COMMUNITY STANDARDS: A NEW SERIES OF GUIDELINES FOR PLANT SCIENCE Community standards for Arabidopsis genetics

s or publications on related mutants appear at the Checklist for publications same time, authors should exchange seeds for complementation tests. If allelism is confirmed, then the proCommunity standards for research publications dealing with Arabidopsis mutants are needed to identify potential cedures outlined above should be followed to establish a conflicts in gene nomenclature. The following section is common symbol. Authors are requested to complete alleldesigned to assist editorial offices by defining recomism tests before publishing another abstract or paper mended standards for publications involving mutant anaon the mutants in question. Editors and reviewers are lysis. Authors should be encouraged to document their encouraged to request evidence that appropriate crosses reasons for not meeting any of these requirements upon have been performed. submission of a manuscript. Reviewers might then be asked to comment on the validity of the explanations presented. Authors are requested to meet the following 3. Refer to synonyms for a given mutant in the text standards for publication. When a mutant is known by more than one name, manuscripts should include clear references to synonyms at 1. Choose mutant gene symbols that do not conflict with appropriate places in the text, for example in the abstract, existing symbols introduction and methods, but elsewhere the accepted name alone may be used. This directs the reader to related Editors and reviewers may wish to consult the updated list work from other laboratories without the distraction of of mutant gene symbols by accessing the Internet address redundant symbols. For example, a paper on amp1 might shown in Table 1. Authors can avoid conflicts by registering new symbols in advance of publication. describe in the introduction its allelism with pt, cop2 Nomenclature and mapping in Arabidopsis 251 and hpt, but then use amp1 and not amp1/pt/cop2/hpt 9. Submit information to relevant databases throughout the remainder of the text. Authors should provide documentation that information presented in a manuscript will be submitted to the Arabidopsis thaliana database (AtDB) and other relevant 4. Characterize inheritance patterns and provide thorough sources upon acceptance for publication. descriptions of mutant phenotypes A superficial description of mutant phenotypes should not be considered appropriate for publication in major journals. Approaches to mapping The analysis of more than one mutant allele should be Mapping of cloned sequences and mutant genes must be encouraged but not required. Phenotypes described should a common goal for the Arabidopsis community. Mapping be compared with those of existing mutants. procedures in Arabidopsis have been reviewed elsewhere (Koornneef, 1994; Franzmann et al., 1995) and will not be 5. Determine the number of genes represented in a repeated here. Our purpose instead is to summarize the mutant collection types of maps, markers and strategies that are currently available. With respect to cloned genes, one standard This can be demonstrated through complementation tests, approach is to identify a sequence polymorphism that a provided the total number of mutants and genes involved given clone detects between Columbia and Landsberg is small enough to make this practical. ecotypes and then map this clone on recombinant inbred (RI) populations obtained from the stock centers. Results obtained from individual plants within this population 6. Assign each mutant to a linkage group and preferably are then compared with data available for other mapped to a chromosomal region markers. The methods involved have been described by This must become a standard requirement for publication. Lister and Dean (1993) and the updated map is maintained Authors should submit estimated map locations to the by the Nottingham Stock Center (http://nasc.nott.ac.uk). curator of mutant gene symbols at the time of publication Mutants can be added by identifying a linked molecular for posting on the Internet. marker that is already on the map or by cloning the disrupted gene. A second approach for mapping cloned genes is to use hybridization or PCR methods to identify a 7. Perform allelism tests with related mutants that map YAC or BAC that contains the sequence and has also been to the same chromosomal region anchored on the physical map. Information on YACs and Mutants should not be assigned a novel name unless BACs can be obtained from the Ohio State Stock Center they define a gene not previously identified. The limited and from the Arabidopsis database (AtDB) noted