Probe : newsletter for the USDA Plant Genome Research Program

42 Pages·1994·2.9 MB·English

by  USDA Plant Genome Research Program

Historic, Archive Document
Do not assume content reflects current
scientific knowledge, policies, or practices.

Newsletter for the USDA Plant Genome Research Program
Volume4, No. 1/2 July 1993-July 1994
USD
As
Office of Agricultural
Biotechnology
Jean A. Larson M.A.
,
USDA
Office ofAgricultural Biotechnology,
Washington, D.C.
Can bioengineered organisms of agricultural importance Secretaries, and the Biotechnology Council,
be released safely into the environment and the market- composed of senior agency staff.
place? Will consumers' desires for labeling ofbiotech OAB has provided leadership for the development of
products impact on the proposed Food and Drug -biotechnology guidelines for agricultural research;
Administration's policies? What will be the impact of -scientific exchanges involving biotechnology;
BST on the dairy industry? Will biotechnology technolo- -environmental assessments for transgenic fish;
gies help revitalize rural America? Can this new -performance standards for research with transgenic
technology be useful in preventing and detecting fish and shellfish;
food safety problems? These and other questions -advice when requested by regulatory agencies;
are routinely being addressed by the USDA -a biotechnology consumer information plan for
Office of Agricultural Biotechnology. USDA;
The Office of Agricultural Biotechnol- -coordinated responses on regulatory and
ogy (OAB) was established in 1986 by a research issues to other Departments;
Secretary's Memorandum 1020-27. Its -international conferences/workshops on
role is to coordinate the development animal and plant biotechnology, includ-
of consistent biotechnology pohcies ing three international conferences on
and procedures within USDA. The Biosafety Results of Field Tests
Current OAB functions include: of Genetically Modified Plants and
• Under a Presidential Initiative, Microorganisms";
OAB is the USDA action office for a multi-year -staff papers and speeches for the Office of the Secretary.
Federal initiative on biotechnology research. Since the implementation of the January 31, 1992,
• OAB staffs a Federal advisory committee, the Presidential Initiative on Biotechnology Research, OAB
Agricultural Biotechnology Research Advisory has been the action office for USDA. Twelve Federal
Committee (ABRAC). This Committee pro- agencies participate in the activity. Their efforts on the
vides a public forum for issues in agricultural biotechnology crosscut are coordinated by the Biotech-
biotechnology. nology Research Subcommittee (BRS) of the Committee
• OAB staffs the Committee on Biotechnology in on Fundamental Science and Engineering Research and
Agriculture (CBA), composed of six USDA Development of the National Science and Technology
Agency Administrators and two Assistant Council. As a participant, OAB has collected research
program and budget data from the Agricultural Research
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2 Volume4, No.1/2
Service, Cooperative State Research mayinclude: management of resis- mail, through USDA's Computerized
Service, Economic Research Service tance to biopesticides in crop plants; Information Delivery System, and on
and the Forest Service and eight non- production of pharmaceuticals in Internet through the National Agri-
USDA agencies which are involved plants and animals; use and effects of cultural Library's Gopher; provided
in agriculturally related programs synthetic sequences in organisms of by the Biotechnology Information
and assembled data into a consistent agricultural importance; risk man- Center. From time to time the Office
format for reporting. agement and risk communications; has sponsored national and interna-
The ABRAC consists of 15 and public attitudes, perceptions, tional conferences and workshops on
experts from academia, industry, and acceptance of genetically engi- biotechnology topics.
government, and public interest neered products. The international and trade
groups with knowledge and experi- In addition to the scientific implications of agricultural biotech-
ence in one or more of the following aspects of modern biotechnology, nology are ofgrowing concern to
areas: recombinant DNA research in OAB clearly recognizes the public many U.S. economic planners and
plants, animals, and microbes; relations dimension ofbiotechnology. policymakers. On the international
ecology and environmental science; A well-informed public isbetterable front, OAB is involved in studying
agricultural production practices; to participate in the decision-making research and technology transfer
biological containment and field process about biotechnology. Toward programs in competing nations;
release; applicable laws and regula- this end, OAB shares information with promoting international consensus on
tions; standards of professional the media, participates in public the scientific principles that underlie
conduct and practice; public atti- affairs activities around the country, the environmental and human safety
tudes; public health/epidemiology; and contributes articles on biotechnol- ofagriculturalbiotechnology; and
and occupational health and ethics. ogy to the generalas well as the working with the U.S. Trade Repre-
Fifteen ABRAC members have been scientific press. The Office publishes a sentative, the Food and Drug Admin-
recently appointed by the Secretary monthly newsletter. Biotechnology istration and the Foreign Agricultural
of Agriculture. Notes. The newsletter highlights Service to provide information to
The purpose of ABRAC is to activities on biotechnology issues at trading partners regarding U.S. food
advise the Department, through the USDA and in the private sector. The safety procedures.
