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Genetic data tells the tale of peppers

Researchers studied over 10 000 Capsicum annuum pepper samples from gene banks worldwide to gain insight into the history of this common food.

Food and Natural Resources icon Food and Natural Resources

To the layperson, genetic diversity might seem like an abstract concept that only concerns scientists, but the reality is very different. If a population becomes less genetically diverse, it loses its ability to adapt and evolve in response to environmental changes, as a result facing a higher risk of extinction. So, when about a century ago scientists became aware of the increasing loss of genetic diversity in crops, they began to establish gene banks. Plant gene banks collect cuttings and seeds as a repository of genetic material for conservation and breeding purposes in order to preserve genetic diversity in plant species. Today there are more than 1 750 gene banks worldwide, and together they maintain about 7.4 million accessions (groups of related plant material representing a cultivar, breeding line or population). Researchers supported by the EU-funded G2P-SOL project have now analysed genetic data from major international gene bank collections to explore the genomic diversity and population structure of wild and domesticated peppers. Their study investigates the plant’s evolution and provides a model of Capsicum annuum species distribution that reflects human trade and historical and cultural influences. “We conducted a huge genomic scan of over ten thousand pepper (Capsicum spp.) samples from worldwide genebanks and used the data to investigate the history of this iconic staple,” stated study co-first author Dr Pasquale Tripodi of G2P-SOL project partner Council for Agricultural Research and Economics, Italy, in a news item posted on ‘’.

The implications of duplicate plant material

The team genotyped 10 038 accessions from 14 pepper species and subspecies that originated from 130 countries across 5 continents. According to the study authors, when germplasm – the living tissue from which new plants can be grown – is shared and inconsistently documented, it often leads to the creation of hard-to-identify duplicates within and amongst gene banks, possibly affecting population genomic analyses. The genomic data generated in the study made it possible to identify duplicate accessions – a total of 1 618. “This significant level of duplication should motivate the development of genetic pre-screening protocols to be used in genebanks for documenting the potential duplicate samples upon first acquisition,” noted senior author Prof. Dr Nils Stein of project partner Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany. By analysing the genetic diversity of Capsicum annuum and investigating its history, the team found a considerable overlap between the kinds of peppers collected in broad regions around the world. To supplement traditional population genetic analyses, a method called ReMIXTURE was developed to quantify the similarity between peppers from a focal region and those from other regions. The results indicate that human preferences have greatly influenced domesticated pepper genetic structure. They “reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes,” observed co-first author Dr Mark Timothy Rabanus-Wallace, also from the Leibniz IPK. “A large factor in pepper’s initial appeal was certainly its pungency, especially in nontropical Europe where hot spices were rare and imported black pepper could fetch good prices.” The G2P-SOL (Linking genetic resources, genomes and phenotypes of Solanaceous crops) study was published in the ‘Proceedings of the National Academy of Sciences of the United States of America’. For more information, please see: G2P-SOL project website


G2P-SOL, pepper, gene bank, genetic diversity, plant, genomic, Capsicum annuum