Advancements in genomics, next-generation sequencing, and genome editing are driving forward a new era of crop breeding. About 75% of the world’s food comes from 12 plants. However, scientists estimate up to 30,000 species are edible. One opportunity in broadening our food supply lies in exchanging genotype-to-phenotype knowledge between globally and locally cultivated crops. However, many genetic variants are species-specific. And methods of selecting for advantageous traits can produce different results in related species.
“There’s a lot of wonderful food crops out there,” said Zachary Lippman, PhD, Cold Spring Harbor Laboratory (CSHL) professor & HHMI investigator. “How many of them have not received the attention they would benefit from, compared to ‘major’ crops?”
Now, CSHL researchers and colleagues around the globe have established a pan-genome of the crop-rich genus Solanum. The team sequenced dozens of complete genomes for the plant genus that includes tomatoes, potatoes, and eggplants. The new, high-quality pan-genome was then used to map the genes behind specific traits of agricultural significance across the genus, and target those genes to create desirable mutations.
This work is published in Nature in the paper, “Solanum pan-genetics reveals paralogues as contingencies in crop engineering.”
The team’s research reveals the importance of understanding the evolution of paralog genes in predicting genome editing outcomes. How paralogs relate to physical changes across species has not been deeply studied—until now. And, in this study, the biggest breakthroughs came from the African eggplant: a tomato relative indigenous to the sub-Saharan region, African eggplant varies highly in fruit shape, color, and size.
The authors wrote, “Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression, and function. By augmenting our pan-genome with African eggplant cultivars and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size.”
Lippman and longtime collaborator Michael Schatz, PhD, professor of computational biology and oncology at Johns Hopkins University, turned to a breeder in Uganda to exchange ideas and expertise. Mapping tens of thousands of paralogs, the team identified a previously unknown gene in African eggplant that affects fruit size. The paralog has the same function in tomatoes. The researchers discovered they could influence tomato size by editing it.
“Reciprocal exchange between indigenous and major crops creates new, predictable paths for better breeding,” said Benoit. “This is key to boost the diversity and resilience of the food system.”
The findings, the authors suggest, demonstrate that “paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.”
“Crop diversity benefits nutrition, choice, and health,” Lippman added. “Determining how related paralogs function across species could help improve crop yields, flowering times, and food selection. In other words, it’s a win-win-win for scientists, farmers, and consumers everywhere.”