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Probe : newsletter for the USDA Plant Genome Research Program PDF

24 Pages·1991·1.8 MB·English
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Preview Probe : newsletter for the 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 (202) 401-5022or NRICGP anticipates publishing the fewmonths by NRICGP's Plant FAX (202) 401-6480 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 (202) 401-5114 or 1.NationalScienceFoundation FAX (202) 401-6488 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

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Most books are stored in the elastic cloud where traffic is expensive. For this reason, we have a limit on daily download.