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Historic, Archive Document Do not assume content reflects current scientific knowledge, policies, or practices. ??/. y ? 7 (? Newsletter for the USDA Plant Genome Research Program Volume 2, No. 1 Spring 1992 Arabidopsis Database Nears Completion Co Drs. Sam Cartinhour, J. Michael Cherry, S. Hanley, B. Hauge, and Howard Goodman Department ofMolecular Biology, Massachusetts General Hospital, and MA Department ofGenetics, Harvard Medical School, Boston, A specialized genome databaseon thesmall plant ofrelated tasks and presentthe results ofaqueryon the Arabidopsis thaliana is expected to be available this spring computerscreenastext. toassistmolecularbiologists,geneticists,and other Forexample,onedatabasemayretrieveand analyze DNA researchers. ScientistsattheMassachusetts General sequences, whileanotheroffersbibliographic Hospital (MGH) in Bostondeveloped thedatabase, information, and still another tracks down the availabil- knownas AATDB (AnArabidopsis thalianaDatabase). ityof mutant strains. The database is one objective of the Multinational This segregation by data type mayseem to be an CoordinatedArabidopsisthalianaGenomeResearchProject. efficient way to manage information. However, the Itwas initiated primarily toencourageacoordinated specific focus—ofthe "divide and conquer" strategy is not research effort to useArabidopsis as a model system for without cost the user who needs to followan informa- studying thebiologyofflowering plants. tion trail through several databases will find the experi- TheArabidopsisgenome project has reached the point enceawkward and frustrating. where thephysical map is taking form. Because thegenome ofArabidopsis is Data Integration small, about 1/30th thesize ofthe Thebroad scopeofthegenome initiative humangenome, the projectis advancing creates a demand fora newkind of — rapidly. Thus, the need fora database is database onethataccommodates acute. manydifferenttypesofinformation.The variousgenomeprojects'intentionsare Specialized Database Needed tocorrelategeneticinformationwiththe Why the need fora specialized data- underlying physical structure ofthe base?Existing databasesaresimply not chromosome. Ineffect, this means — adequateto managegenomicinforma- bLending information suchasgenetic tion in a useful way. Molecular maps, collections ofcloned DNA biologistsandgeneticists routinely segments, and DNA/proteinse- — usecomputers and databases to quencedatabases that, until organizeand interpretcomplex recently, was maintained biologicalinformation; however, separately. thesedatabasesaretypically As thousandsof intended toperformasingleset overlappingcloned . Probe 2 Spring 1992 DNAsegmentsarematched with Macintoshcomputerallows the user Central Feature each otherand aligned intolarge, toretrieveinformation.Information Thecentral featureofAATDBis the continuous "physical maps," the in AATDB is always available in integratedpresentationofthegenetic need to integrate thedata inapracti- windows, whetheritissimple text map, the physical map, and the DNA cal waybecomesnecessaryfor (forexample, abibliographic refer- sequencesthathavebeendetermined bookkeepingpurposesand forthe ence) orapictorialrepresentationof forArabidopsis. Thegeneticmap convenienceofaccess.Management something moreabstract (suchas a consists ofover500 markers on5 ofa large-scale combined cloningand genetic orphysical map). Ineither chromosomes; the physical map DNAsequencingeffortrequires that case, users find outmore information currentlycontains nearly 15,000 itbe possible to visualize at a glance ormovetocompletelynewcategories clonedDNAsegments.TheDNA therelationshipsbetweencloned ofinformationby "clicking on" hot sequencecollectioncontains over300 DNA segments, thegeneticmap,and spots, which can be eitherwords or entries