Probe : newsletter for the USDA Plant Genome Research Program

24 Pages·1991·1.8 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
Volume 1, No. 1/2 Spring/Summer 1991
Genome
Strengthening Plant Research
—
New USDA
Efforts Goal of Program
The program is a cooperative effort ofseveral
JeromeMiksche, Director USDA agencies — the Agricultural Research Service
Plant Genome Research Program, USDA
(ARS), the National Agricultural Library (NAL), the
Cooperative State Research Service (CSRS), and the
TT
1 / (U.S. Departmentof Agriculture) Forest Service (FS). ARS has the lead role in directing the
/ / Plant Genome Research Program, estab- program. With a budget of$14.7million for FY'91, the
m jM lished last October, w—ill facilitate the im- Plant Genome Research Program is managed through
provementofplants agronomic, horticul- grants, contracts, and inter- and intra-agency transfers of
—
tural, and forest species by locating importantgenes funds.
and markers on chromosomes, determining the structure
of thosegenes, and transferring the genes to improve Competitive Grants
performance. The end product will be superior plant CSRS' Competitive Grants Research Office will manage
varieties that more closely meet marketplace needs and thegrants portionof the program in cooperation with
niches, while creating a positive effect on the environ- ARS. Grants will be peerreviewed and mission oriented.
ment. Scientists from industry, academia, and government may
Plant Genome Research Program
Goal;Facilitatethegeneticimprovementofplants(agronomic,horticultural,andforestspecies)bylocatingimportant
genesandmarkersonchromosomes,determiningthestructureofthosegenes,andtransferringthegenesto
improveperformancetomeetmarketplaceneedsandniches.
StartOct 1.1990 1991 1992 1993 1994 J82L 1996
Grants awarded for and evaluation ofprogress on
Mapsofthe
gasescoding
Broadmapsat25centimorgan gaps foreconomic
traitsofcrop
Specificregionsandgenes andforest
speciesready
DNAtechnologies, newvectors,PCR, etc: forbreeding
andabilityto
usethegenes
Contracts and agreements for
Genericdata-
Databases basesystemfor
plantgenome
mappingand
Automationrobotics automated
DNAsequenc-
1Centimorgan=acommonmeasurementingenemapping.
Jse.
.
Probe
2 Spring/Summer 1991
economicgainto Americanagricul- gene transfer, and expression. This
ture. Knowledge acquired from one objective is important because it will
commoditycan be transferred to generate results that offer products
another crop species. to the agricultural community. The
In this phase of the program, analysis of factors ingene systems or
proposals anticipated will represent gene families that regulategene
the following commodities: com, expression is required.
soybean, tomato, wheat, barley, rice, 3) Progress in the PlantGenome
pine (conifer), potato, garden bean, Research Program is tied to develop-
cotton, pea, peach, oat, sorghum, ing new mapping and sequencing
sweet potato, carrot, onion, apple, technologies. The following are
rose, sugarcane, citrus crops, and examples of new technologies that
otheragriculturally important need development: A new method
species. to tag sequences, which will elimi-
Dr.JeromeMikschewasnamedDirectorofthe 2) Grants will be awarded to develop nate the need to store mapping
PlantGenomeResearchProgramin 1989. more specific information on crops probes, innovative applications of
Priortojoiningthe U.S. Departmentof
for which some data have already the polymerasechainreaction (PCR),
Agriculture(USDA),Dr.MikschewasHeadof
theBotanyDepartmentatNorthCarolinaState been acquired. Many ofthe major newmethodologytoidentifyQuanti-
University. In 1985,hewasnamedNational acreage crop species such as corn, tativeTraitLoci(QTL's),creative
Program LeaderforPlantPhysiologyand soybean, wheat, and rice come under computersoftwaredesigned specifi-
Biotechnologywithin theAgricultural this category. cally forplantgene systems, insitu-
ResearchService(ARS),whichisaNational Scientists will determinegene hybridizationtechnologies forplant
ProgramStaff(NPS)appointment,the
construction relative to important chromosomes,methods thatallow
advisorybodyforARS. Dr.Mikschehas
maintainedhisinvolvementwithNPSwhile specific traits such as yield, heat and mapping ofpolyploid genomes,
undertakinghisroleinthePlantGenome cold tolerance, disease resistance, chromosomalsorting and separation
ResearchProgram qualitychanges, drought tolerance, Cont. on page 21
apply forgrant funding.
TABLE OF CONTENTS
Multidisciplinary submissions will
begiven favorable consideration.
