Rice Plant: DNA Mapped

W. Richard McCombie
Professor, Cold Spring Harbor Laboratory
Wednesday, August 10, 2005; 2:00 PM

Scientists are reporting this afternoon that they have completed a genetic map of the rice plant, a scientific milestone that they hope will accelerate efforts to feed the hungry by improving the world's most important food.

Read the story: Scientists Crack DNA Code of Rice (Post, Aug. 10)

Rice is the first crop plant whose complete genetic sequence, or genome, has been ascertained and placed in computer data banks around the world. It will be a key tool for researchers working on improved strains of rice as they struggle to stay ahead of human population growth. A major paper describing the genome is to be published Thursday in the journal Nature.

Professor W. Richard McCombie of the Cold Spring Harbor Laboratory in New York was online Wednesday, Aug. 10, at 2 p.m. ET to discuss genetic mapping of the rice plant and explain what it means for the world's population.

A transcript follows.

____________________ Professor McCombie, thanks for joining us today.

The DNA mapping of the rice plant ... please explain how important you have found this to be and what it means to the average person in this country and to the world's population.

W. Richard McCombie: The importance of this is that it provides a detailed basis for understanding on how a rice plant grows, develops and reproduces. That allows rice researchers to more intelligently and rapidly understand how the plant responds to different conditions and improve the plant.


Long Beach, Calif.: Unfortunately it is a near guarantee that this technology will be used for "roundup-ready" type of pesticide resistance, with massive controls on the farmer's cleaning and gleaning of seed for re-planting, rather than improving the yield of public domain varieties of rice to feed the world.

What kind of business model incentives could change that within the GM food industry?

W. Richard McCombie: This isn't technology. It is information. It provides basic knowledge of the genetic components of this important crop. It is not necessary for what you say. Rather it is useful information for better understanding of the plant, and it will change the way that research can be done on rice. The concerns you have are things that already are concerns and are concerns with plants that aren't sequenced. They really don't relate to this information directly.


Brighton, N.Y.: As a former biologist I think of plant chromosomes as having a lot of repetitive DNA sequences. Was this true for the rice genome? If so did you find anything interesting about the repetitive regions?


W. Richard McCombie: Yes, rice has quite a it of repetitive sequence; considerably more than Arabidopsis thaliana, the first plant sequenced. However, it is less than in corn (based on estimates of corn). Considerable work is underway on the role of the repeats in the genome, especially in Arabidopsis, but we really don't know the answer yet.


Washington, D.C.: How long did this take to decipher?

W. Richard McCombie: About 6 years.


Arlington, Va.: Now that the rice plant genome is mapped -- how far away are we from completing corn and wheat DNA maps?

W. Richard McCombie: Those are still in the early or planning stages, so it is a bit difficult to tell. These projects almost always have been done ahead of schedule. With new technology becoming available I expect sooner rather than later.


Alexandria, Va.: What alterations to rice do you think are most likely to appear first? What can we look forward to (or for some, dread) on shelves in 10 years?

W. Richard McCombie: I don't do rice breeding, however, an educated guess would be rice that has better nutritional balance, is resistant to pests and is better able to grow in marginal soils.


Washington, D.C.: A lot has been said about the benefits of GM rice for the poor, in particular with Golden Rice and Golden Rice 2. But I have not yet heard of their use in developing countries. What is the status of their field tests and/or regulatory/legal processes? When will poor people begin to realize their benefits?


W. Richard McCombie: Im not involved with the Golden Rice projects. I would think that the poor people who need the nutrition are much more acutely aware of their value than are the people who don't need them.


Northern Va.: What does the world need to ensure that food engineering does not get abused in the future? Is anything like an effective regulatory framework in place now, even in embryonic form?

W. Richard McCombie: Regulations vary by country. I think that regulations in the US are developing in a reasoned, manner.


Washington, D.C.: What other foods' genetic maps might be revealed next? What determines the priority for research, and is there any pressure on the scientific community to look at any particular organisms?

W. Richard McCombie: There are several projects underway at various stages, and in different countries. Several countries, including the US are engaged in developing genome resources for a plant with a small genome that is related to soybean, called Medicago. Corn is also progressing very rapidly, with pilot studies completed in the US. A number of animal genomes are also being, or have been determined with agricultural importance.


Washington, D.C. Ethically speaking, how do you assess the risk-benefit balance in this sort of work?

W. Richard McCombie: In the sequencing itself or in the modification of the organism by various means? The sequence itself will without doubt be very important in better understanding plants and in increasing the food supply in the face of population growth and possible future famines. It is important to put this into perspective: people have been genetically modifying plants for nearly 10,000 years. It isn't clear that there are significant dangers in doing so. It is clear that we need to increase food supply significantly in the medium term.


Palo Alto, Calif.: What was your most unexpected finding in the rice sequence?

W. Richard McCombie: I think, for me, that there was as much difference as there turned out to be between rice and the first plant sequenced Arabidopsis. I thought they would be not as different as they are.


Virginia: Can you describe, in layman's terms, what the technical process is for decoding a genome like this? I hope the scientists have more to do than wait for a bunch of computers to finish quadrillions of calculations.

W. Richard McCombie: No, this is lots of hands on lab work, but we use computers and robots. The people in our lab, and the others working on the project carry out biochemical reactions in the lab and then analyze them on the computer. Much of their time goes into sorting out what is confusing after the initial computer analysis. This involves both computer analysis and carrying out experiments in the lab.


Washington, D.C.: How would you improve rice over what has already been done?