fromtheGenBankDNA theDNAsequencedatabase.The symbols. database, including theirannotation. DNA overall status ofthe projectcan then Second, informationin the Foreach sequence, theresults bemonitored.Ultimatelytheinfor- databaseis linked togetherbya large of"similaritysearches" are also — mationrecipients thegreater numberofinterconnections.Thereis available (obtained bycomparingall — scientificcommunity need the nosinglestarting point foraskinga possible amino acid translation same tools iftheyare to use the question, norareusers required to products foreachDNA against informationeffectively move through theinformation ina severalproteinsequencedatabases). single direction alonga single path. Inaddition to thegeneticand AATDB Design Consequently, specific information in physical maps, AATDB contains AATDB isdesigned along the thedatabasecan be found inavariety bibliographicreferencesforjournal broadly-inclusive principles de- ofways. articles, books, theses,and symposia, scribed earlier.The databaseallows a AATDBalso featuresaquery whichareorganized byauthor, researchertobrowsetheenormous language thatcan be used todirectly journal, and accession number. Many varietyofinformationassociated search forkey words,phrases,or references havebeen provided bythe with theArabidopsisgenomeand zero values in specific fields. National AgriculturalLibrary (NAL) in on specific details. The process is fromtheAGRICOLAbibliographic simplified by using graphics. Genetic database as well as from other maps, physical maps, and the DNA features of sequences are Table of Contents drawnas pictures in the way that molecularbiologistsareaccustomed Arabidopsis DatabaseNears Completion 1 toseeingthem,ratherthanpresented Plant GenomeResearch GrantProgramFirstAnnualReport - 1991 4 as columnsoftextand numbers. TheClassof1991 Plant GenomeGrantRecipients 6 TheArabidopsisdatabasegoes wellbeyond the "single purpose" Canada's Wheat GenomeMapping Efforts 10 biologicaldatabases mostscientists TriticeaeGene-MappingScientists Unite 12 areaccustomed to usingtoday TheFederal BiotechnologyCommitment 14 becauseoftwoimportantfeatures. CornDatabaseAidsResearch FundingDecisions 16 First,usersobtaininformationfrom the databasebyusing a mouse to Short TandemRepeat DNAPolymorphismsas GeneticMarkers 18 "clickon" objects in windows, in ImprovingEnd-UserComputerSearches 23 much thesame way the Apple CalendarofUpcomingGenomeEvents 26 IntroducingDr. GeorgeJen 30 Probe Spring 1992 3 AATDB sources. Information forstrains from Obtaining Distribution sites willalso be estab- theNottinghamStockCentreSeed The database currently runs as a lished overseas. Electronicmailand Cataloghasbeenprovided by the stand-alonesystemonSun the same FTP mechanism will be StockCenterat Nottingham, En- Microsystems workstationsas an X- used todistribute updates to the gland. Also included are the contents Windows application. Plans are to software and data. Eventually, a CD- of"The Greenbook" forArabidopsis make available an Apple Macintosh ROM version will be available from by Meyerowitzand Pruitt (with version.Currently, Macintoshand NAL. gene, allele, and bibliographic entries Microsoft Windows users, orindi- The USDA Plant Genome cross-referenced to the rest of the viduals with access to X-Windows Research Program is providing database). In addition, the database serversoftware, canuse AATDBvia funding through NAL to support the includes contact information for over a networkconnection toaUNIX database development forArabidopsis 350 researchers and segregation data computerthatruns thedatabase thalianaand fouradditional plant for many RFLP markers. software. species: wheat, pine, soybean, and Plans are to add more informa- AATDB is a stand-alone maize. Eventually the information tion, includingscanned images, to distributed, rather than a centralized, from the five