The programgrants consists of Strengthening Plant Genome Research Efforts—Goal ofNew USDA Program I
three components: NAL's Plant Genome Center—A New Directionfor Library Services 3
1) Support will be committed to A Look at USDA's Competitive Grants Process 4
constructing broad maps that locate Plant Genome Database—Update 5
importantgenes orgenesystems in Planning Underwayfor USDA Soybean Genome Database 7
crops and forestspecies. This will be Lorest Tree Genome Database—Development Begins 7
—
achieved using a technology that Information Superhighway Envisioned Legislation Pending 8
allows scientists to determine rather TrenchJoin theInternational Human Genome Effort 10
broad geneticsimilarities and ImprovingAccess to Standardized Biological Terminology 11
differences, initiate assignment of Libraries Link Users With Specialized Databases 13
DNA
fragments on chromosomes, Theory andApplication ofYAC Technologyfor Genome Research 14
and then begin the mapping process. ParserAvailablefor GenBank5 Elat Tile 18
Budgeted dollars will not be allo- Genome Sequencing Conference III Setfor September 18
cated on a commodity basis, but on Introducing Dr. Stephen Heller 19
targeted gene systems or traits of Calendarof Upcoming Genome Events 20
some of the commodities that yield Beltsville Symposium 22
—
Probe
Spring/Summer 1991
Genome
NAL's Plant Center
A New
Direction for Library Services
Joseph H. Howard
Director, National Agricultural Library
U.S. Department ofAgriculture
This newsletteris butone
When the National Agricultural exampleofthevariousservices
Library (NAL) opened in Beltsville, offered byPGDIC.Inaddition,
Maryland, in 1967, all the techno- PGDICstaffwill provide information
logicaladvances in information onallaspects ofplantgenome
management that would develop mapping; identifycurrentgenome
overthenext24years wereprobably mapping research; referusersto
notenvisioned bythestaff. organizationsorexperts in theplant Since1983,JosephH.Howardhas
NAL servedasDirectoroftheNational
But, since that time, has genomesubjectarea;performbrief Agricultural Library(NAL). With2
workeddiligentlytostayabreastof AGRICOLA (AGRICulturalOnLine millionvolumes,NALisoneofthe
thenewtechnologies and toadapt Access)databasesearchesona largestagriculturallibrariesinthe
those thatmostbenefitusers.These complimentarybasis orexhaustive worldandisoneofthreenational
technologicaladvancescombined searchesonacost-recoverybasis; librariesintheUnitedStates.
with the talents and dedicationof furnish users witha QuickBibliogra-
librarystaffhaveenabled NALto phy(QB), Special Reference Brief AGRICOLA computerized database
improveand expand itsservices to (SRB),oruserguide to literature; and and as the foremost agricultural
bettermeetthe needsofusers inthe assist users inaccessing NAL's library in the world, with nearly 2
agricultural community. extensivecollection. millionvolumes and subscriptions to
RecentlyNALopened thePlant These services1 are available to 26,000 periodicals, NAL is the ideal
Genome Data and Information anyoneinterested inplantgenomes, location forestablishing and main-
Center (PGDIC), which offers a new including scientists, breeders, educa- taining the database.
direction for the library in archiving tors,students,legislators, information NAL staffanticipates that
and in providing the public access to professionals, administrators,and the PGDIC will lead the way foraddi-
a national scientific database. An general public. tional centers and databases in other
initiativeofUSDA's Plant Genome Plans are underway todevelop agriculturally related areas.
Research Program, the Center's a newdatabase that will contain For more information on
primarygoal is to make information plantgenome data on fouragricul- PGDIC, contact Susan McCarthy,
—
onplantgenomeresearchreadily tural commodities soybean, com, coordinator for the Center, on (301)
available in usefulformats to users. wheat, and pine. As producerof the 344-3875.
1.All programsoftheUSDAareavailabletoanyonewithoutregardtorace,creed,sex,ornationalorigin.
Probe
Spring/Summer 1991
Competitive Edge
A
Look USDA's
at
Competitive Grants Process
Anne Datko, Program Director, National Research Initiative responsible, in consultation with the
Competitive Grants Program, (NRICGP), CSRS, USDA chiefscientistofNRICGP, forselect-
ing panel members withappropriate
scientificexpertise,reviewexperi-
National Research Initiative turalResearch Service (ARS) would ence,andbreadthofknowledge.
USDA has announced a national bethe lead agency fortheUSDA Written reviewsarealsosolic-
research initiativeonagriculture, PlantGenomeResearchProject, the ited from thescientificcommunityon
food, and theenvironment.The need competitivelyawarded researchgrant anad hocbasis. The peerreview
foran increased investmentin componentwould beadministered panel, chaired by the panelmanager,
competitively awarded research was byCSRS and funded within the considers thejudgementofpanel
—U
identified by the National Research Program's PlantSystems Divisionat
Council ofthe National Academy of a level of$11 million.
