Designing an Agricultural Genome Program (1998) / Chapter Skim
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Summary of Proceedings
Summary of Proceedings
Pages 4-22
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From page 4... ...
Mapping and sequencing a genome is the same task whether the genetic material comes from yeast, people, or rose bushes the genes of all are composed of the same chemical building blocks, just put together in different ways. This means, said Daniel Drell, a biologist with the Department of Energy' s Human Genome Program, that the advanced genomics technologies developed for other species can easily be put to work on an agricultural project.
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From page 5... ...
On the broad end, there is general agreement about the right way to approach mapping and sequencing of multi-cellular organisms. The recommendations of Christopher Somerville, director of the Department of Plant Biology of the Carnegie Institution of Washington in Stanford, California, were typical: "When we began developing the Arabidopsis program, we realized the sequencing had to be preceded by other forms of information, particularly a very good map, because sequenced information is most useful when it is used in conjunction with mapping information on individual genes and mutants." In mapping a genome, researchers piece together a large-scale picture of where genes and larger chunks of the chromosomes are.
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From page 7... ...
was actually directed toward mapping. I think that is a good model to follow for the other genomes." For the Arabidopsis program, the map of choice was a "physical map," a set of overlapping stretches of chromosome that covered the entire genome.
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From page 8... ...
Future genome projects may want to use a slightly different type of physical map, suggested Neal Copeland, a mouse researcher at the National Cancer Institute. "As people [working on the mouse genome]
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From page 9... ...
Integrating the databases from those two species would be valuable for the same reasons that integration among agricultural genomes would be valuable, but so far such coordination is more hope than reality. "Quite frankly," he said, "we're still catching up." Finally, the early consideration of social and ethical issues for an agricultural genome project is a step that other genome projects have proven to be valuable (see Box 2: Considering Social and Ethical Issues)
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From page 11... ...
So the major question facing an agricultural genome project becomes: Which fraction of all the genetic information available should be tackled first to get the most bang for the buck? A number of the participants in the workshop agreed that there is no better way to get bang for the buck than to sequence the entire genome of a representative organism, as is now being done for humans and for the weed Arabidopsis thaliana (see Box 3: Saved by the Weed)
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From page 13... ...
A gene might be very close to a particular marker in Arabidopsis but nowhere near the corresponding marker in, say, soybeans. As a result, Bennetzen said, "You are not going to be able to transfer information across species quite that simply based on map position." For that reason, many workshop participants agreed that one of the goals of any agricultural genome program should be to develop target species other than Arabidopsis.
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From page 14... ...
"What a lot of us in the field think now is that we are going to need a number of nodal organisms, organisms that will allow you to study a whole series of species that are closely related." Agricultural genome research would be apportioned into groups of related species, each with its own nodal organism, he said. Because completely sequencing a genome is expensive, there is a limit to how many target species or nodal organisms can be delineated down to the last
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From page 15... ...
That is, if a researcher has isolated a gene from, say, potatoes and wishes to discover its function by comparing it with a collection of known genes from Arabidopsis or another target species, the chances of success are only about five percent greater if the researcher works with a completely sequenced gene than with ESTs. The use of ESTs makes it feasible to amass a surprisingly large amount of information about even those plants and animals that are not chosen as target species.
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From page 16... ...
"I would argue," Venter said, "that this comparative data is going to be far more valuable to have than to completely sequence any one species." Given the value of obtaining complete genomes for target species and the possibility of using ESTs to skim the cream off several dozen genomes for a relatively small investment, the researchers at the workshop thought the best approach to an agricultural genome project would be a multi-tiered one. At the top tier would be a few target species, such as Arabidopsis and rice or corn, whose genomes are sequenced completely.
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From page 17... ...
The project should include not just crop plants, but also livestock, crop trees, and even microorganisms, each group with its own target species. The microorganisms are often overlooked in discussions about an agricultural genome project, noted Jim Cook of USDA's Agricultural Research Service at Washington State University, but they are of crucial importance to agriculture.
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From page 18... ...
"Looking back at the mouse, if we knew about this technology we could have done it a lot cheaper and a lot faster." Another key will be coordination. Since only a few genomes will be sequenced completely, comparison of genetic information across species will play a major role in an agricultural genome project, and the maps will have to be made with that in mind.
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From page 19... ...
"One of the successes of the Arabidopsis group," he said, "has been the development of coordinating committees at both the national scale and an international scale to make sure that we do not engage in any wasteful duplication of effort and to resolve issues that range all of the way from nomenclature to allocating work to the different groups, organizing meetings and [running] databases." Neal Copeland of the National Cancer Institute, who has worked on the mouse genome, echoed the importance of such communication.
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From page 20... ...
They channel a lot of resources into a few centers, rather than NSF' s or NIH' s more distributed system." But whether the Human Genome Project or the highly concentrated programs that DARPA runs serve as the model, many participants believed that one tier of an agricultural genome project should be a directed, technologically intensive effort aimed at mapping and sequencing as much of as many different
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From page 21... ...
To date, much of the individual-investigator funding for agricultural genome research has come from the USDA's National Research Initiative (NRI)
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From page 22... ...
started in 1991," he said, "there has been money put toward about 50 different species." NRI also funds research into animal genomes. But whether the support comes from NRI or as part of a broader agricultural genome project, workshop participants agreed that investigator-initiated research will be the most effective way to pursue such specialized investigations as how a gene's structure is related to its function.
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