Genome reconstruction opens door to transforming potato breeding

The potato is increasingly becoming an integral part of diets around the world, including even Asian countries like China, where rice is the traditional staple. Building on this work, we can now implement genome-assisted breeding of new potato varieties that will be more productive and also resilient to climate change – this could have a huge impact on food security in decades to come. to come,” says Professor Korbinian. Schneeberger on the potential unleashed by his study.

By buying potatoes in a market today, it is quite possible that the buyer will walk away with a variety that was already available more than 100 years ago. This speaks to the enduring popularity of traditional potato varieties. However, it also highlights the lack of genetic variation in the dominant potato varieties. This can have dramatic consequences, most dramatic during the Irish famine of the 1840s, when for several years almost the entire potato crop rotted in the ground, and millions of people in Europe suffered starvation simply because the only variety grown was not resistant. to the newly appeared tuber blight. During the green revolution of the 1950s and 1960s, scientists and plant breeders managed to dramatically increase the yields of many of our major staple crops like rice or wheat. However, the potato has not experienced a comparable boom, and efforts to create new varieties with higher yields have remained largely unsuccessful to date.

Potato plant flowers

Before the potato was recognized as edible, it was grown in Europe as an ornamental plant. Pollen from large flowers is normally collected by bumblebees for pollination. In the present study, the genomes of individual pollen grains were analyzed to produce the first complete map of a potato genome. Credit: Ulrich Pollmann, 2022

The reason for this is simple but has proven difficult to tackle – instead of inheriting one copy of each chromosome from both father and mother (as in humans), potatoes inherit two copies of each chromosome from each parent, making it a species with four copies of each chromosome (tetraploid). Four copies of each chromosome also means four copies of each gene, which makes it very difficult and time-consuming to create new varieties that harbor a desired combination of individual properties; Moreover, the multiple copies of each chromosome also make reconstructing the potato genome a much more difficult technical challenge than was the case for the human genome.

Researchers in Professor Korbinian Schneeberger’s group overcame this long-standing hurdle and were able to generate the first complete assembly of a potato genome using a simple yet elegant trick. Instead of trying to differentiate between the four, often very similar, chromosomal copies, Korbinian Schneeberger with Hequan Sun and colleagues got around this problem by sequencing the DNA of a large number of individual pollen cells. Unlike all other cells, each pollen cell contains only two random copies of each chromosome; this allowed scientists to reduce the complexity of the problem and ultimately reconstruct the entire genome sequence.

An overview of the complete DNA sequence of the cultivated potato has the potential to greatly facilitate breeding and has been an ambition of scientists and plant breeders for many years now. With this information in hand, scientists can now more easily identify genetic variants responsible for desirable or undesirable traits, a first step towards incorporating or excluding them during breeding.

Reference: “Chromosome-wide and haplotype-resolved genome assembly of a tetraploid potato cultivar” by Hequan Sun, Wen-Biao Jiao, Kristin Krause, José A. Campoy, Manish Goel, Kat Folz -Donahue, Christian Kukat, Bruno Huettel and Korbinian Schneeberger, March 3, 2022, Natural genetics.
DOI: 10.1038/s41588-022-01015-0