In search of the perfect pepper

Technological innovation for agricultural advancement

The taste, vitamin content and firmness of the pepper are largely determined by the plant’s genotype. Video: Videezy

Estimated reading time: 7 minutes

What genetic properties does the plant have that grows from a particular seed? That information is stored in gene banks around the world. Scientists at Wageningen University & Research are collaborating on a European project to create a single catalogue covering all those collections. That will facilitate the search for more climate-proof crops.

If you buy a pepper in the supermarket, you probably don’t think about the extensive selection process that preceded the production of this vegetable. Breeders look at all the possible options and select the pepper varieties that best meet the demands of the market. In Western Europe, that is a plant that grows easily, has high yields and fruit that tastes fresh and sweet but not hot and spicy. In Asia they like hot chili peppers, close family of ‘our’ bell pepper. The taste, vitamin content and firmness of the pepper are largely determined by the plant’s genotype – its hereditary characteristics. Gene banks around the world contain collections of the genetic material of thousands of plant species. Wageningen also has one of these gene banks, with the seeds of more than 23,000 cultivated and wild accessions. Plant breeders use the gene banks to breed crops that are resistant to diseases and pests, for example.

This has become possible because there are now such good, cheap options for applying DNA sequencing techniques

Although most crops have many varieties, growers usually only grow comparatively few. Photo: Arnaud Bovy

That sounds useful. But up to now there was one problem: information about the traits in the genebank was often lacking and difficult to access. “Each gene bank recorded the data in its own way,” explains Wageningen Research scientist Arnaud Bovy. “So we didn’t know which plant data could be found where, or how many duplicates there were in the collections. What is more, they only recorded a limited number of phenotypic – physical – characteristics and genotypic information was usually lacking completely.”

From potatoes to aubergines

Bovy works in Wageningen University & Research’s Plant Breeding department, where his team participated in a large collaborative European project called G2P-SOL. The name stands for ‘genotype to phenotype for Solanaceous crops’. Bovy: “The Solanaceae are the nightshade family, which includes potatoes and tomatoes. They are important food crops all over the world. Our consortium consists of partners who have been working with these crops for years.” G2P-SOL aims to improve the cataloguing of the genetic diversity in gene banks around the world and make the information more accessible. Researchers across the globe are working together under European leadership. They have characterised more than 50,000 genotypes of four Solanaceae crops: tomatoes, peppers, potatoes and aubergines. “50,000 genotypes is an incredible number”, stresses Bovy. “This has become possible because there are now such good, cheap options for applying DNA sequencing techniques.”

WUR’s gene bank contains seeds of well over 23,000 breeds and wild populations. CGN distributes around 6000 samples to hundreds of users annually. Photo: Guy Ackermans

Why is such a worldwide gene bank catalogue so useful? Bovy: “We face major challenges in the years ahead, both in Europe and beyond. There is climate change, of course, as well as the question of how we can produce enough food for the growing global population. That is why we are looking for crops that will perform well under the new conditions. They can be found in the gene banks.”

At present, growers only make use of a small proportion of the available variation in a particular crop. “That has developed over the centuries: you select genotypes that best fit with what you want – for example, plants with a higher yield. But there might be other variants that do better in a warmer planet.” The gene bank catalogue could also be useful for companies that are exploring new applications in agriculture. “An example is vertical agriculture where you grow plants on top of one another in storeys,” says Bovy. “In this research project, we found a pepper plant that stays small, with all the fruits growing at the top of the plant.”


How did the scientists combine all the genetic information in one system? First, seedlings were grown in the research centres for the thousands of selected genotypes. “Then we created a ‘fingerprint’ with the plant’s DNA. That meant we could compare the various DNA profiles. This showed us for example that some genotypes were stored under different names but were in fact the same.” The researchers selected a ‘core collection’ from all the data with about 400 genotypes for further investigation. “We grew the plants in various locations, including France, Israel and Italy. That showed us how they performed under different conditions. Which properties are stable and which are heavily influenced by the environment?”

The project teams looked at aspects such as how the plant grows and flowers, as well as the colour, size and shape of the produce and whether the crop can cope with heat stress and diseases. “Here at Wageningen Research, we mainly studied the quality and nutritional value,” says Bovy. “We know a lot about the properties of plants and the substances they contain. We want to learn more about how those substances are made and how they relate to one another. That is incredibly important in letting us identify the underlying genes.”

We used to grow vegetables in different locations — that showed us how they performed under different conditions

The gene bank can be consulted to find varieties that are suitable for new applications, such as vertical farming. Photo: Shutterstock

Thus Wageningen scientists discovered that certain pepper aromas are only found in peppers that also contain capsaicin, the substance that makes them taste hot. Bovy: “Of course the next question is why? Is there an enzyme that makes the hot compound and also plays a role in the formation of aromas? We have also found a gene for high concentrations of flavonoids, a group of natural oxidants. There is a lot of interest in flavonoids because they may be good for people’s health.”

Professor Giovanni Giuliano, is the coordinator of the project and explains in this video what G2P-SOL is researching.

While G2P-SOL is a European project, it involves organisations from all over the world. There are also a few plant breeding companies involved in addition to the research institutes. “Of course they are very interested in what we are doing. A big project like this gives you lots of new contacts and ideas, which in turn leads to new projects.” The project finished at the end of 2021. Bovy: “In the final stage, we were investigating which parts of the plant’s DNA are responsible for its properties. That is the icing on the cake.” But he emphasises that this is also really only the start. “G2P-SOL has turned up lots of pointers for follow-up research. We never used to do much with aubergines in Wageningen but now we have a solid foundation of knowledge for that crop as well. When we started the project, a lot of the participants were quite sceptical – including me. The number of genotypes we wanted to analyse was so large and the budgeted costs per sample so low that we wondered whether we would ever manage. Yet we did. That is amazing.”

European research context

From Genotype to Phenotype – Solanaceae (G2P-SOL) addresses the following European policy challenges:

  • Improve the cataloguing of the genetic diversity in gene banks around the world and make the information more accessible
  • Healthy, safe and sustainably produced food for everyone

Wageningen University & Research groups involved: Wageningen Plant Research, Laboratory of Plant Breeding and Centre for Genetic Resources, the Netherlands (CGN)

European and other countries involved: Bulgaria, France, Germany, Israel, Italy, the Netherlands, Peru, Poland, Spain, Taiwan, Turkey and United Kingdom

Duration 2016 – 2021

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