Assistant Secretary for Science and dissemination of the newsletter is via
Education, with respect to policies,
programs, operations, and activities Table of Contents
associated with questions of biosafety,
USDA's Office ofAgricultural Biotechnology 1
the development ofguidelines and
Summary ofthe 1993 Plant GenomeAwards 4
performance standards for research
RBNET(Electronic Mail Networkfor Rice Biotechnologists) 7
with genetically modified organisms,
New Capabilities and Connectionsfor the Plant Genome Database 9
and, in response to a specific re-
Plant Genome II Conference Report 22
quest, the development of recom-
Soybase News 24
mendation for the food safety
The Class of1993 Plant Genome Grant Recipients 25
evaluation of transgenic livestock. A Primeron Images and the Internet 20
The most important issue that
Maize Genome Database, a USDA-ARS Plant Genome Database 22
will be addressed by the new Com-
Introducing Dr. Edward Kaleikau 24
mittee in the coming months will be
AnnouncingPlant Genome IIIMeeting 25
to complete the development of
Calendar ofUpcoming Genome Events 27
performance standards for outdoor
SurveyofSynonymous Codon Usage in Nuclear Genes ofArabidopsis, Soybean andMaize .30
research with genetically modified fish
Plant Genome Analysis by SingleArbitrary PrimerAmplification 32
and shellfish. Other important issues
Distinctive Biology ofForest Trees Highlightedat Sixth International Meeting 37
Probe
July1993-July1994 3
Agricultural Biotechnology Research Advisory Committee Probe
Dr. Walter A. Hill Dr. Ronald R. Sederoff
School of Agri. & Home Economics Dept, of Forestry
Tuskegee University North Carolina State Univ. ISSN: 1057-2600
The official quarterly publication of
Dr. Anne R. Kapuscinski Dr. James Lauderdale the USDA Plant Genome Research
Dept, of Fisheries and Wildlife The Upjohn Company Program. This newsletter is aimed
University of Minnesota at facilitating interaction throughout
the plant genome mapping commu-
Dr. Pamela G. Marrone Dr. Susan Harlander nity and beyond.
Entotech, Inc. Director, Dairy Foods Probe is a publication of the Plant
Land O'Lakes, Inc. Genome Data and Information
Center, National Agricultural
Dr. Deborah K. Letourneau Dr. Stanley Pierce Library.
Board of Environmental Studies Rivkin, Radler, Bayh, Hart, & Managing Editor
Univ. of California Kremer Susan McCarthy, Ph.D.
Editor
Dr. Rudy Wodzinski Dr. Fernando Osorio
Joanne Meil
Dept, of Molecular Biology and Department of Veterinary
Production Manager
Microbiology Biomedical Sciences
Terrance Henrichs
Univ. of Central Florida Univ. of Nebraska
Layout andDesign
Dr. Roy Fuchs Dr. H. Alan Wood Terrance Henrichs
Monsanto Agricultural Company Boyce Thompson Inst, for Plant Special Thanks to:
Research Barbara Buchanan
Andrew Kalinski
Stephanie MeGee
Dr. James Tiedje Dr. Walter Reid
Marcia Norfleet
NSF Center for Microbial Ecology World Resources Institute
Michigan State Univ. Articles, announcements, and
suggestions are welcome.
Correspondence Address
Dr. Paul Thompson Susan McCarthy, Ph.D.
