One giant step

SEQUENCING THE CORN GENOME: A MONUMENTAL ACHIEVEMENT THAT IS ALREADY BEGINNING TO ACCELERATE BREEDING IMPROVEMENTS

corn researchers around the world are very excited these days – and growers should be as well.

A talented group of US Department of Agriculture (USDA) scientists and their colleagues have recently presented what is by far the most complex and largest plant genome to date – that of corn. During the past four years, the hardworking team sequenced over 2.3 billion nucleotides (base pairs of DNA), and although some gaps still exist, the achievement is very significant indeed.

Almost everything a grower wants – hybrids with higher yields and better tolerance of droughts, pests and diseases – will now be developed more quickly. Having this resource should also help produce hybrids that are much better suited to creating biofuels.

Plants previously sequenced include rice, sorghum, poplar, grape and Arabidopsis thaliana, a plant widely studied as a model organism.

Doreen Ware (pictured on the cover), a computational biologist at the USDA Agricultural Research Service’s Robert W. Holley Center for Agriculture and Health in Ithaca, New York, is one of the project leaders. Other key participants in the project were based at the University of Arizona in Tucson and the USDA Cold Spring Harbor Laboratory in New York.

When asked how it felt to arrive at this milestone, Ware highlighted the many different facets which such a project presents. “A genome is never really complete,” she explains. “Having said that, I’m relieved to have some of it done, and it feels good to have produced something that will have high utility for a long time. What we have now is an excellent resource for both the public and private sectors to forge on and leverage the knowledge. Using this resource will allow for accelerated breeding, and also help answer evolutionary questions about corn.”

overcoming challenges
Some of the many challenges to getting the job done were expected. “It’s a complicated genome, and it was technically challenging overall in terms of the repetitiveness of the task,” Ware observes. “It was also tough in the sense that we had certain resources and technology available at the time. But we leveraged resources, used our individual skills while lending a hand where needed, and we now have a great resource where, even though it’s not complete, we have good ideas as to the approximate orientation of genes and where they end and begin, to move forward with.”

However, other challenges were somewhat unanticipated – such as managing of people’s expectations. This resource, in combination with other resources, will certainly accelerate things – the more information you have overlaid, the more you can accomplish what you want,” Ware notes, “but when you release a resource such as this, we’ve discovered you also have to do some education and training about what it provides and how to use it.”

The project also created a lot of discussions about what approach was best to take, requiring, in the end, a decision that all those involved had to believe in. “The strategy that we chose to use turned out to be the best and most appropriate strategy,” Ware says. “Even as new sequencing technologies move forward, our strategy I think will still be the overall one that will be used.”

In addition to sequencing, Ware worked with Edward Buckler, a geneticist also based at the Holley Center, using sequencing data to assemble a haplotype genetic map of the corn genome. A haplotype is a combination of alleles (alternative forms of genes) which are found in close proximity on the same chromosome and usually inherited together.

 The ‘HapMap’ lays out portions of the corn genome that are shared by 27 diverse inbred lines of the crop. These lines were chosen on the basis of best representing the vast majority of corn’s genetic diversity. The map, along with the sequenced genome itself, is available for researchers to search, and will also help to significantly accelerate breeding.

reaction from ontario
Lewis Lukens, a corn geneticist in the department of plant agriculture at the University of Guelph, is excited by the achievement. “Having this will have a huge impact on basic research, and this will also help applied research as well,” says Lukens, who studies corn maturation, drought tolerance and gene expression patterns. “We have specific genes that control important traits that we’re trying to identify and sequencing the genome will make this much easier.”

Steven Rothstein, a professor in the Department of Molecular and Cellular Biology at the University of Guelph, is also quite thrilled. “Now that the sequencing is complete, we can now find out much more inexpensively and quickly which genes and variations of those genes are of interest,” he says. “Farmers will begin to see results from this achievement about ten years from now and onward.”

While researchers know what the genes are, Rothstein says, how they affect the plant is still to be determined. “Complicating this is the fact that there can be multiple interacting genes for traits such as how a corn plant reacts to drought stress,” he notes. “This achievement also means that we can more easily conduct research on other corn lines than the one they sequenced.”

Over the next four years Rothstein and other researchers in his department and the Department of Plant Agriculture will receive more than $8.5 million to continue their corn genomics studies. Working with agricultural biotech company Syngenta, Rothstein is looking for genes that control plant growth. “Using molecular and genetic tools, we are aiming to alter certain traits that will hopefully make plants more efficient at absorbing and using nitrogen,” he says. “The world’s population continues to increase, and corn use per person is also growing, so we need to double corn yields over the next three to four decades.” •