By Chloe McIvor of Nature magazine
A global effort has finally cracked the complex genome of the potato, which is published today in Nature.
The not-so-humble potato (Solanum tuberosum) is the world's fourth most important food crop and is vital for global food security. It has proved surprisingly economically stable compared with major grain crops such as rice, wheat and maize (corn): when wheat prices more than doubled on the international markets in 2008, and peaked again in 2010, potato markets stayed the same.
Despite its importance, sequencing has been delayed by the genetic complexity of the common commercial potato. Its genome comprises more than 39,000 protein-coding genes, and it is a highly heterozygous autotetraploid -- this means that it has four copies of every chromosome, and often considerable variation among the corresponding four copies of each gene. This is in contrast to the two copies in most human cells.
According Glenn Bryan of the Scottish Crop Research Institute in Dundee, UK -- one of the 26 research institutes that came together from around the globe to form the Potato Genome Sequencing Consortium -- several factors made the sequencing possible. The meeting of minds within the consortium and the use of next-generation sequencing technologies were vital for success. "Having access to these next-generation technologies is just fantastic, it's a little quantum leap in our ability to generate data quickly," Bryan says.
But the key was finding a type of potato with a genome that could be adequately simplified. The researchers used a variety of S. tuberosum that the paper refers to as DM. This differs only slightly from another variety that the researchers studied, RH, which more closely resembles that found in most supermarkets. DM, cultivated in South America, has a diploid genome, meaning that it has a more manageable 2 copies of every gene. Using this potato, geneticists selected one copy of each chromosome and duplicated these to produce a double-monoploid clone -- in which the two genes that make up each pair are identical, or 'homozygous' -- that they could sequence almost completely.
The scientists also sequenced substantial sections of the heterozygous diploid variety RH, although due to its heterozygosity were not able to assemble it into a complete genome. "It's quite nice actually, now we've got data on two types of potato, it gives us quite a good handle on the biodiversity of the potato as well," says Bryan.
The most important finding of the consortium's initial analysis is the identification of more than 800 disease-resistance genes, each of which has potential for use in fighting devastating diseases such as the potato cyst nematode and the potato blight pathogenPhytophthora infestans, famous for causing the Irish potato famine of the 1840s. Singling out these genes will make it easier to develop new varieties of potato because, thanks to its complex genetics, the tuber has been notoriously difficult to improve through breeding.
And the researchers are wasting no time in getting started. "Most of the people in the group are now asking how we can use The possibilities for improvement through marker-assisted breeding and genetic modification could make the potato a more viable alternative to grain crops, especially in developing countries, says Sarah Gurr, a molecular plant pathologist at the University of Oxford, UK, who was not part of the consortium. "Potatoes are more nutritious in terms of complex carbohydrates, they've got more protein and more fibre than rice, with no fat," says Gurr. "They've also got more vitamin C, vitamin B complexes and trace elements."
This article was reprinted with permission from Nature magazine. It was first published on July 10, 2011.