databases will be fed documentboththecharacteristicsof database.Toobtain AATDB, users into a main database at NAL. mutantstrainsand the hybridization will copy the database software and patternsproduced byRFLPprobes; data from an archive on the Internet Contact anexpanded listofkeywords; raw worldwidecomputernetwork.Once Readers who desire additional data fromgenetic crosses; informa- the local copyof AATDB is installed, informationabout AATDBcan tion on characteristics of mutant users can run thesoftwareon their contactDr. Sam CartinhourorDr. J. alleles; allseed, stock, and clone workstations and have access toall MichaelCherry inProfessorHoward information from thenewOhio State the collectiveArabidopsis information. Goodman'slaboratoryviaInternet University/MichiganStateUniversity Initially, the database will be distrib- computer mail at ArabidopsisBiologicalResource uted via Internet anonymous FTP [email protected], or Center;andotherinformationperti- procedure from sites in the United via FAX (617) 726-6893. + nenttotheArabidopsiscommunity. States, including NAL and MGH. Database Software Thesoftwareforthedatabasecame fromDr.Richard Durbin(MRC, Cambridge, UK) and Dr.Jean Thierry-Mieg(CNRS-CRBM, Montpellier,France).Lastyearthey released adatabasetoaccommodate the rapidly accumulating information generated bytheC.elegansgenome project. Animportantfeatureofthe C. elegansdatabase,called ACEDB (A CaenorhabditiselegansDatabase),is thatitis easilyadapted to meet the informaticrequirementsofa wide varietyoforganisms.Thisversatility makes itrelatively easy to reconfigure ACEDB to manage information for Arabidopsis thaliana. Probe Spring 1992 Competitive Edge Genome Plant Research Grant Program First Annual Report - 1991 Dr. Susan McCarthy, Coordinator Plant Genome Dataand Information Center USDA NationalAgricultural Library, MD Beltsville, -W "W-SDA's 1992Plant The Plant Systems Division of supportawards made in two pro- m I GenomeGrantsPro- the NationalResearch Initiative grams in the PlantSystems Division: gram is well underway. Competitive Grants Program The PlantGenome Programand the ; / Proposalssubmitted are (NRICGP) inUSDA's Cooperative Plant Genetic Mechanisms and nowin the reviewprocess.The StateResearchServiceadministers MolecularBiology Program. Plant following is a summary ofthe 1991 the plantgenomegrants. In 1991, the genome funds alsosupported some programresults. bulkofplantgenome funds wentto awards in the Division's remaining fiveprograms.While theprojects that were funded covera diversityof Figure 1 topics, all aredirected toward Mapping vs. Technology Development advancing the understanding ofplant geneticstructureand mechanisms. In all, 1991 plantgenome — funds totalling $10.5 19.0% — million currentlysupport77 researchprojects. The funds also have supportedoneconference.Over250 applicants competed forthegrants. A 53.0% listofawardeesand theirresearch topics is included in this issue. Nearly90percentoftheawards wereforprojectsontheagronomic 28.0% crop species. Table 1 provides a breakdown by plantspecies, and depicts the numberofindividual Broadmap25cM awards, total money awarded, and FineMap1-5cM percentage of the total. TechnolDev Probe Spring 1992 Table 1 Oftheplantgenomeawards, 64 Species, Number of Grants, and Funding Level percentwere unidisciplinaryprojects while 36 percent were multidisciplinary. Overall forNRJCGP, Percentageof multidisciplinary awards averaged Species NumberofGrants GrantAmount GrantTotal 28 percentofthe total. Mission-linked Corn 21 $ 2,642,000 25 grantsaccounted for26 percentofthe Tomato 13 2,387,000 23 total 1991 program. Bean 4 270,000 3 Cotton 2 260,000 2 Figure 1 shows the plant genomegrantsbreakdownformap- Soybean 3 306,000 3 pingand technologydevelopment. Wheat 2 176,000 2 Sorghum 1 210,000 2 Broad- orlow- resolutionmapping Barley 1 