Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology (2008) / Chapter Skim
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From page 20... ...
Examples of the traits that plant genome scientists would like to understand and control include disease resistance against a wide range of plant pathogens, nematodes, and insects and tolerance to environmental stresses (for example, salt, toxic soil chemistries, drought, extreme temperatures, and soil nutrient utilization)
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From page 21... ...
It also requires a daunting level of intellectual growth in biologists' perception of how genetic networks control physiological traits, how natural genetic variability in important traits within and across plant species is manifested, how environmental signals are transduced into adaptive responses, and how evolutionary processes lead to network diversification, optimization, and creation of trait novelties. Scientific AND SOCIETAL Impacts OF NPGI Impacts and Outcomes from NPGI-Funded Research At the beginning of NPGI in 1998, there was little dedicated federal funding for plant genomics research beyond the then rapidly expanding Arabidopsis genome project and its associated research community, and various projects funded by ad hoc grants to principal investigators (PIs)
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From page 22... ...
Genome Sequence, Structure, and Organization NPGI has contributed to revolutionary breakthroughs in plant genome se quencing. The initial priority in plant genomics research is to have a high-quality finished genome sequence of the relevant organisms.
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In addition to using "sequencing for hire" in some projects, NPGI has recently benefited from an extremely successful interaction with the Department of Energy's (DOE) Joint Genome Institute (JGI)
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From page 24... ...
Full-length cDNA clone sequences are even more useful to understand gene function and evolution; complete collections of full-length cDNA clones are important tools for subsequent functional experimentation. Completed and Ongoing Land Plant Reference Genome Projects Table 2-1 includes known ongoing plant genome sequencing projects, many of which support the mission of NPGI through in-kind support from JGI.
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From page 25... ...
Rice (indica and 0.4 BAC 2005 International consortium japonica) 3 Populus trichocarpa Black cottonwood 0.5 WGS 2005 Joint Genome Institute 4 Vitis vinifera Grape 0.5 WGS 2007 Genoscope 5 Physcomitrella patens Club moss WGS 2006 Joint Genome Institute 6 Medicago truncatula Barrel medic 0.5 BACb 2007 International consortium 7 Sorghum bicolor Sorghum 0.7 WGS 2007 Joint Genome Institute 8 Carica papaya Papaya 0.4 WGS 2007 University of Hawaii 9 Ricinus communis Castor bean 0.4 WGS 2007 The Institute for Genomic Research 10 Zea mays (x2)
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From page 26... ...
Another calculation of the number of putative unique transcripts (PUTs) for these and other species can be found at the Plant Genome Database (Plant Genome Database 2007)
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From page 27... ...
Glycine max Soybean 392,321 24,018 36,399 Malus x domestica Apple tree 255,097 16,903 26,757 Medicago truncatula Barrel medic 236,819 16,211 20,414 Lotus japonicus Trefoil 150,631 13,640 14,461 Populus trichocarpa Black cottonwood 89,943 14,059 12,687 Populus tremula x Hybrid aspen 76,160 7,519 11,593 Populus tremuloides Prunus persica Peach 70,972 6,306 6,596 Ricinus communis Castor bean 53,402 NA 4,524 Populus trichocarpa x Populus Hybrid poplar 53,208 NA 7,803 deltoides Euphorbia esula Leafy spurge 47,543 NA 9,905 Arachis hypogaea Peanut 40,627 NA 1,491 Trifolium pratense Rotklee clover 38,109 NA 4,347 Populus tremula European aspen 37,313 NA 5,961 Manihot esculenta Cassava 36,120 NA 5,189 Phaseolus vulgaris Common bean 22,847 NA 2,941 Bruguiera gymnorrhiza Burma mangrove 20,373 NA 2,031 Populus trichocarpa x Populus nigra Hybrid poplar 20,130 NA 3,531 Phaseolus coccineus Scarlet runner bean 20,120 NA 2,315 continued
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From page 28... ...