Center for Biotechnology Policy and Ethics NAL, 4th Floor
Texas A&M Univ. 10301 Baltimore Blvd
MD
Beltsville, 20705
Phone:[phone]
Minutesfrom ABRAC meetingare published andavailablefrom the OAB on request. FAX: [phone]
_
[phone] email: [email protected]
Needless to say, the OAB transfer, regulations, environmental
USDA Program Office
program is a very dynamic office that impact, economics, public relations, and
Dr. Jerome Miksche
maintains timely responsiveness to the international affairs havebeen supplied USDA/ARS/NPS/PNRS
ever-changingbiotechnology scene. to OAB by cooperating agencies. At the Room 331C, Bldg 005
BARC-WEST
All the above activities are done completion oftheir assignments, says MD
Beltsville, 20705
with a small core ofpermanent staff, Young, "these individuals take their Phone:[phone]
but OAB DirectorDr. Alvin Young newbiotechnologyknowledge and FAX: [phone]
says that "much of my staffworkis experience with them backto their
doneby individuals on temporary agencies and everyone benefits."
assignment to OAB from other USDA For additional information or to
agencies." Specialists in agricultural request OAB published materials,
NationalAgriculturalLibrary
OAB
research, extension/technology contact the at [phone].
Probe
Volume4, No.1/2
$
CompetitiveEdge
Summary Genome
of the 1993 Plant
Awards
Dr. Ed Kaleikau, Program Director
National Research Initiative Competitive Grants Program
USDA
Cooperative State Research Service,
DC
Washington, 20250
Table 1
n 1993, Congress appropri- SPECIES REPRESENTED BY PLANT GENOME AWARDS 1993
7 ated $97.5 million for the
NUMBER OF DOLLAR
National Research Initiative
SPECIES AWARDS AMOUNT
Competitive Grants Pro-
gram (NRICGP), of which $12.1 Agrobacterium 2 250,000
million was made available for plant Alfalfa 2 220,000
genome research. The Plants Divi- Apple 1 276,000
Arnbidopsis 8 539,000
sion of the NRICGP in USDA's Barley 5 961,000
Cooperative State Research Service Bean 2 370,000
administers the plant genome Blueberry 1 118,422
Brassica 4 262,000
grants. In addition to the NRICGP Cotton 2 299,013
allocation, $3.67 million was appro- Douglas Fir 1 223,000
priated to USDA's Agricultural Lettuce 1 200,000
Maize 20 2,405,700
Research Service (ARS) for program
Millet 1 120,000
management, setting targets for Mungbean 1 115,000
genome mapping research, and Oats 2 300,000
database development for agricul- Peach 1 200,000
Peanut 2 262,000
turally important plants. After Petunia 2 211,000
program administration costs, the Pine 3 453,000
net amount available for all plant Poplar 1 120,000
Potato 2 190,000
genome research totalled $15.1 Rice 3 570,000
million: $3.0 million for the ARS Sorghum 4 297,200
and $12.1 million for the NRICGP. Soybean 3 500,000
Tobacco 11 1,392,400
Mission-oriented research proposals
Tomato 7 846,900
that address the goal of improving
Wheat 6 1,145,200
agronomic qualities through ge- Wild Rice i 40,000
nomic research were submitted to
the NRICGP by scientists from the Totals 91 12,126,238
research community. Each proposal ARSG.A.Smith,J Miksche
was peer-reviewed by experts in the
area of genomic research and was * Summations ofaward numbers and dollar amounts do not
sum to the actual values presented because some ofthe awards
Continuedpage7 utilized more than one species.