NRICGP
Sciences and broadly endorsed by These researchgrants support anticipates publish-
the agricultural, scientific, and users researchprojectsjudged tofurther ing the 1992 solicitation in
communities. In the 1990 Farm Bill, USDA programs. Asolicitation the Federal Register early in
the initiative was authorized at a full announcing each program's guide- October 1991 with postmark
funding level of$500 million per lines is published in the Federal
deadlinesfor proposals being
year.The OfficeofManagementand Registeratthebeginningofeach
earlier than in 1991.
Budget endorsed the full funding fiscal year. Proposals forsuchawards
leveland is committed to reaching maybe submitted byanypublicor 99-
this levelbyphased growthoverthe private institution, or individual.
nextfewyears.ForFY'91,Congress membersand thead hocreviewsto
funded the initiative at $73 million; Peer Review provide advice to the NRICGPas to
thePresident'sFY'92budgetrecom- Ingeneral terms, peerreviewis used thescientific meritofeach proposal.
mends funding at the level of$125 to provide the best possible scientific Theprogramrecommendationfor
million. advicebeforeexpendingFederal funding,based onthepanel ranking,
funds. Peerreviewis arranged bya is presented to thechiefscientistwho
NRICGP's RoleinSupporting program director— a USDA scientist recommendstheawards.
Plant Genome Research responsible foroverseeing the review
In 1991, the NationalResearch process, upholding the highest Plant Genome Proposals
Initiative CompetitiveGrants Pro- standards ofconduct, and providing Morespecifically, the 1991 NRICGP
gram subsumed the previously assistance and advice to the panel solicitation identified research in the
existingUSDACompetitiveResearch manager. A panel manager, an active broad area ofplantgenomestudiesas
GrantsProgram. Further, itwas researcherintheappropriatescien- having the potential tosignificantly
announced thatwhile the Agricul- tificcommunitychoseneachyear, is improve agriculturaland forest
Probe
Spring/Summer 1991 5
Home Base
\y
—
productivity, and described the areas
in which proposals would be ac- Plant Genome Database Update
cepted. Inresponse to thesolicitation,
alargenumberofproposals were
submitted bythepostmarkdeadline
Douglas Bigwood, Database Manager
ofJanuary28, 1991 Dr. Maureen
. Plant Genome Data and Information Center
Hanson, directorofthe NSFVDOE2/ USDA
National Agricultural Library,
USDA PlantScience CenteratCornell
University, was named panel man-
agerforthePlantGenomeProgram Providing users with fast, easyaccess agricultural species—maize, soybean,
for 1991, while Dr. Anne Datko, of to plantgenome mapping and wheat, and loblollypine. In addition,
the NRICGP staff, served as program related information is a primarygoal procedures will be implemented to
director. of USDA's Plant Genome Research ensure that the information provided
The peerreviewpanel has Program. Currently plans are under- is up to date.
alreadymettoreviewproposals way to develop a plantgenome
submitted;awardrecommendations database system at NAL's Plant Project Activities
havebeenmade toDr.PaulStumpf, Genome Data and Information Initial activities ofthe database
chiefscientistofNRICGP.Becauseof Center (PGDIC). The Center's project include site visits by PGDIC
hisjointresponsibilityforNRICGP database manager will direct the staff to several institutions also
and thePlant Genome Research implementation of the plantgenome involved in developinggenome
Program, Dr. Miksche was notonly database, which will contain public information systems. Institutions
consulted as to panel memberselection plantgenome information for four visited include the NationalCenter
butalso received theaward recom-
mendations.Thegrants funded willbe
published inJanuary 1992inthe "Food automatically receive a copy of the Forsolicitation information,
and Agriculture Competitively 1992 solicitation. Other interested contact thefollowing:
Awarded Researchand Education individuals may request the Solicita- Attn: 1992 Solicitation
Grants" publication prepared by tion (in September 1991, see the NRICGP/CSRS/USDA
USDA's CSRS. addressbelow). Room 323, Aerospace Building
A vacancyannouncement Washington,DC20250-2200
is
1992 Solicitation expected tobe issued withinthe next Phone [phone]or
NRICGP anticipates publishing the fewmonths by NRICGP's Plant FAX [phone]
1992solicitation in the Federal SystemsDivision forthepositionof ForGenomeProgramDirector
RegisterearlyinOctober 1991 with PlantGenomeProgramDirector. vacancyinformation,writeto:
thepostmarkdeadline forproposals Persons interested in applying for Attn: Dr. Sally Rockey,
being earlier than in 1991. All institu- this full-time, permanentUSDA PlantSystemsDirector
tions thatreceived the 1991 solicita- positionmaycontactCSRSat the NRICGP/CSRS/USDA
tion and all 1991 applicants will address below foradditional infor- Room 323, Aerospace Building
mation. Washington, DC 20250-2200
Phone [phone] or
1.NationalScienceFoundation FAX [phone]
2.U.S.DepartmentofEnergy
Probe
Spring/Summer 1991
for Biotechnology Information at the reliability, management, and accessi- related datasourcessuchas
National Library ofMedicine bility ofdata important to all fields of GenBank®, AGRICOLA, and the
(Genlnfo®Backbone), the Los Alamos science and technology. Germplasm Resources Information
National Laboratory (GenBank®), the Network (GRIN).
