An international team of scientists has developed the entire set of genes or a “pan-genome” for crops like potatoes, tomatoes, and aubergines by sequencing the genomes of 22 Solanum species. This breakthrough could result in higher-yielding and more resilient crops. 

Global agricultural systems are extremely vulnerable to extreme environmental events like drought, flood, and disease since over 75% of the world’s food supply comes from just 12 extensively bred commodity crops, according to the Natural History Museum (NHM), which has supported the study.

The researchers, affiliated with multiple universities and organizations across Europe, the US, and Uganda, note that increasing the variety of crops used for food production is crucial as we navigate climate change, deforestation, and other planetary emergencies.

However, they point out that genetic complexity has traditionally gotten in the way. Even if the plants are closely related, properties that can increase output in one crop species may not translate to others.

Dr. Sandra Knapp, merit researcher at the NHM and an author on the paper, reflects on the significance of this discovery.

“Plant breeding has taken place for thousands of years to increase yields, but this comes at a cost.”

“The focus on production has narrowed the genetic diversity of many crops, limiting their ability to adapt to challenges like climate change. This pan-genome allows us to explore how wild relatives might help improve our crops and determine how feasible those improvements are,” she explains.

According to the research team, the Solanum pan-genome is an advanced genetic map already offering insights into local crops like the African eggplant, a vital food source in Africa and Brazil.

The findings are published in the scientific journal Nature.

Implications for African eggplant

Solanum is one of the largest plant groups, comprising over 1,200 species. This presents opportunities to leverage wild relatives to enhance yields and quality, but challenges due to genetic complexities remain.

According to the NHM, one of these is the presence of paralogues, a pair of genes that derive from the same ancestral gene but evolve differently and can lead to unpredictable results in closely related species, including crops.

As part of the study, the authors collaborated with local breeders and combined indigenous knowledge with research to identify a yet-unknown gene influencing fruit size in the crop. This development can improve harvests and productivity of the African eggplant.

Knapp emphasizes understanding taxonomic relationships, which can be defined as links between scientific classifications and between species to advance innovation in food security and biodiversity.

“Taxonomy is a challenge in groups as large as Solanum, and it took a lot of effort from our colleagues at Cold Spring Harbor to get high-quality genomes so that we could do this work,” Sandra says.

“But it was worth it, as every time we team up across disciplines like this, we understand how the world works a little better,” she concludes.