Scientists from McGill University in Montreal have created a super pangenome of potato, which plant breeders can use to produce potatoes that are more nutritious, disease-free and climate resilient.
Martina Strömvik, an associate professor and chair of the plant science department at McGill, led the research, which was published in Proceedings of the National Academy of Sciences in July 2023.
“Our super pangenome sheds light on the potato’s genetic diversity and what kinds of genetic traits could potentially be bred into our modern-day crop to make it better,” says Strömvik, who collaborated with researchers in Canada and United States as well as from the International Potato Center in Lima, Peru.
Read Also
PepsiCo nearly doubles regenerative scope
Another 240,000 farm acres managed through regenerative agriculture will be supported by PepsiCo across Manitoba and Saskatchewan by the end of 2025.
“We wanted to see the whole diversity of everything that is potato and everything that we could potentially breed into the potato.”
This broad spectrum of genome sequencing data offers the potential to produce improved potato varieties by using traditional breeding methods as well as gene editing techniques.
To produce their potato super pangenome, Strömvik and her team assembled the genome sequences of nearly 300 varieties of potatoes and their wild relatives, making it the most extensive compilation of such data to date.
“A lot of public money in different countries has gone into sequencing genomes,” says Strömvik,
“We took everything that’s available from Canada, the United States, from Europe, from China, from South America … and we basically said, ‘here’s the family tree.’”
Creating that family tree was a monumental task, requiring supercomputers to crunch genome sequencing and gene expression data sourced from public data banks all over the world — a process that lasted a year.
“We had to figure out where the genomes go in individually, but then also how do they all fit together. That’s very, very computationally intense,” says Strömvik. “It took a few iterations for us to figure out exactly how we wanted to go about this and what data to include.”
So, what exactly is a super pangenome? A genome is an organism’s complete set of genetic instructions, known as the DNA sequence. A pangenome strives to capture the complete range of genetic diversity with a species, while a super pangenome does this across multiple species.
Most of the 60 wild relatives in the potato super pangenome hail from the Andean highlands of Peru and Bolivia, an area of great genetic diversity and the place where potatoes were first domesticated and cultivated by indigenous peoples about 10,000 years ago.
Strömvik stresses it was essential to include wild species, even though most of them are inedible and in fact toxic.
That’s because many have useful traits like built-in tolerances to extreme conditions related to climate change, such as excess heat or cold, droughts and floods. They could also have disease resistance genes, which could prove momentous for potato breeding as well.
“We know that wild potatoes have been used for many, many years to integrate important traits into what we have cultivated and what we’re eating,” Strömvik says.
“We work with breeders in Canada and also internationally who have been working with reference genomes for many, many years, and are interested in specific traits.”
According to Strömvik, these traits include producing “a future climate-smart potato” that’s better equipped to deal with dramatic weather events associated with climate change. She notes traits that reduce potato losses due to climate events as well as disease would increase food security for many nations.
Strömvik says another possible beneficial trait relates to sustainability; specifically, reducing commercial potato production’s reliance on nitrogen fertilizer.
That’s something she’s been investigating along with one of her collaborators, Helen Tai, who co-authored the potato super pangenome research paper. Tai is a potato genetics and genome research scientist with Agriculture and Agri-Food Canada in Fredericton, N.B.
Strömvik says she has participated in Tai’s studies analyzing nitrogen response genes in potato for the purpose of developing a more focused approach to fertilizer applications — for example, by applying nitrogen when it’s most needed and provides the greatest benefit to the crop.
“That’s something that’s very important,” she says.
The research paper on the potato super pangenome can be found on the PNAS website.
