SA: How did you get started looking at genomes and what attracted you to rice?
SG: The choices were: looking at expressed genes or entire genomes. Rice is evolutionarily related to corn, wheat, barley and the other major cereals. Its is also the smallest genome430 million basesof all the cereals. If you just look at crop production worldwide, about 60 toIve read as high as72 percent is three species: corn, wheat and rice. So, if youre going to focus on something, then the focus would be on the cereals, because the cereals are the major production, and they are evolutionarily related. We knew from previous work that there was some colinearity of the genomes. In other words, the positions of the genes along the chromosomes of rice were similar to the positions in corn and in wheat and in barely and in other cereals. The sequencing technology was advancing to the point where it made sense to not just look at expressed genes, but actually look at the genome. It was kind of the right time at the right place.
SA: When you were working on the sequence for rice, did you already know what a big splash it would create if you succeeded?
SG: We knew that rice was politically sensitive, because its the major crop in Asia. But, we actually didnt know whether or not we would even publish it. Theres a lot of additional work that goes into a publication thats not really necessarily the goal of a company. At the same time, its something that you want to complete and get out there because its important for developing countries and for sustained or subsistence farming. There's a lot of uses that go well beyond what a company can use it for. We are getting our use out of it, but it seemed appropriate to try to make it useful for other groups of people.
SA: One of the keys to this work was using shotgun sequencing. If you wanted to give someone an intuitive feel for this approach, what would you tell him or her?
SG: You just chop up the whole genome and computationally reassemble it after youve sequenced small pieces of it. Its a computational challenge. There are positive and negative parts about shotgun sequencing. You dont get complete coverage, but its a lot cheaper than other sequencing techniques. The computational challenge is big enough that people were really concerned about it. Now, I think its agreed that is can be done on large genomes. When we started this project, the largest genome that had been sequenced by this method was really pretty small, a bacterial genome.
SA: What is the next research hurdle for knowledge related to the rice genome?
SG: Now its a question of what do all the cereal genes do. Sequencing just gives you the raw information that allows you to predict the genes, and the gene predictions give you some hints from previous studies of what the proteins encoded by those genes may be doing. Then you need to prove it, and theres a lot of unknowns.
When Arabidopsis was sequenced, for example, only eight percent of the genes had been studied in a lab. Theres a lot missing there. And its probably a much smaller number for rice or any of the cereals. Even when you take in all the wheat information, all the maize information, compile it all with rice and say what the function of all those genes are, theres a very high percent that we still dont have any idea what they do. We might have some hints from pieces of the proteins that are encoded by those genes, but an actual piece of information on what they do is still not in anybodys notebooks or published any where. Theres a lot more to learn. So, whats ahead? Its the functional genomics hurdle.
Mike May is based in Madison, Ind.