There are as many hybrids and varieties as there are soil types, environments, and taste preferences already. If you wish to make the rice untasty to insects, then the seed will just cost more proportionately to the yield increase. Then the bugs that like the untasty rice will flourish. If the RoundUp plan is used, that too requires more pesticides which means increased costs. Otherwise, this is a very good breakthrough and I don't want to complain too harshly about progress on feeding the world's humans, livestock, and insects.

W. Richard McCombie: Well, just as an example...

One of the real problems facing agriculture in the world, especially the developing world, is inadequate amounts and quantity of soil and fresh water. Developing rice that could grow well with lower quality inputs would be very beneficial.

Likewise, here in the States, we have available to us a balanced diet. If rice does not have adequate amounts of some nutrients that doesn't present a problem to us because we get those from other sources. In the developing world, that may not be the case, in fact it often isn't. So having rice with a better nutritional balance would be of great benefit to those parts of the world that depend disproportionately on rice as a food.


Washington, D.C.: Does this sequencing change the taste at all?

W. Richard McCombie: The sequencing does nothing to the plant, well except for the ones we sequenced which at one point got ground up and destroyed. But it is really just information on the computer, it has no effect on the plant at all unless it is used to change the plant in the future.


Bethesda, Md.: What do the robots do?

W. Richard McCombie: A number of things. In particular they carry out certain biochemical reactions at fairly high throughput and at every low volume (to save costs of supplies). Essentially lots of liquid handling.


Washington, D.C.: Just curious ... why exactly did it take so long to map ...

I would have thought that with the mapping of the human genome that gene mapping speeds would decrease.

Of course this comes from a NON-biologist.

W. Richard McCombie: You are correct. However, the amount spent on the project determines the rate at which it proceeds.


Memphis, Tenn.: When would be the rice genome available for use to the scientific community?

W. Richard McCombie: The current version is freely available now.


I'm Confused ...: Hello, I am a biology college student and we were taught that the complete sequence for rice had already been completely mapped. Were we taught incorrectly?

Thank you.

W. Richard McCombie: There were several rough, incomplete versions that have been available for a couple years. This is the first complete one.


Long Beach, Calif. : Gosh, the compartmentalized answer you've offered is a bright window into the larger problem.

Isn't how the information is to be used by industry as it studies development options soon-to-be-available via the new information of any concern to your segment of agribusiness?

W. Richard McCombie: Of course it is of concern. But in fact, the information is of enormous potential benefit both for basic science and for crop improvement. Including crop improvement that can be done using standard breeding.


Lanham, Md.: Are you a mad scientist?

W. Richard McCombie: Sometimes, I must confess, that I respond with impolite verbal statements to things I observe in traffic.


Washington, D.C.: Has there been any international reaction to the mapping of the genome?

W. Richard McCombie: This was an international collaboration that was led by the Japanese. Given the time difference, I expect that it will be later today before there is much of a reaction from Asia to the announcement of the publication. The release date of the information was determined by the scientific journal in which it is being published, which is headquartered in London.


Herndon, Va.: How many labs have been working on this with the rice? Is the work all coordinated?

W. Richard McCombie: It has been coordinated by the Japanese group at the Rice Genome Program, headed by Dr. Takugi Sasaki, in Tsukuba Japan. Ten countries participated in the sequencing.


Washington, D.C.: So what's your next project? Will you continue to refine the rice genome or are you on to other food items?

W. Richard McCombie: Right now we are working to both refine the rice sequence and to determine in detail the information it encodes. We are still doing some of the really tough parts of the genome. We are also working to determine the start sites of a large number of rice genes and to figure out how to scale up efforts to determine the interactions between the products of the genes.


Oakton, Va.: How big of a milestone is it to have mapped the rice genome? It's a necessary step, but aren't there many more difficult steps that have to be accomplished before this turns into practical benefit for people? Is this a bit over hyped, or am I missing something?

W. Richard McCombie: All science progresses by steps built on the steps before. This is only a step, but a rather big one. It now makes the complete set of information available. That will change the way people do rice research, that is why it is a pretty big step.


Washington, D.C.: I'm skeptical that rice varieties haven't already been "pushed" to grow in any soils and water conditions possible. After all, tons of rice are lost to drought each planting. So wouldn't the best seeds already be "selected" out by nature?

Monsanto has increased the nutrients that rice can pull from the soil, but doesn't that just leave tired soil that eventually requires more and more fertilizers?

My conclusion is the only way to improve rice is to improve the efficiency of photosynthesis, which is the way plants convert sunlight into various sugars. Sunlight seems to be a resource that's more cheaply available than water and soil nutrients. Sunlight is something rice growers don't usually worry too much about having a scarcity of, since rain clouds are usually the alternative (except when neighbors are burning the forests to make a new patty).

What do you think?

W. Richard McCombie: Water is a real issue from what the rice breeders say. Certainly improving other things, such as the efficiency of photosynthesis will help as well. Likewise, more yield will be important because the amount of area that can be farmed is finite.


Bethesda, Md.: How does this compare to the "Miracle Rice" news back in the 60's, which was supposed to eliminate world poverty and hunger?

W. Richard McCombie: Those improved strains did much to provide more food for people in the 60s. In the long term, this will provide information that will allow significant improvement to rice in the future.


Alexandria, Va.: With the knowledge you have of rice's makeup, are you capable of artificially creating rice or any other grain in the lab?

W. Richard McCombie: Not at all. We are not trying to do so.


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