Oryza sativa Rice 1,211,418 40,259 49,870 Zea mays Maize 1,159,264 57,447 64,601 Triticum aestivum Wheat 1,050,926 34,505 62,121 Hordeum vulgare + subsp. vulgare Barley 437,713 21,418 30,171 Saccharum officinarum Sugarcane 246,301 15,586 26,894 Sorghum bicolor Sorghum 204,308 13,547 20,714 Festuca arundinacea Fescue 41,869 NA 6,297 Zingiber officinale Ginger 38,139 NA 7,850 Hordeum vulgare subsp.
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From page 29... ...
Patens Moss 174,908 13,688 18,707 Marchantia polymorpha Liverwort 33,692 NA 3,874 NOTE: All plants with more than 20,000 ESTs are shown, as listed in dbEST. gene function, defining regulatory genes and networks, understanding patterns of gene expression, comparative analysis of gene expression, gene expression resources and databases, and epigenetics and RNA-based regulation.
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From page 30... ...
Comparative analysis of gene expression. Comparative analysis of expression patterns could be a major outcome of functional genomics applied to a wide va riety of plant species.
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That website has an estimated 25,975 unique visitors and 269,323 page impressions, excluding robot requests. SOURCE: Examples of Websites were obtained from the Interagency Working Group on Plant Genomes.
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Domestication, Diversity, and Natural Genetic Variation The 2002 NRC report noted that while sequencing costs were too high for deep sequencing across the plant kingdom, EST sampling, development of mapping tools, and the coalescence of focused, community-supported projects of evolution ary and ecological interest were worthy of support. NPGI-funded studies of natural variation and crop domestication have led the way in the understanding of selec tion and in the dissection of complex traits.
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From page 33... ...
The available plant genomics databases have already led to concrete benefits in the plant research community, as summarized above. From an analytical perspective, the gains are clear: Collection of large data sets from multiple sources has led to metadata analyses, though comparisons of data that span technology
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From page 34... ...
Comparative studies exploiting the basal plant genomes now available provide the basis for phylogenetic models of gene and genome structure. To enable these and other studies, the data resource projects typically offer downloading datasets such as physical maps, genetics maps, computed gene predictions, microsatellite sequences, the database content (as tab separated-value files or as database dumps)
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That newly proposed area of research was intended to empower both public and private scientists to use the basic discoveries from other research areas of NPGI for crop improvement. The report mentioned the following as critical enabling technologies and goals: the development of genetic maps, physical maps, transcript maps, and germplasm collections with molecular genotypes; the discovery of chromosomal intervals that possess gene conditioning important agronomic, compositional, and pest resistance traits; the design of "breeder-friendly" DNA markers; and the analysis of fungal genomes and the sequencing of the gene-rich regions of major crop plants.
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From page 36... ...
Arabidopsis 2010 Project are the engines of basic plant genomics discovery that power intel lectual and practical furtherance of plant biology in both the public and private sectors. Hence, the committee also monitored scientific output of NPGI-funded grants (as provided by IWG)
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These data are also compared to plants that serve as broad models for all of basic plant biology (bottom of the tables in Appendix B)
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. There are no TABLE 2-4 Number of Undergraduate Students Trained and the Sector in Which They Now Hold Positions, as Reported by the 165 NPGI-Funded Investigators Who Responded to the Committee's Questionnaire Number of Sector Students Academia, including undergraduate and graduate schools and other positions in academia 438 Government 8 Industry 79 Still in investigators' laboratory 198 Other, including professional schools such as medical, dental, and law school 115 Unknown 658 Total 1496 NOTE: Number of undergraduate students among the 1,496 known to have left the country = 10.
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From page 39... ...
Specialized individual fellowship programs provide incentive for the best students at any level to seek and win competitive fellowships and have proven to bring new talent into a field. For example, the NSF Plant Biology Post-doctoral Fellowship Program (1983–1994)
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From page 40... ...
