Taking part in an immersive visitor experience can be invaluable to researchers. They allow us to learn new approaches and ideas from others, share our own knowledge and experience directly, and they strengthen the relationships that underpin team science on a global level.
The Earlham Institute recently welcomed Lina Maria Lopez and Paula Espitia from the International Centre for Tropical Agriculture (CIAT) in Colombia for a three-month placement in the De Vega Group.
In this Q&A, they share their experiences - from bioinformatics training to eating pigs in blankets - and why they’d encourage others to take advantage of these opportunities when they arise.
Paula Espitia: I’m an Associate Researcher in the Tropical Forage Breeding Program at the Alliance Bioversity and CIAT in Cali, Colombia.
Since I joined the Alliance as an Undergraduate intern four years ago, I have been studying host plant resistance in Brachiaria grasses to pests in tropical America and Africa using phenotyping methods.
More recently, our aim is to develop new molecular breeding techniques to optimise the selection of resistant hybrids to spittlebug attack.
Lina Maria Lopez: I’m a senior research associate at the Alliance Bioversity and CIAT.
I’m working in the Digital Genebank group located in Palmira, Colombia, and my role is to support the data analysis for the tropical forages collection. Currently we started to genotype the Brachiaria collection to characterise diversity within our materials.
Lina Maria Lopez
Paula Espitia
LML: As a visiting researcher, I participated in De Vega’s group, where I received training in association mapping (GWAS) in a diversity panel of Panicum maximum accessions using bioinformatic pipelines.
My expectations were to learn more about bioinformatic tools, development of pipelines, and getting to know more about the research done by the Institute through the seminars in different areas.
Naturally, the skills I developed at the Earlham Institute exceeded my expectations. I’m very grateful for the opportunity granted.
PE: Our group has collaborated with De Vega’s group before, in better understanding relevant traits for Brachiaria breeding, such as apomixis and aluminium tolerance.
Thus, I came to the Earlham Institute in November 2022 to work on a project to build a bioinformatics pipeline for genetic mapping and to identify QTL associated with spittlebug resistance.
This included learning the basics of bioinformatics and then applying that knowledge in real Brachiaria mapping populations.
Panicum maximum, a type of forage grass that Dr Maria Lopez is working on.
What saved me a lot of time and made my learning process much easier, was that there were people that were working on similar projects or that had the ability to quickly identify the pitfalls in a determined process - and they were just one office away!
Dr Paula Espitia
PE: As an early-career researcher who has been working in the field or in the greenhouse, I had to learn bioinformatics from scratch.
During my first weeks with Jose’s group, we designed a workflow to analyse the raw sequencing data using different software and planning alternative paths, while I was becoming more familiar with programming and using different tools.
For this, the help of all the group members was very important! As we advanced in the pipeline, I also learned some of the genetics behind the mapping process, so, at the end of my research stay, I was able to try and tell which alternative and tool was more accurate to obtain better results.
LML: During my training, I had the opportunity to work with Panicum maximum. This Tropical grass is very important, because it is used as forage for cattle grazing and cutting, being known for their high nutritional quality for livestock systems.
In this project, we used previous phenotypic data collected by the tropical forages team at CIAT, as well as sequencing data and genomic information assembled by the De Vega group. With these data, we explored different ways to do association mapping in a diversity panel of P. maximum accessions.
The main result of this work was the identification of significant associations (QTL’s) related to biomass production, which is a very desired trait for breeding. However, we continue to obtain more interesting results.
I had the chance to learn from each member of the group, whose contribution was crucial to my learning process. In addition to their support in my own training, I was also able to learn from the work they have been doing in their own projects.
Thanks to the Earlham Institute’s Advanced Training programme, I had the opportunity to participate in different courses on data carpentry and acquire knowledge and tools about data analysis, using programming languages such as R and Python, the Unix Shell command interpreter, and database management.
Paula and Lina with the De Vega Group at the Earlham Institute
LML: Currently my work is focused on the analysis of tropical forage data, so the knowledge I acquired about bioinformatics tools at Earlham Institute will be incredibly useful for my work at CIAT.
In addition, with the association mapping methodology José de Vega’s group taught me, significant associations with traits of interest in other collections and data generated by the digital genebank can now be found.
I hope to be able to share the knowledge acquired with my current research group in Colombia.
PE: When I go back to CIAT, I will start analyzing a new Brachiaria mapping population data for spittlebug resistance and apomixis.
Also, I’ll add the genetic mapping technique to the set of molecular breeding tools that we are incorporating in our program and share all the knowledge I learned with my research group back home.
Dr Espitia is working on resistance to spittlebug (pictured)
PE: Outside work, I really enjoyed my time in the UK despite the cold weather! I could travel to iconic cities - such as London, Edinburgh and Liverpool - and saw at first hand a Peaky Blinders immersive play, the Cavern Club, and the beautiful seals in the Norfolk Coast.
As I spent December in Norwich, I went to the Christmas market and had pigs in blankets, jacket potato, and berry custard crumble on boxing day.
LML: Having the chance of being in such a great country I had to take advantage of the time and visit the surroundings. I went to London and Edinburgh, which are stunning cities with a lot to offer. In London I visited the all time classics while navigating in a cruise through the Thames: Big Ben, The Tower Bridge, things I had only seen in the movies! And speaking of movies, I explored the Harry Potter set at Warner Bros Studios which was an incredible experience.
I also loved living in such a beautiful city as Norwich. The cathedrals and downtown markets were lovely, as well as the food (fish and chips jacket potatoes) and the people. I got a very good impression of the UK and I can’t wait to come back.
I could learn from each member of the group, whose contribution was crucial to my learning process. Besides their support in my own training, I could also learn from the work they have been doing in their own projects.
Dr Lina Maria Lopez
PE: I would definitely recommend doing placements like the one I did because it is a great way to acquire new skills - not only because the Earlham Institute is among the top research centres in genomics but also because it is a great opportunity to share and learn with people involved in different fields of science and with lots of experience.
Actually, what saved me a lot of time and made my learning process much easier, was that there were people that were working on similar projects or that had the ability to quickly identify the pitfalls in a determined process - and they were just one office away!
I would like to thank all of the De Vega group - Camilla, Juliana, Jonathan, Carolina, Kate, and Jose - for their support and their warmth in having me during this time.
I will definitely miss my weekend walks in the Norwich city centre and the funny lunch times at Centrum!
LML: Absolutely. My time at the Earlham Institute has hugely enhanced my professional and personal growth, expanding the range of challenges and opportunities within my work, as well as my communication and social skills with a community that has a very different culture. Besides, being immersed in an english-speaker environment pushes you to practise the language despite the challenge that this could represent to me!
This experience has resulted in the rewarding acquisition of necessary and compelling abilities, as well as the fortune of knowing new wonderful people. So I recommend it 100%. I am always going to be thankful to De Vega's group for everything they taught me: Carolina, Jonathan, Camilla, Juliana, José for the support throughout my training and I want to highlight the mentoring of Kate during my process. None of this would have been possible without the amazing team responsible for this project.
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