in Table resolution of existing maps should be considered when 1. A third approach is to determine whether the clone in choosing appropriate mutants for allelism tests question has been assigned a chromosomal location as (Franzmann et al., 1995). Manuscripts that describe part of the multinational genome sequencing project. Intercommon phenotypes without map data or results of allelnet links to the major sequencing groups can be obtained ism tests should be returned to the authors unless an through AtDB. exceptionally strong case can be made for immediate Mapping of genes identified by mutation can be accomppublication. In the case of dominant and gametophytic lished with either molecular markers or visible markers. mutants, where complementation tests are not informative, When molecular markers are used, mutants are localized recombination data should be used in the absence of relative to other markers already placed on the recombinant sequence information to address the likelihood that a single inbred (RI) map. When visible markers are used, mutants gene is involved. are localized on the classical genetic map. These two maps do not correspond exactly in chromosome length. Integration will become easier in the future as more mutant 8. Make seeds of published mutants available to other genes are cloned and incorporated into both maps. In the investigators for allelism tests interim, one rapid method for approximating gene location is to use the ratio: [total length of classical chromosome/ Seeds for most established mutants can already be obtained through stock centers. Authors should document total length of RI chromosome] to convert the estimated location of a gene on the RI map to the corresponding their plans to make seeds available to the community upon acceptance of a manuscript and should include accession location on the classical genetic map. However, this method may further increase the considerable uncertainties in map numbers of appropriate stocks to facilitate ordering from existing resource centers. locations that are characteristic of all genetic maps. 252 David Meinke and Maarten Koornneef Meinke laboratory has been supported by grants from the USInformation on visible markers available for mappingNational Science Foundation and the S.R. Noble Foundation.purposes can be obtained from the stock centers. SeveralTodd Nickle manages the Arabidopsis Genetics/Meinke Laboratoryrecent publications have outlined procedures for mapping WWW page. Research on Arabidopsis in the Koornneef laboratorymutations with visible markers (Franzmann et al., 1995; has been supported by the Biotechnology Programs BRIDGE andPatton et al., 1991). The current classical map can be PTP of the European Union.accessed through the Internet as described in Table 1.Periodic updates are made to this map after sufficientReferencesinformation has been collected from the community. Link-age information on mutant genes not yet placed on the Bell, C.J. and Ecker, J.R. (1994) Assignment of 30 microsatelliteloci to the linkage map of Arabidopsis. Genomics, 19, 137–144.map can be obtained from the linkage table also availableCastle, L.A. and Meinke, D.W. (1994) A FUSCA gene of Arabidopsisthrough the Internet. Although the original genetic mapsencodes a novel protein essential for plant development. Plantof Arabidopsis were constructed by computer using com-Cell, 6, 25–41.bined recombination estimates for all visible markers Chang, C., Bowman, J.L., DeJohn, A.W., Lander, E.S. and(Koornneef et al., 1983), mutant genes have more recentlyMeyerowitz, E.M. (1988) Restriction fragment lengthpolymorphism linkage map for Arabidopsis thaliana. Proc. Natlbeen placed on the map by hand using recombinationAcad. Sci. USA, 85, 6856–6860.estimates with a more limited set of linked markersChapple, C.C.S., Vogt, T., Ellis, B.E. and Somerville, C.R. (1992) An(Franzmann et al., 1995). An integrated map that combinedArabidopsis mutant defective in the general phenylpropanoiddata for classical and molecular markers obtained frompathway. Plant Cell, 4, 1413–1424.different mapping populations was published several years Chin-Atkins, A.N., Craig, S., Hocart, C.H., Dennis, E.S. andChaudhury, A.M. (1996) Increased endogenous cytokinin inago (Hauge et al., 1993) but proved to be somewhatthe Arabidopsis amp1 mutant corresponds with de-etiolationinaccurate with respect to the order of linked markers inresponses. Planta, 198, 549–556.certain regions of the genome.Cnops, G., den Boer, B., Gerats, A., van Montagu, M. and vanSeveral types of molecular markers can be used to mapLijsebettens, M. (1996) Chromosome landing at the Arabidopsismutants. These include RFLPs (Chang et al., 1988; NamTORNADO1 locus using an AFLP-based strategy. Mol. Gen.Genet. 