. Although the numbers of students involved in those IGERT programs are low, the three programs are a first of what could be an expanding set of steps towards addressing a key recommendation of the 2002 NRC report that "the plant biology community needs to expand training opportunities into disciplines that are not traditionally associated with plant biology and crop sciences, such as computer science, mathematics, chemistry, and engineering." At the undergraduate level, NPGI provides partial support for 12 summer internship programs through its Research Experience for Undergraduate Program (REU)
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programs led by North Carolina State University and by the Uni versity of Connecticut offer opportunities for diverse populations of students to gain hands-on experience in plant genomics research (NSTC 2005)
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In the first year of the Wheat Coordinated Agricultural Project (CAP) , USDA provided workshops or information sessions on marker-assisted selection at more than 40 field days and industry meetings, and mounted a symposium at the Crop Science Society of America meeting that reached more than 120 people (USDA-CSREES presentation to the committee, April 26, 2007, Workshop)
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From page 43... ...
. The committee enthusiastically endorses this concept and concluded that NPGI has set an example for other federal programs by appointing a professorial or an affiliate faculty-level education coordinator for each of its Coordinated Agricultural Projects (Interagency Working Group on Plant Genomes, personal communication, September 18, 2007)
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Building on the success of the rice genome sequencing project, an Interna tional Rice Functional Genomics Consortium was convened with leaders from 18 institutions representing 10 countries and two international agricultural research centers. The goals of the initiative are to work cooperatively to elucidate gene
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http://cnia.inta.gov.ar/lat-sol/ SOURCE: Interagency Working Group on Plant Genomes. function, integrate databases, establish bilateral or multilateral partnerships, and enhance rice production (IRFGC 2007)
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From page 46... ...
that are resistant to the parasitic weed Striga. • Establishing comparative markers to link the genetic maps of chick pea, cow pea, and pigeon pea to the Medicago genome sequence map, enabling breeders in India and Africa to identify disease resistance genes and develop improved cultivars of their local crops.
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From page 47... ...
. The CGIAR Generation Challenge Program is dedicated to alleviating constraints in agricultural productivity that contribute to global poverty and hunger, with an emphasis on harnessing genomic technologies to make rapid progress in the area of drought tolerance (CGIAR Genomics Task Force 2006)
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From page 48... ...
Plant Genome panel into a translational genomics program in recent years, with a different crop focus each year, and with a major emphasis on outreach and extension of research efforts. USDA-ARS has also refocused some of its internal programs to complement and support NPGI research.
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From page 49... ...
bThe program budget presented for the Bioenergy Research Center includes funding for plant and microbial research and technology development. multimillion-dollar Coordinated Agricultural Project from USDA-CSREES and USDA Forest Service (USFS)
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From page 50... ...
. Examples of plant genome sequencing by DOE's Joint Genome Institute through CSP include Physcomitrella in 2005; Selaginella, sorghum, Arabidopsis lyrata, Capsella, Mimulus, and the chlo roplast of Campanulales in 2006; and Brachypodium, Aquilegia, Gossypium, cas sava, maize, soybean, and Eucalyptus in 2007.
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From page 51... ...
Although NHGRI does not fund plant genome sequencing directly, parts of some plant genome sequencing projects have been done at one of the NHGRI-supported sequencing centers, and many of the fungal pathogen genome sequences noted above were done as part of the Broad Institute's Fungal Genomics Program. NHGRI also supports the advancement of sequencing technology, development of bioinformatics tools, and identification of all functional elements in the human genome.
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From page 52... ...
For example, the Maize Genetics Corporation was expanded to provide long-term curation of maize mutant genetic stocks developed by NPGI awardees. The Ge netic Stocks -- Oryza Collection was established as a result of NPGI when the rice genome was sequenced and the need for a collection of rice seed mutant genetic stocks was recognized.
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