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July1993-July1994 5
Table 2
GENE SYSTEMS OF TRAITS, NRI PLANT GENOME GRANTS, 1993
AC/DC transposons Anthocyanin biosynthesis
AC/Ds mutagenesis and integration Aphid resistance
Alcohol dehydrogenase Blight resistance
Amylase activation Endodormancy chilling requirement
Apomixis Ethylene biosynthesis
Bacterial blight resistance Fertility
Ca+ Modulated leaf receptor protein Fiber quality
Cytokinin response Fruit quality
Disease resistance Hessian fly resistance
Drought tolerance Inflorescence development
Floral homeotic genes and sterility Kernel starch
Flowering Kernel sucrose metabolism
Gene targeting for excision of foreign DNA Leaf epidermal growth
Lipid desaturation Mildew resistance
mRNA Mitochondria protein synthesis
stability
Phytochrome A mRNA degradation Nematode resistance
N
Plasmid directed conjugation Nodulation and fixation
Polyamines and stress tolerance Phaseolin and seed protein
QTLs for wood quality Photorespiration
QTLs for yield Plastid light response
Ribosomal protein synthesis Rust resistance
Rust resistance Seed oil synthesis
Seed maturation Self incompatibility
Stable transformation Ubiquitin ligation
Starch synthesis Vigor and plant morphology
Targeted DNA integration Virulence genes
Trichomes and insect resistance Virus resistance
T-DNA transport and integration Wood specific gravity
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6 Volume4, No.1/2
Table 3
GENETIC PHENOMENA NRI PLANT GENOME GRANTS 1993
DESCRIPTION SPECIES
Amylaseactivation&repression Barley,Maize
Annualgrowthrate Douglasfir
Anthocyaninbiosynthesis Maize
Apomixis,asexualreproduction Pearlmillet
Cellgrowth Tobacco
Chromosomerecombination Wheat
Chromosomesortinglibraries Tomato
Cloningdiseaseresistancegenes Rice
Cytokininresponse Arabidopsis
Developmentalregulation Tomato,Tobacco
Droughttolerance Grainsorghum
Edthylenebiosynthesis Tomato
Endodormancy&chillingrequirement Blueberry
Geneeffectsonchromatinstructure Maize
Genetaggingforinsectresistance Maize
Geneticengineeredsterility Poplar
Gene/chromosomeidentification Wheat
Homologousrecombination Arabidopsis
Homozygousdeletionstocks Wheat
Hormonalcontrolofseedmaturation Tobacco
Inflouresencedevelopment,flowering Maize,Tobacco
Lipiddesaturation Peanut
Mappingcold,diseaseresistance Peach
mRNAstabilityindicots Tobacco
Mutationvia transposableelements Tomato
Nodulation&Nfixation Bean,Medicago
NucleartargetingofDNA Agrobacterium
Nuclear&organelleDNAvariation Barley
Nuclear-plastidcommunication Tobacco
Photorespiration,nitrogenassimilation Ambidopsis
PhytochromeA,mRNAdegradation Oats
Plasmiddirectedconjugation Agrobacterium
Phytochromegenecontrol Tomato,Rice,Sorghum
Repeatinducedgenesilencing Arabidopsis
RNAediting Petunia
Seedoilsynthesis Maize,Brassica
Selfincompatibility Brassica
Sequencerepeats,microsatellites Soybean
Sitedirectedmutagenesis Maize
Spatialorganizationofgenome Maize,Sorghum
Starchmetabolism&transport Maize
Tandemrepeatsequences Rice
TargetedDNAintegration Tobacco
Transformationdiseaseresistance Potato
Transformationdroughttolerance Pine
Transformationinsectresistance Tomato
Transformationvirusresistance Peanut
Transposableelements Maize
Transposontagging Maize
T-DNAtransfer,andtransport Tobacco,Maize
Ubiquitinactivatingenzymes Arabidopsis
Woundinducibleinsectresistance Tobacco
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July1993-July1994
Awards—Continuedfrompage4 made in two programs in the Ninety-one awardswere made to
judged on its scientific and technical NRICGP Plant Division: the Plant scientists from 34 States (See article,
merit, qualifications of proposed Genome Program and the Plant "The Class of 1993 Plant Genome
personnel, and relevance to Genetic MechanismsProgram. A small Grant Recipients" in this issue).
sustainability and stated research
portion offundsalsosupported Nineteen agronomic, horticul-
objectives in the solicitation for
proposals. genome-related research inother tural, and forest tree species are
In 1993, the majority of plant progamsofNRICGP. Research projects undergoing genetic and physical
genome funds supported awards beingsupportedinFY1993aresumma- mapping procedures (Table 1). Fifty-
six genes and gene systems are being
rizedin tireaccompanyingtables.
Table 4 studied (Table 2), as well as genetic
phenomena in various plant species
TECHNIQUE DEVELOPMENT NRI PLANT GENOME GRANTS, 1993 (Table 3). Many new molecular
techniques are being pursued (Table
Antibody synthesis for proline DNA 4). The data were supplied by the
Biolistic transformation with high molecular weight NRICGP staff, and compiled into
Chromosome painting
Construction and insertion of chimeric gene tables by Dr. G.S. Smith and Dr. J.P.
