The genome sequence of the humble potato was published in Nature last week (Nature 475, 189–195 (14 July 2011) and the story was taken up by the world’s media. As ever, hyperbole ruled, with claims that the new genome information would solve the problem of serious diseases of the crop and prevent starvation in the developing world. But given the fact that next generation sequencing technologies mean that whole genome sequencing is now both cheap and quick, why was this particular genome paper afforded the accolade of a place in Nature? Part of the answer is undoubtedly the ‘newsworthy’ nature of the work. Potato is the world’s fouth most important food crop and is especially important in the developing world. But there are two particular parts of the science presented in the paper that represent genuine breakthroughs.
The first is related to the difficulty of sequencing the genome. Like many of our crops potato is polyploid – meaning it has more than two copies of each chromosome – and is highly heterozygous with considerable variation between the same gene present on each of the 4 copies of each chromosome. This is a result of the fact that commercial tetraploid potato varieties are infertile and are propagated exclusively clonally through the tubers or stem cuttings. Without the homologous recombination that occurs between chromosomes during sexual reproduction, mutations in an individual copy of a gene are not redistributed to the other copies, permitting substantial differences between the four gene copies to accumulate. For technical reasons, this makes it much harder to reassemble the genome from the short fragment sequences that are obtained using current sequencing methods. The international consortium behind the potato genome sequencing solved this problem by creating an artificial ‘double monoploid’ clone (called ‘DM’) in which there were only two copies of each chromosome and more importantly, each copy was identical. This allowed them to completely sequence this simplified genome which then formed a framework for comparison and assembly of a more complex diploid genome (from a variety called ‘RH’ which closely resembles varieties that we consume).
The second breakthrough was the comparison of the DM and RH genomes revealed possible explanations for two major problems of potato: inbreeding depression and susceptibility to disease. Inbreeding depression in the phenomenon whereby a lack of genetic diversity in a population leads to reduced fitness of individuals. Although there is wide genetic diversity amongst the many thousands of species in South America, only a limited number of species were introduced from Europe and these formed the genetic base from which all modern farmed potatoes were derived. Inbreeding depression is apparent in the two sequenced varieties: DM is much less vigourous than the RH variety. By examining the sequences, the consortium were able to show that there was a greater prevalence of genome mutations that disable gene function in the DM variety suggesting a possible reason for the reduced vigour. The sequencing also revealed a possible explanation for the susceptibility of modern potato to devastating pests such as potato cyst nematode and diseases such as potato blight. More than 800 disease resistance genes were identified in the sequenced genome and importantly, many appeared to be broken due to mutation. While a second potato famine is unlikely to afflict the modern world, blight still is a cause of major losses of the crop every year and the genome sequencing now provides a possible route to a genetic fix.