Lawrence Berkeley Laboratory Species Groups
(Chromosome Information System), The taskofcollecting and Future Plans
the Welch Library atJohns Hopkins evaluating the data that will com- By the time this newsletter is printed,
University (Genome Data Base), the prise the plantgenome database thefirstmeetingofthePGDIC
Massachusetts General Hospital system is the responsibilityof the Technical Committee will havebeen
(Arabidopsis mapping project), and principal investigators for the four held Composed ofgeneticand
.
Agrigenetics(commercialbreeding plant species and their advisory informationexperts, thecommitteeis
projects). NALstaffbenefited from committees. The principal investiga- expected tobevaluablein ensuring
the wealthofknowledgeand experi- tors are Frank Greene and Olin that the plantgenome database is the
enceprovided by thesegroups. Anderson (wheat), David Neale bestpossibleresourceforusers.
Hopefully, as a result of this informa- (pine), Ed Coe (maize), and Randy PGDIC staffare also establish-
tion sharing, some of the pitfalls and Shoemaker(soybean).Eachgroup ing computerand communication
problems faced byotherinstitutions will have its own database require- systems. Initial development will be
can beavoided in the USDA project. ments.Cooperatorsintheproject performedonUnix1workstations
TheCenteralso has beenactive havemadeaconcerted effortto using the Sybase1 relationaldatabase
in twoCODATA projects: Biological ensurethatalldatabase-related managementsystem. These have
Macromolecules (seeking toimprove activities are performed in acoordi- essentially become de factostan-
coordination among institutions that nated manner.The ultimategoal is to dards in the genome community. The
DNA
compile protein and sequence providea masterdatabase design that database system's major network
data) and Standardized Terminology is as generic as possible. If this goal is access will be through Internet viaa
—
for Access to Biological Data Banks achieved and effortsso farare T1 line.
—
(headed by Lois Blaine, whose article encouraging data froma numberof The database analysis and
appears elsewhere in the newsletter). additional species may be easily designare proceedingas planned.
CODATA
is an interdisciplinary incorporated in thedatabase in the Implementation will begin in the
scientificcommitteeoftheInterna- future. Furthermore, plansare to near future.
tional Council of Scientific Unions develop an open system so USDA's
thatseeks to improve thequality, databasecan forgedata links with
1.Mentionofa tradenameorbrand namedoesnotconstituteendorsementorrecommendation
bytheDepartmentoversimilarproductsnotnamed.
DESERT STORM RAINS ON PLANT GENOME GRANT PROPOSALS
January 28, 1991, was the deadline for plant genome grant proposals. Prior to the Persian Gulf
crisis, express mail was delivered directly to the Aerospace Building. High-level security
protocols were engaged with the commencement of hostilities in the Gulf. The express mail
was subsequently routed to the main USDA mailroom two blocks away and X-rayed. A few
grant proposals were inadvertently returned to the senders. All of these proposals were subse-
quently accepted for consideration.
