University of Wisconsin-Madison scientists are part of an international consortium that has successfully sequenced and analyzed the potato genome. The consortium's work, which is described in the current issue of Nature, turned up more than 39,000 genes and is expected to speed potato research and breeding projects around the globe.
The Wisconsin team's contribution involved uncovering important information about the structure of potato's 12 chromosomes.
"The most important part of this project was actually finding the genes. That was the main goal," says UW-Madison plant geneticist Jiming Jiang, one of 20 principal investigators from 14 countries who worked on the project. "But the group still needed our expertise to help solve some of the puzzles."
Jiang is an expert in cytogenetics, the study of the structure and function of chromosomes. He and fellow UW scientists Marina Iovene and Giovana Torres used microscopic tools to reveal unique physical characteristics of each of the potato plant's 12 chromosomes, such as the location of gene-rich and gene-poor regions and - particularly important - where each chromosome begins and ends within the genome sequence.
"Through sequencing alone, it is difficult to reveal this kind of information. But cytogenetic analysis can help connect the sequence information to individual chromosomes. Cytogenetic mapping provides a bird's-eye view of the potato chromosomes," explains Jiang, who made similar contributions to international efforts to sequence the rice, corn (maize) and papaya genomes.
Potato is the world's most important non-grain food crop. Each year, more than 200 million tons are eaten worldwide. In Wisconsin potatoes are grown on more than 63,000 acres, making the state the third-largest producer in America.
Historically, potato has been notoriously difficult to work with. It is a tetraploid, meaning its cells contain four copies of each chromosome, which makes it difficult to breed. Despite decades of improvement work, the crop remains susceptible to pests, pathogens and inbreeding depression (where new potato lines are weaker than their parents). Sequencing of the potato genome should speed efforts to address these issues.
"It will take researchers awhile to use the genome information to improve its agronomic traits, such as improved quality, yield, drought tolerance and disease resistance. But our most recent research will accelerate efforts to improve potato varieties and help close the gap in bringing a better potato to the farmer," says Robin Buell, a plant biologist at Michigan State University, one of three co-leaders of the potato genome project.
Jiang says the availability of potato's genetic code will get him back in the game of hunting - or cloning - genes of value to the potato industry. He had sworn off such work in the early 2000s after an agonizingly slow quest to find the gene responsible for a wild potato's resistance to late blight, the pathogen that caused the Irish Potato Famine. The effort was ultimately successful, but it took three postdoctoral researchers more than five years to accomplish.
"Back then I said I would never clone a potato gene again until the genome is sequenced, because without the sequence it was so difficult and time-consuming. We just lacked the resources to work with-the markers, the maps," says Jiang. "Now that there's a reference genome, it's going to be so much easier for all future work-identifying, cloning and characterizing potato genes."
Jiang plans to search for more disease-resistance genes, as well as genes that affect potato quality. Based on what happened after other crops were sequenced, he expects this will feel a bit like a gold rush among potato gene prospectors.
"Before the rice genome was sequenced, it was also very difficult to clone a gene in rice," he says. "After the publication of rice's genome sequence in 2005, you started to see paper after paper by people cloning all sorts of genes-genes responsible for yield, abiotic stress-and it was all because of the sequence."
The Potato Genome Sequencing Consortium, an international team of 39 scientists, began work on the potato genome project in 2006. The complete sequence is estimated to be 840 million base pairs, about one-quarter the size of the human genome. The draft sequence, which covers 95 percent of potato genes, is available at www.potatogenome.net.