Miksche in ARS.
Develop target probes for fly resistance
DNA
vector synthesis
Functional cloning of disease resistant genes
Identification of effective sterility genes
Isolate nuclear skeletal structures Plant Genome
Map based cloning system for Rice Grant
DNA
Megabase isolation
Molecular probe and reagent development Deadline Dates
Regeneration after transformation for Pine Announced
Substrate features required for enzyme activation
Transfer teosinte chromosomes to maize
Transformation system for Peanut See page 8
Transposon tagging
in this issue
Wound induced transformation
Offthe Wire
RBNET
Mail Network
(Electronic for
Rice Biotechnologists)
For those colleagues in coun-
tries where electronic mail service is
not currently available, attempts are
With support from the Rockefeller ogy Center, 1060 Carmack Road,
being made to deliver a message by
Foundation, an electronic mail Columbus, Ohio 43210 USA. To
network has been established to address all users of the networkyou fax. If any one ofyou are in this
situation and wish to communicate
increase communication among the may send a message to:
to the RBNET users, you may fax
international rice biotechnology [email protected]. To
community. This network (RBNET) add your name to the RBNET your message to the attention of
Professor Verma at [phone]
is being managed by Professor mailing list, please send your E-Mail
and your message will be posted on
Verma at the Ohio State Biotechnol- address to:
the RBNET for distribution.
[email protected].
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Volume4, No.1/2
NRI
1995 Grant Deadlines
Postmarked Program Program Contacts
Dates Codes Areas (202)
November 14, 1994 31.0 Improving Human NutritionforOptimalHealth 205-0250
52.1 PlantGenome 401-1901
52.2 Plant GeneticMechanisms 401-5042
November21, 1994 22.1 Plant Responsestothe Environment 401-4871
December5, 1994 51.1 Plant Pathology 401-4310
54.1 Photosynthesisand Respiration 401-6030
December 12, 1994 25.0 SoilsandSoil Biology 401-4082
December 19, 1994 26.0 Water ResourcesAssessment and Protection 401-4504
51.5 BiologicalControl Research 401-5114
January 9, 1995 51.2 Entomology 401-5114
51.3 Nematology 401-5114
51.4 Weed Science 401-4310
44.0 Sustaining Animal Healthand Well-Being 401-6303
January 17, 1995 71.1 FoodCharacterization/Process/Product Research 401-1952
71.2 Non-Food Characterization/Process/Product Research 401-1952
72.0 Biofuels Research 401-1952
41.0 EnhancingAnimal Reproductive Efficiency 401-6234
January23, 1995 23.0 Forest/Range/Crop/Aquatic Ecosystems 401-4082
53.0 PlantGrowth and Development 401-5042
January30, 1995 32.0 Ensuring Food Safety 401-4399
51.6 Assessing Pest Control Strategies 401-5114
100 Agricultural Systems 401-1901
401-6303
February 6, 1995 54.2 Nitrogen Fixation/Nitrogen Metabolism 401-6030
61.0 MarketsandTrade 401-3487
62.0 Rural Development 401-3487
February 13, 1995 73.0 Improved UtilizationofWood and Wood Fiber 401-4871
February21, 1995 42.0 Improving Animal Growthand Development 205-0250
43.0 Identifying Animal Genetic Mechanismsand Gene 401-4399
Mapping
February27, 1995 80.1 Research Career Enhancement Awards 401-6234
80.2 EquipmentGrants 401-6234
80.3 Seed Grants 401-6234
The 1995 program solicitation and and the NRICGP application kit. All Genome Grants Program,
application kit will be available in others may request copies from: contact:
September. Please note that potential National Research Initiative Com- Dr. Ed Kaleikau
applicants who are on the competi- petitive Grants Program (NRICGP) Program Director
tive research grants mailing list, who c/o Proposal Services Branch NRICGP/CSRS/USDA
sent in applications in fiscal year AMD/CSRS/USDA AG Box 2241
1994, or who recently requested AG Box 2245 Washington, DC 20250-2241
placement on the list for fiscal year Washington, DC 20250-2245 Telephone: [phone]
1995 will automatically receive Telephone: [phone]
copies of the program solicitation For more information about the Plant