Additionally, beekeepers in the UK have a large interest in the native honey bee, as there was a large importation of bees in the 20th century. Using sequencing we are able to identify how certain native bees are compared to others.
And of course the bee decline is causing great concern.
What causes the bee decline?
The bee decline is a big problem. In the past few years there has been a large focus on the decline of honey bees in Europe and North America. One of the main causes is loss of forage. Up to the 1950s wildflower meadows were used to feed animals. However, with the development of nitrogen fertilisers, grass was used instead, so there has been a massive disappearance of flower meadows.
Another large problem are the pests and diseases which are spread around the world by beekeepers who transport their bees around the world. An example is Varroa destructor, a small parasitic mite that attaches itself to honey bees and transmits disease. Varroa destructor started as a parasite of the eastern honey bee and the story goes that Russian servicemen in World War II travelled with their bees to Indonesia and that the mite crossed species from the eastern honey bee to the western honey bee. As the western honey bee has not evolved to protect itself, if infected, there is a very high chance the whole colony will be decimated. This eventually led to the distribution of the mite around the world, with only a few places still safe, like Australia. It's a big problem!
How can science help?
We’re currently in a situation where we have to keep this thing at bay and that is not a good situation to be in.
However, there are certain options being explored. Varroa-resistant honey bees can be selectively bred once traits are identified by analysis of variation, such as the Varroa Sensitive Hygiene trait. These bees are more hygienic, helping to keep the mites out.
We have also been involved in a collaboration in Portugal, working with Alice Pinto from the Instituto Politécnico de Bragança. Alice has a low cost genotyping platform and she was looking at genetic variation (SNPs) to differentiate between native and imported bees. That work has just been published in Nature’s Scientific Reports.
My final questions are not bee-related. What’s your favourite story from your time at the Institute?
My favourite story is from when I was co-supervising a PhD student. The first time Bill Gates came to the Institute and was waiting to get up the stairs in the cafeteria, the student looked up from the table and very dramatically and loudly said “Oh my God, it’s Bill Gates!”, it was just like something from an episode of the Simpsons!
And finally, if you weren’t a scientist, who would you be?
I’d be a bee farmer or a singer/songwriter. So pretty much what I currently do in my spare time.