—
Probe
Spring/Summer 1991
Touching Base with Randy Shoemaker
USDA
Underway
Planning
for
Genome
Soybean Database
Randy C. Shoemaker Agricultural Library (Susan
Research Geneticist, Field Crops Research Unit McCarthy). In addition, Mary Berlyn,
Iowa State University acooperatorintheUSDAProgram
USDA
Agricultural Research Service, and co-developer and curatorof the
E. coli genetic stock center database
Until recently, informationon and established a priorityforaccom- at Yale University, provided useful
soybeangenetics hasdeveloped plishing the tasks required todevelop inputand facilitated discussions.
slowlyinrelation todatagathered adatabase.
onothermajorcrops.However, the Thegroup included scientists Working Committees Formed
increased speed with whichgenetic from Stateand Federal institutions Sevencommitteeslistedbelowwere
dataon thesoybeancurrentlyis and privateindustry, and representa- formed during theconference to
being accumulated rivals that ofany tives from theGermplasm Resource addressspecificconcerns according to
othergeneticsystem. Information Network (Mark theirareasofexpertise.Thecommit-
The importance ofthe soybean Bohning), the American Soybean tees will determinetheprobable
as a majorworld oilseed crop plus Association (Keith Smith), the USDA relationshipsbetweentheirrespective
the increased volume ofgenetic Plant Genome Research Program segmentofthedatabaseand theother
information accumulating have (Jerry Miksche), and the National Cont. on page9
made the soybean an important
focus ofthe USDA Plant Genome Touching Base with David Neale
Research Program's thrust to
develop a plantgenome database Forest Tree Genome Database
management system. The database,
to be located at the National Development Begins
Agricultural Library (NAL), will
include information on fouragricul-
—
tural commodities soybean, com,
wheat, and pine. David Neale, Molecular Geneticist project is part of USDA's Plant
Institute ofForest Genetics (IFG) Genome Research Program effort to
Soybean Conference Held USDA Forest Service, Berkeley, CA provide users with fast, easy access
Ataconference held recently in St. to plantgenome data. USDA plans
Louis, Missouri, over 30 partici- are to develop a plantgenome
pants from 14States and Canada database system at NAL's Plant
Plans are underway by USDA's
met to discuss developing a proto- Genome Data and Information
type soybeangenome database. Forest Service (FS) staffto develop a Center, which will contain plant
prototypegenome mapping database
Participants provided information genome information on the loblolly
for the loblolly pine, an important
onthelong-termneedsoftheproject pine and three additional
forest tree species. The database
Cont. on page9
Probe
8 Spring/Summer 1991
From the Hill
Information Superhighway
Envisioned— Pending
Legislation
to Establish National Computer Network
Susan McCarthy, Coordinator
the congressional calendar.
Plant Genome Data and Information Center
Under the proposed legislation,
USDA
National Agricultural Library,
the National Science Foundation
would provide leadership in estab-
lishing the new fiber-optic computer
A national superhighway for infor- needed to facilitate access to genome network in cooperation with the
mation maysoon become a reality if data. NREN would link libraries, Department ofDefense, the Depart-
Congress passes the proposed government research laboratories, ment ofEnergy, the Departmentof
legislation needed to establish the industry, and universities. The Commerce, the National Aeronautics
National Research and Education National Agricultural Library and and Space Administration, and other
—
Network (NREN) a high-capacity, the National Libraryof Medicine are agencies.
high-quality computer network that cited in the proposed legislation as A third bill introduced this year
supports a broad set ofapplications focal points in the information proposes to establish a Federal High-
and networkservices for the research distribution networks. These libraries Performance Computer Network,
and education community. play vital roles in thegenome which would serve many ofthe same
NREN would expand and programs forhumans, plants, and purposes envisioned forNREN.
upgrade the existing interconnected animals. SenatorJ. BennettJ—ohnston (D-LA) is
array ofprimarily scientific research sponsoring the bill the Department
networks thatcomprise Internet, Proposed Legislation of Energy High-Performance Com-
including the nationwide NSFNET Senator Albert Gore, Jr. (D-TN) puting Actof 1991 (S343). The
(the backbone), regional networks introduced a bill (S272) in the Senate DepartmentofEnergy is designated
such as NYSERNET and SURANET, this yearto establish NREN under lead agency under the proposed
and local area networks. NSFNET, the High Performance Computing legislation.
perhaps the best known of the Actof 1991. Recently, Representative
Internet networks, allows researchers George Brown (D-CA) introduced a Increased Funds and Support
and educators to exchange up to 1.5 companion bill (HR656) in the A new Presidential Initiative,
million bits ofdata persecond. The House. Legislation was first pro- "Grand Challenges: High-Perfor-
proposed NREN is expected to be at posed by SenatorGore in 1988. Last mance Computing and Communica-
least a thousand times faster. yeara revised version ofthebill was tions," issued by the Office ofScience
unanimously passed by the Senate, and TechnologyPolicycalls fora 30-
Facilitating Genome Research but the House failed to act on the percentincrease infundingforFY'92.
Fast, high-quality networks (gigabit companion bill. The current Senate The funds will support high-perfor-
persecond transmission rate) are and House bills have been placed on mancecomputingsystems, advanced