Research by German scientists into the genetic makeup of European potato varieties has revealed that, despite significant differences between chromosomes, these varieties share a narrow genetic base. The findings, from a study that also involved Wageningen University & Research, will help inform new strategies for breeding more resilient potato varieties.
The researchers from the Ludwig Maximilian University of Munich (LMU) and the Max Planck Institute for Plant Breeding Research, in collaboration with researchers from Wageningen, selected ten heritage potato varieties, some of which were already being cultivated in the 18th century. According to Ronald Hutten, the curator of the Potato Pedigree Database, which includes lineage data for almost 10,000 potato varieties, these varieties represent the 'Founding Fathers' of modern potatoes. They date from the first phase of European breeding programmes.
A narrow base
Because a potato has four sets of chromosomes, these 10 varieties could theoretically contain a maximum of 40 different sources (unique haplotypes). However, it turns out that large regions of many chromosomes are identical. On average, there are no more than nine different haplotypes. And that covers 85 percent of the genetic variants (haplotypes) found in modern European potatoes. Wageningen potato geneticists Ronald Hutten and Herman van Eck say they cannot explain this based on lineage data alone. Written sources on lineage only go back as far as 1820. So, the European potato has a very narrow genetic base, derived from a small number of plants originally introduced into Europe. Or could various bottlenecks have reduced genetic variation? Any plants that were poorly adapted to the European climate and to our long daylight hours would have been lost. Potato blight wiped out the most susceptible plants. In 1845, this disease caused a devastating famine, especially in Ireland, but also in other parts of Europe.
Large genetic diversity
So, while there aren't many haplotypes, paradoxically those haplotypes are actually very diverse. On average, in a stretch of DNA there are variants at a frequency of in one in 50 nucleotides, the building blocks of DNA. This is substantially more than in other crops. The genetic distance between the potato haplotypes is almost as great as the differences between tomato, potato and aubergine chromosomes.
It's likely that this variation preceded the arrival of the potato in Europe. Indigenous peoples in South America began domesticating tuber-bearing Solanum species between 10,000 and 7,000 years ago. Crossbreeding among different species increased the diversity.
The Haplotype Graph
The researchers combined their data into a "haplotype graph" based on mathematical graph theory. The linear DNA chain of a chromosome can be visualised as a railway line going from A to B. Two chromosomes jointly form a double track, with switches connecting the tracks, so a train can run on either the left or right lane. All the potato chromosomes in the study collectively form a complex network resembling a rail yard.
This haplotype graph is a useful tool for reconstructing the tetraploid genome of other potato varieties, even when only limited information on the DNA sequence is available. A small amount of specific DNA variants from Russet Burbank - a favourite potato variety for chips - enabled the identification of the four tracks in the rail yard. Each track then represents the reconstruction of the chromosome.
New methods for potato breeding
According to potato geneticist Herman van Eck, the research findings confirm insights that had already been suspected based on previous limited data. These insights are very useful in the development of new methods of potato breeding.
Ordinarily, new potato varieties are selected from crosses between potatoes with four sets of chromosomes. In Wageningen, co-author Ronald Hutten has spent decades working on a breeding programme using diploid potatoes (two sets of chromosomes). These diploids are essential for developing a new breeding method to create F1 hybrid potato varieties. One of the challenges of this method is that diploid potatoes must be inbred through self-pollination. "We now have a better understanding of which tracks in the chromosomal rail yard we can use to build suitable chromosomes for F1 hybrids. After all, each potato variety has a unique combination of chromosomes. If mutations lead to certain genes no longer functioning, vigorous plants will compensate for this using functional variants on another chromosome."
In the long run, the researchers expect to be better able to predict which parent combinations can produce offspring with the desired chromosome variants. This will enable more efficient and targeted development of robust potato varieties.
