Science - July 7, 2011

Potato researchers solve an enormous Sudoku

Five years ago, few people thought it would be possible to map the potato genome, but now it has been done thanks to new technology. The researchers will soon be publishing their findings.

The potato has a very complex genome. It is a tetraploid crop: the potato's cell nucleus contains four examples of each of the twelve chromosomes. In other words, each gene is to be found at least four times in the genome. That makes it very difficult to find the position of those genes if you consider that a potato has around 36,000 genes. 'You always have four different sequence options for any one position on the genome. The general opinion was that it would never be possible', says Christian Bachem, a researcher at Wageningen UR Plant Breeding and the project manager for the Potato Genome Sequencing Consortium.
The old technique involved the geneticists cutting up the genome into 80,000 fragments, with around 130,000 base pairs each, and then sticking them together to make a complete chromosome. Before that, the fragments were put in a medium, after which a chromatograph recorded the base sequence and the researchers started puzzling over an enormous Sudoku. Fortunately, they already knew the chromosomes on which many of the genes were to be found, which enabled them to find the right position for many DNA fragments. After three years, the researchers had found about twenty percent of the genome sequence.
Next generation
They looked to be facing a long, tortuous process of cutting and pasting pieces of potato genome, but in 2008 a new generation of techniques came on the market. This allowed them to sequence many more tiny pieces of DNA. By assigning colours to the different base sequences, they could let the computer stick the fragments together. The chip technology used for this works a factor 200 times faster than the old technique. What is more, they were able to collect the potato sequences for the entire genome in one go and use that to assemble the twelve chromosomes.
This 'next-generation' approach had one disadvantage: it was not able to deal with tetraploid genomes with four variants of a chromosome. That is why the researchers changed to studying the wild variety Solanum phureja. American geneticists had made an unusual version of this potato, the double monoploid (DM). This potato contains only one variant of each chromosome, in duplicate. The DM is not to be found in nature but is ideal for genome analyses.
The Solexa machine in the Beijing Genomics Institute got through the entire genome in less than a year. That is, 85 percent of the genome is now known. Now, researchers can compare the genome of potatoes in the field with the genome of the DM potato that has been studied, which makes it easier to find genetic markers for useful properties. The wild potatoes in the Andes in particular show enormous genetic diversity, which should make it possible to find genes for resistance to diseases and pests, for instance. Such genes can then be used in crossbreeding.
That is still not a simple task, as the potato has four chromosomes that can lead to different outcomes in generative reproduction, so that it is not certain whether the favourable property will be inherited. That is why potato breeding takes a long time and plant breeding companies work primarily with vegetative reproduction (cloning) using top-quality tetraploid potatoes. 'That way they are fixing the genetic information', says Bachem. Knowing the potato genome makes it possible to get a more focused and predictable outcome to plant breeding.