The Maize Genome Project is the culmination of a century of maize research at Cold Spring Harbor Laboratory that began with George Shull and continued with Nobel Laureate Barbara McClintock.

Jason Williams: A team of US scientists announced this week the completion of the maize genome; the entire set of genetic information that encodes the corn plant. Scientists from Cold Spring Harbor Laboratory joined with colleagues from Washington University in Saint Louis, and Arizona and Iowa State Universities in this multi-million dollar project, almost 4 years in the making. I discussed the significance of the project with Cold Spring Harbor researchers Doreen Ware and Rob Martienssen. Robert Martienssen: Cold Spring Harbor played a very important role in the sequencing itself. Dick McCombie was involved in finishing many of the banks that we used in the process and Doreen Ware and her group did most of the annotation and much of the assembly and repeat analysis and so on which is crucial for a genome which is very complicated. It is the most complex plant genome that has yet been sequenced. Doreen Ware: So maize, or corn, is a very important agricultural crop in this country. It represents $47 billion in revenue last year and last year 12 billion bushels of corn went to feeding livestock and more and more we’re using this corn as an alternative to energy fuel in the form of ethanol. The objective was to focus on the relatively unique portions of the genome that are usually going to be associated with the things that we think about as the protein-coding genes, and our objective then was using this template to predict those protein-coding genes, and in order to do that we actually use a series of information from other species – everything including protein-coding information from humans to model plants like Arabidopsis and we have to overlay that on the existing sequence. It’s interesting because from my perspective I actually have two farms. I have the farm where I plant my corn in the field and I have the farm that actually represents the computer farm where I send all the information and I run the computes. So in our case today biology is really associated with the necessity of managing the sequence as well as integrating additional information on that sequence. Jason Williams: Cold Spring Harbor’s participation in the project was in fact a continuation of a century of maize genetics here at the Lab. Working in a small cornfield on the banks of the harbor, George Shull showed that crossing two inbred lines of corn produces a hybrid with uniformly high yield. In fact, all modern hybrid corn today is produced using the method Shull first outlined. I talked with Nobel laureate James Watson about Shull’s discovery. James Watson: I think in a true sense corn genetics really started in Cold Spring Harbor when George Shull came here, almost at the very start of 1905, and started growing corn, and there already had been corn breeders. But the main thing he did was to cross two of them and find that the product grew better. Jason Williams: One of the difficulties of sequencing the maize genome was large quantities of highly repetitive DNA, segments of DNA that are repeated over and over, perhaps thousands of times. Half a century after Shull, and starting out in this same cornfield, another Cold Spring Harbor researcher, Barbara McClintock, showed that most of this repeated DNA is created by movable genetic elements, or transposons. Although we think of it as only being yellow or white, some corn in fact produces purple and red pigments that give rise to colored kernels. The purple pigment, which is expressed on the outside of the kernel, is produced by a gene on chromosome 9. McClintock found that yellow kernels are produced when a particular transposon jumps into the purple pigment gene, disabling color production. Robert Martienssen: And this ear of corn actually demonstrates – I’ve got it here – chromosome breakage caused by transposable elements, and you will see a much better version of this in the maize poster, but what’s illustrated here is the presence of a transposon called dissociation or Ds, which is causing the breakage of chromosome 9 at a very specific location, and when that chromosome is broken it results in a spot of color on the kernel. That breakage is controlled by another transposon called Activator, and the relationship between those two classes of transposons really defined the discovery. This ear is in fact…the position of Ds on the chromosome in this ear represents the first recorded transposition of a transposable element, so it is a really precious ear. This ear is 60 years old this fall; it was harvested actually probably about a month ago, 60 years ago so it is a very special ear. James Watson: All the people who knew Barbara knew that she was probably right, but it wasn’t until jumping genes began to be found in yeast here [at CSHL], and we had recombinant DNA. So Barbara… her jumping genes were seen through recombinant DNA methods I guess by 1980, and Barbara went to Stockholm for the Nobel Prize in 1983, for work which had started 40 years earlier. Jason Williams: Although the early pioneers like Shull and McClintock didn’t have access to the genomic tools of today, they actually foresaw many key elements of the genome, which are only now being confirmed. The completion of the maize genome marks the beginning of a second century of maize research at Cold Spring Harbor. Robert Martienssen: Barbara absolutely adored molecular genetics. She thought it was just fantastically exciting and couldn’t get enough of it. However I have to say that, speaking from my perspective, I’m not sure they would have been surprised by that much in terms of the structure of the genome. They knew the chromosomes were very large. I think maize geneticists are excited just to see all the genes in order along the chromosome, as they would have been a hundred years ago. These days of course we can associate many different types of trait with genes and we can map them genetically, and having that trait associated with specific sequences in the genome is enormously valuable both for more theoretical geneticists like myself, as well as for breeders who can now identify the traits with incredible accuracy really, really quickly as genes along the chromosome, and I think that has really been the most exciting for most people.

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