The National Plant Genome Initiative Objectives for 2003-2008 (2002) / Chapter Skim
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3 Maximizing the Return from Reference Sequencing: Translational Agriculture
3 Maximizing the Return from Reference Sequencing: Translational Agriculture
Pages 23-30
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From page 23... ...
This is greatly preferred over moderate Investment In many plant species because it concentrates research efforts on identification of genes and key biologic functions in experimental contexts where those coals can be achieved economically. Our proposal will leverage the power of comparative and functional genomics to understand the biology of the selected crop species and their relatives.
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From page 24... ...
We recommend identification of a set of several hundred conserved genes that can be used as anchor markers for comparative map construction and phylogenetic studies across relevant taxonomic distances. If possible, sets of conserved genes should be chosen on the basis of the biologic significance of the underlying genes and pathways and of genomic distribution; map positions should initially be defined in a reference genome.
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From page 25... ...
~nding levels increase, and that the appropriate prerequisites (see Chapter 2J are met, it will be possible to begin sequencing the gene-rich regions of additional key crop species. Translational agriculture will eventually be simplified by the availability of genomic DNA sequence.
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From page 26... ...
The genomic sequencing efforts, and the building of translational tools delineated above, are already supported by EST projects, some of which are being generated in ongoing NPGI projects from normalized libraries of different tissues, different developmental time points, or system perturbation contexts (see Table 3.1~. More-extensive use of alternative gene-discovery technologies such as serial analysis of gene expression and microbead-based and other representational methods should be considered to complement EST projects.
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From page 27... ...
Total plant ESTs Total ESTs in GenBank 263,737 215,71A 1 75,836 1 7A,62A 165,518 1 62,7A 1 1 A8,3~6 112,~87 1 0A,59A 9A,257 1,61 7,85A 1 2,323,09A SOURCE: NCBI 2002. Therefore, we advocate sequencing of full-length cDNAs from all the Arabidopsis genes to generate a baseline "plant Open Reading Frame reference set" the ORFeome that represents the set of genes from which protein is made.
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From page 28... ...
For example, EST sequencing of the oil-gland secretory cells of peppermint plants demonstrated a substantial enrichment, compared to leaf tissue, in expression of genes involved in oil production. In a simple analogy, the virtual plant should include the ability to make it "grow a tuber" or "develop a cotton boll." To reach the goal of incorporating important plant phenotypes (such as cotton fibers, tuber formation, apomixis, perennial habit, fleshy fruit development, nitrogen fixation, heterosis thybrid vigor]
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From page 29... ...
Stock centers might be organized to manage a variety of resources developed for a specific family of plants (such as the Arabidopsis Genome stock center at Ohio State University) , or they may be organized to distribute a specific type of reagent or resource for a wide range of plant families (such as BAC Resource Center currently located at Clemson University)
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From page 30... ...
. Expanding the level of international collaboration and exchange would enhance access to information, germplasm and technology for scientists throughout the world and motivate the formation of partnerships that would generate novel opportunities for innovative genomics research.
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