Scientists decode 300 potato varieties for better crops

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Potatoes are one of the most widely consumed food crops in the world, but they face many threats from climate change, such as drought, frost, and diseases. How can we make them more resilient and nutritious for the future? A team of scientists from McGill University has come up with a novel way to find the answer: by creating a potato super pangenome.

A pangenome is a collection of all the genetic variations within a species, while a super pangenome includes multiple related species. The researchers have created the most extensive potato super pangenome ever, covering 60 species of potatoes and their wild relatives. They used supercomputers to analyze data from public databases, including gene banks in Canada, the United States, and Peru.

The potato super pangenome reveals the rich genetic diversity of this crop that was first domesticated by Indigenous peoples in the mountains of southern Peru about 10,000 years ago. It also helps identify the genes that are responsible for important traits, such as resistance to diseases, tolerance to extreme weather, and enhanced nutritional quality.

The researchers hope that their super pangenome will be a valuable resource for improving the potato crop using traditional breeding or gene editing techniques. They aim to develop a super spud that can cope with the challenges of climate change and ensure food security for millions of people around the world.

The study leader, Professor Martina Strömvik, explained that their super pangenome revealed the potato’s genetic diversity and the potential to improve the modern-day crop by breeding in some genetic traits. She added that wild potato species could offer valuable insights into how to adapt to climate change and extreme weather, as well as enhance nutritional quality and food security.

The study is part of a larger project called Potato Genome Resources, which aims to provide genomic tools and data for potato research and breeding. The project is funded by Genome Canada, Genome Quebec, Agriculture and Agri-Food Canada, and many other bodies.

The study was published in the Proceedings of the National Academy of Sciences.

Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.