European potato genome: small gene pool with large differences

A research team has decoded the genomes of historic potato cultivars and used this resource to develop an efficient method for analysing hundreds of additional potato genomes. 

Potatoes are a staple food for over 1.3 billion people. But breeding successes have been modest despite their importance for global food security. Some of the most popular potato cultivars were bred many decades ago. The reason for this limited success is the complex genome of the potato: there are four copies of the genome in each cell instead of just two.

This challenges traditional hybridisation-based breeding. A team led by Professor Korbinian Schneeberger, head of the Genome Plasticity and Computational Genetics research group at LMU and the Max Planck Institute for Plant Breeding Research, has now made an important breakthrough. As the researchers report in the renowned journal Nature, they were able to reconstruct the genome of ten historic potato cultivars. They then used this knowledge to develop a method that would make it much easier and faster to reconstruct further potato genomes. 

In collaboration with researchers from Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Groß Lüsewitz, and the Xi’an Jiaotong University in China, the team selected historical varieties, some of which were already cultivated in the 18th century. 

Korbinian Schneeberger:

"Since these potatoes come from a time when European breeding programs were beginning, we wanted to figure out how much diversity exists in these potatoes in order to understand the genetic potential of our potatoes."

The answer was: not very much. The genetic pool of the potato is extremely limited. The ten potato varieties covered around 85 percent of the genetic variability of all modern European potatoes. 

Bottleneck effects after introduction from South America

The researchers attribute their findings to bottleneck effects. Potatoes were imported from South America from the 16th century onward. The number of different individuals was low and most were unable to cope with the European conditions. This reduced gene pool was then further reduced by diseases. The most famous example is the potato late blight outbreak of the 1840s, which caused harvests to collapse and led to catastrophic famines, most notably in Ireland but also in the rest of Europe. At the same time, the study revealed – to the researchers' surprise – that the differences between individual chromosome copies can be huge.

Flowers of a potato plant

Korbinian Schneeberger:

"Because the gene pool is so limited, there aren't many different chromosomes, but when the chromosomes do differ, they diverge to an extent never before observed in domesticated plants. The differences are about twenty times greater than in humans."

These differences presumably arose before the arrival of the potato in Europe. The indigenous peoples of South America started to domesticate potatoes about 10,000 years ago, and the differences are likely the result of crossing between wild species. Finally, the researchers developed a novel approach that can be used to analyze the genomes of the around 2,000 potatoes registered with the European Union.

Instead of laboriously generating the data needed to reconstruct a genome, easily generated data are compared with the currently known genomes to determine which of the known chromosomes are present in a cultivar. The researchers showed that their approach works with the Russet Burbank cultivar, which has existed since 1908 and is still the standard variety for French fries to day.

Korbinian Schneeberger:

"Knowledge of genome sequences forms the basis for many approaches in plant breeding, from traditional breeding to the latest methods of genome engineering. In future, we won’t have to work without this information anymore."