120,000 1 for the less well defined species Alfalfa 3 437,151 4 accounted for53 percentofthe 1991 Pea 2 325,000 3 awards. Cabbage 1 180,000 2 Intermsofgenesystems or Potatoe 1 180,000 2 traits, 76 NRIgrants weregiven in the Rice 1 60,000 1 followingareas: Insectresistance, Pepper 1 260,000 2 nematoderesistance,diseaseresis- Brassica 4 318,374 3 tance, yield (QTL's), ripening, floral Lettuce 1 265,000 3 traits,triacylglycerols,and technol- Poplar 2 250,000 2 ogydevelopment. Flax 1 150,000 1 Cuphea 1 210,000 2 Carrot 1 118,000 1 Tobacco 2 275,000 3 Pine 3 260,000 2 Chlaymodomonas 1 185,000 2 Arabidopsis 7 885,000 8 Cyanophora 1 150,000 1 Total 76 $ 10,489,525 104 Note:Thetotalnumberofgrantsis76.Thetotaldollaramountis$10,498,525. Thedifferencebetweenthetotalvaluesisduetomorethanonespecies reportedpergrant.Averagepergrantis$138,020. Grant recipients i Marcus Rhoades Memorial Fund Marcus Rhodes, one ofthe world'sdistinguished maizegeneticists,died December30, 1991. A fund inRhoades' memory hasbeensetupatIndiana Universityto financiallyassistgraduatestudents there. Individuals who would like to makeadonation inRhoades' memoryofcansend achecktoTom Blumenthal, Chairman, Depart- mentofBiology,IndianaUniversity, Bloomington, IN47405. Pleasemake thecheckpayable to theI.U. Foundation - Marcus Rhoades Memorial Fund. Probe 6 Spring 1992 Genome The Class of 1991 Plant Grant Recipients Jane Aldrich HansBohnert CaseWesternReserveUniversity UniversityofArizona Isolation of Rust Resistance Genes in Flax The Cyanelle Genome - An Evolutionary Legacy of Plant Genes David Altman USDA/ARSSouthernCropsResearchLaboratory Harvey Bradshaw Glanding-Control Genes of Cotton: A Model System for UniversityofWashington Gene Expression Low-Density Genetic Mapping in Populus Genome FrederickAusubel RoxanneBroadway Massachusetts General Hospital CornellUniversity Use of Genomic Substraction for Cloning Plant Genes Defensive Efficacy and Molecular Characterization of Cabbage Trypsin Inhibitor BarbaraBaker USDA/ARSPlantGeneExpressionCenter GordonCannon Ac and Ds Transposon-Based Genetic Tools for Tomato University ofSouthern Mississippi Biochemical Characterization of Soybean Chloroplast JeffreyBennetzen DNA Replication in Vitro PurdueUniversity Molecular Genetic Analysis of Rpl-Mediated Disease JohnCarman Resistance in Maize UtahStateUniversity Embryogenic Tissue Cultures of Wheat: Production, JeffreyBennetzen Transformation and Regeneration PurdueUniversity Parallel Studies of Genome Organization in Maize and ChristineChase Sorghum UniversityofFlorida CMS Molecular Genetics of Fertility Restoration in Edwin Bingham UniversityofWisconsin - Madison Defining Gene Action for Yield in Autotetraploid Joanne Chory Alfalfa The SalkInstitute forBiological Studies Molecularand Genetic Analysis ofArabidopsis DET2 Gene JamesBirchler UniversityofMissouri-Columbia PremChourey Chromosomal Manipulation in Maize UniversityofFlorida Analysis of Minature and the Two Sucrose Synthase David Bisaro Genes in Maize OhioStateUniversity Molecular Mechanisms of Geminivirus Replication Gary Churchill CornellUniversity Lawrence Bogorad Converting RFLP Linkage Maps into Physical Maps: HarvardUniversity Theory and an Application Functional Features of the Chloroplast Genome Probe Spring 1992 MichaelDevey NoelKeen USDAForestService UniversityofCalifornia -Riverside RAPD Linkage with a Major Gene for Blister Rust Cloning and Mapping of Soybean Genes for Disease Resistance in Sugar Pine Resistance and Other Characters RebeccaDickstein Jerry Kermicle DrexelUniversity UniversityofWisconsin - Madison Nodule Morphogensis Genes of Medicago Transposition of Ac/Ds Mobile Elements in Maize RobertFerl StevenKnapp UniversityofFlorida OregonStateUniversity Chromatin Structure and Gene Expression in Plants A Genetic Map of Cuphea: Fatty Acid Synthesis Loci and