Exploring Horizons for Domestic Animal Genomics Workshop Summary (2002) / Chapter Skim
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3. Identifying Priorities
3. Identifying Priorities
Pages 9-19
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From page 9... ...
The worldwide sequencing capacity is, according to the workshop participants, enough to sequence a complete mammalian genome every four to eight months, given that entire fill-time capacity was devoted to one species. So in theory researchers could sequence the genomes of the major domesticated animals of interest—cattle, pigs, dogs, cats, horses, sheep, chickens—within a few years.
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From page 10... ...
So there's always going to have to be a balance between scientific relevance and things that have a payoff in other ways." Medical Relevance In terms of funding potential, the most important practical criterion is medical relevance, O'Brien noted, since that is what the NIH is most interested in, and it is the NIH that to date has been the major source of funds for genome sequencing. To appeal to the NIH, researchers interested in sequencing the genomes of domestic animals will have to consider which work will address issues of human health.
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From page 11... ...
They have implications both for the task of annotating the human genome, which will have many direct medical benefits, and for a better understanding of how species evolved over tens of millions of years, which, as an issue of basic science, will have more indirect benefits in the future. One key evolutionary factor to consider in choosing which genomes to sequence is how closely related a species is to other species that have been or will be sequenced.
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From page 12... ...
Box 3-1 Phylogenetic Relationships Among Modern Orders of Placental Mammals Cladistics is a system of arranging taxa by the analysis of primitive and derived characteristics, so that the arrangement will reflect a pattern of descent among the species in question. Cladistics attempt to determine which characteristics of the organisms are specialized, derived ones that truly reflect recent common descent and it emphasizes such features, which are called "shared derived characters", in classification.
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From page 13... ...
"That means that three of the four mammalian major clades are unrepresented entirely." That lack, O'Brien argued, offers a strong argument for sequencing at least one or two domestic animals as representatives of the fourth clade, such as cattle and perhaps one of the members of the order Carnivora either a dog or a cat. Evolutionary biologists also would like the sequences of representatives from the first two clades—say, the elephant and the armadillo—but that interest does not help researchers choose among domestic animals, since all of them sit within the fourth clade.
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From page 14... ...
Unlike a wild species like the elephant, where the identifiable disease states would be very limited, domesticated animals are really valuable in that way." Another consideration, Preuss suggested, should be the value of different genomes in helping researchers to understand gene expression and regulation. "In the human genome project," she said, "it was surprising to everyone that there were so few genes, and so a lot of people are now focusing on gene regulation.
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From page 15... ...
It might not be necessary to do a complete genome for each species, Messing said, and so researchers who are prioritizing genome projects should consider whether to sequence the entire genome for a particular animal. "We should look at the extent of sequence coverage that we want to allocate to a particular project," he said, "either a complete sequence or to go for targeted regions, which I think also has great value in terms of comparative genomics" (see Box 3-2~.
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From page 16... ...
16 IDENTIFYING PRIORITIES In addition, Kappes noted, it will be necessary to decide how much redundancy is needed in the genome sequence for each animal.
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From page 17... ...
A number of participants expressed the view that cattle, pig, and, perhaps, chicken genomes should be put at the top of the list for a variety of reasons, including agricultural value and helpfulness in understanding the human genome better. "As far as farm animals are concerned," O'Brien said, "it would be hard not to put the cow up on the top of the list with the people that are here at this meeting, but the people interested in the pig genome make a pretty strong argument, too.
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From page 18... ...
Finally, the human genome and the cat genome are both very primitive for their respective orders. That is to say, the ancestor of carnivores look a lot like a cat, and the ancestor of primates looks a lot like a human." An audience member echoed O'Brien's arguments: "One of my preferences is the cat, and that's because of it being such a good model for FIV and human immunodefiency virus (HIV)
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From page 19... ...
, which is an incredible tool. It has a very short generation interval as well, which is a powerful tool for fine mapping of quantitative trait loci.
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