Transposable Elements Bikram Gill KansasStateUniversity Molly Kyle Molecular Cytogenetic Analysis in Wheat CornellUniversity Genomic Mapping and the Transfer of Broad Spectrum Wilhelm Gruissem Plant Virus Resistance UniversityofCalifornia-Berkeley Regulation ofTomato Fruit Development and Christopher Lamb Differentiation by HMG CoA Reductase SalkInstitute for Biological Studies Gene Activation Mechanisms in the Initiation of Plant Tim Helentjaris Defense Responses UniversityofArizona High Density Genetic Map for Maize Including BrianLarkins Molecular and Phenotypic Loci UniversityofArizona Third International Congress ofPlant Molecular Biology ThomasHodges PurdueUniversity RobertMartienssen Homologous Recombination Between DNA Molecules Cold SpringHarborLaboratory in Plant Cells Molecular Analysis of the lojap Gene in Maize MargaretHoey Douglas Maxwell UniversityofGeorgia UniversityofWisconsin- Madison A Complete Genetic Map for Liriodendron (Yellow Trans-Dorrdnant Interference as a Mechanism for Poplar) Resistance to Plant Geminiviruses Stephen Howell StephanMayfield BoyceThompsonInstitute forPlantResearch, Inc. Research Institute ofScripps Clinic Isolation of Genes Involved in Cytokinin Responses in Nuclear and Chloroplast Gene Interactions Regulating Arabidopsis Expression of Photosystem II Proteins AnthonyHuang DonaldMcCarty UniversityofCalifornia -Riverside UniversityofFlorida Molecular and Cell Biology of Oil Bodies in Maize and Viviparous-1 Mediated Repression of Alpha Amylase Brassica Genes in Maize Aleurone KeithHutchison Shiela McCormick UniversityofMaine USDA/ARS/PWA A Molecular Genetic Linkage Map for Conifers Constructing and Characterizing a Tomato YAC Library to Clone Male Sterile Genes Probe 8 Spring 1992 ThomasMcCoy David Ow MontanaStateUniversity USDA/ARS Use of Molecular Markers to Study Recombination and Generating Site-Specific Chromosomal Deletions and Heterosis in Alfalfa the Cloning of Deletions Loci Richard Michelmore Andrew Peterson A&M UniversityofCalifornia -Davis Texas University A Genetic Map of Lactuca sativa with Sequence Molecular Mapping of the Cotton Genome Using DNA Characterized Amplified Regions Markers Michael Mulligan PeterPeterson UniversityofCalifornia - Irvine IowaStateUniversity RNA Editing in Maize Mitochondria Transposon Tagging of Agriculturally Important Disease-Resistant Genes in Maize MarthaMutschler CornellUniversity Ronald Phillips Genomic Regions Associated with Acylsugar UniversityofMinnesota Biosynthesis and Insect Resistance Molecular and Genetic Analysis of Tissue Culture- Induced Variation June Nasrallah CornellUniversity RobertPlaisted Molecular Analysis of the Cellular Interactions of CornellUniversity Incompatibility in Brassica Potato RFLP Map to Introgress Insect Resistance From Wild Species MyronNeuffer UniversityofMissouri CharlesRick Selection Characterization and Preservation of Maize UniversityofCalifornia - Davis Mutants Analysis ofthe Tomato Genome via Lycopersicon x Solanum Hybrids BrentNielsen AuburnUniversity DonaldRobertson Localization and Characterization of Chloroplast DNA IowaStateUniversity Replication Origins Isolation of Genes for Quantitative Inheritance in Maize Suzanne Nielsen PurdueUniversity RonaldSederoff Molecular Cloning of Soybean Cysteine Proteinase NorthCarolinaStateUniversity Inhibitors for Insect Resistance Molecular Markers to Accelerate Breeding in Loblolly Pine MaryO'Connell NewMexicoStateUniversity Phillip Simon A Mitochondrial Mutation in Tomato Alters Vegetative USDA/ARS/Midwest Area and Reproductive Growth Molecular Markers for a Low-Resolution Genetic Map ofCarrot ThomasOsborn University ofWisconsin - Madison KarambirSingh Cytoplasmic Effects on Genome Stabilization in UniversityofCalifornia - Los Angeles Brassica amphidiploids Analysis of OCS-Element Enhancer Sequences in Arabidopsis