253, 32–41.et al., 1989), RAPDs (Reiter et al., 1992), CAPS (KoniecznyFabri, C.O. and Schaffner, A.R. (1994) An Arabidopsis thalianaand Ausubel, 1993), and SSLPs (Bell and Ecker, 1994). TheRFLP mapping set to localize mutations to chromosomalrelative advantages and disadvantages of these differentregions. Plant J. 5, 149–156.markers have been discussed in many research publicaFranzmann, L.H., Yoon, E.S. and Meinke, D.W. (1995) Saturating thetions. A collection of RFLP markers designed for efficientgenetic map of Arabidopsis thaliana with embryonic mutations.Plant J. 7, 291–300.mapping of mutants has also been described (Fabri andGalway, M.E., Masucci, J.D., Lloyd, A.M., Walbot, V., Davis, R.W.Schaffner, 1994). In addition, the value of AFLP markersand Schiefelbein, J.W. (1994) The TTG gene is required tolinked to a mutant gene of interest has been discussed inspecify epidermal cell fate and cell patterning in the Arabidopsisrelation to map-based cloning (Cnops et al., 1996; Vosroot. Devel. Biol. 166, 740–754.et al., 1995). Our purpose here is not to promote the use Guzman, P. and Ecker, J.R. (1990) Exploiting the triple responseof Arabidopsis to identify ethylene-related mutants. Plant Cell,of one mapping method over another. Investigators should2, 513–523.consider the expertise available within their own labora-Hauge, B.M., Hanley, S.M., Cartinhour, S., et al. (1993) Antories (performing gel-blot hybridizations and PCR ampli-integrated genetic/RFLP map of the Arabidopsis thalianafications versus scoring the phenotypes of visible markers)genome. Plant J. 3, 745–754.and check on materials available at the stock centers before Hou, Y., von Arnim, A.G. and Deng, X.-W. (1993) A new class ofreaching a decision on the most appropriate mappingArabidopsis constitutive photomorphogenic genes involved inregulating cotyledon development. Plant Cell, 5, 329–339.strategy for their mutants and genes of interest. We hopeKonieczny, A. and Ausubel, F.M. (1993) A procedure for mappinginstead to encourage members of the Arabidopsis com-Arabidopsis mutations using co-dominant ecotype-specific PCR-munity to place a greater overall emphasis on mappingbased markers. Plant J. 4, 403–410.both mutant genes and cloned sequences to facilitate the Koornneef, M. (1994) Arabidopsis genetics. In Arabidopsis,integration of classical and physical maps and to aid in the(Meyerowitz, E. and Somerville, C., eds). Cold Spring Harbor,New York: Cold Spring Harbor Laboratory Press, pp. 89–120.analysis of gene function. With continued attention to theseKoornneef, M. and Stam, P. (1992) Genetic analysis. In Methodsissues of nomenclature and genetic analysis in the future,in Arabidopsis Research (Koncz, C., Chua, N.-H. and Schell, J.,it should be possible to maximize the research effortseds). New Jersey: World Scientific, pp. 83–99.of plant biologists worldwide and realize the long-term Koornneef, M., van Eden, J., Hanhart, C.J., Stam, P., Braaksma,objectives of the Arabidopsis genome project.F.J. and Feenstra, W.J. (1983) Linkage map of Arabidopsisthaliana. J. Hered. 74, 265–272.Koornneef, M., Blankestijn-de Vries, H., Hanhart, C., Soppe, W.Acknowledgmentsand Peeters, T. (1994) The phenotype of some late-floweringmutants is enhanced by a locus on chromosome 5 that is notWe thank Carlos Alonso-Blanco and Chun-ming Liu for helpfulcomments on the manuscript. Research on Arabidopsis in theeffective in the Landsberg erecta wild-type. Plant J. 6, 911–919. Nomenclature and mapping in Arabidopsis 253 Lee, I., Michaels, S.D., Masshardt, A.S. and Amasino, R.M. (1994) Ploense, S. (1995) Unscheduled cell division in hauptling mutantembryos results in polyembryony, increased cotyledon numberThe late-flowering phenotype of FRIGIDA and mutations inand shoot apex enlargement in Arabidopsis. 6th Int. Conf. onLUMINIDEPENDENS is suppressed in the Landsberg erectaArabidopsis Research. Abstract 77.strain of Arabidopsis. Plant J. 6, 903–909.Price, C.A. (1994) A nomenclature for sequenced plant genes: aLister, C. and Dean, C. (1993) Recombinant inbred lines forbrief description. Plant Mol. Biol. Rep. 12S, 4–9.mapping RFLP and phenotypic markers in Arabidopsis thaliana.Quail, P.H., Briggs, W.R., Chory, J., et al. (1994) Spotlight onPlant J. 4, 745–750.phytochrome nomenclature. Plant Cell, 6, 468–471.Mayer, R., Raventos, D. and Chua, N.-H. (1996) det1, cop1, andReiter, R.S., Williams, J.G.K., Feldmann, K.A., Rafalski, J.A., Tingey,cop9 mutations cause inappropriate expression of several geneS.V. and Scolnik, P.A. (1992) Global and local genome mappingsets. Plant Cell, 8, 1951–1959.in Arabidopsis thaliana by using recombinant inbred lines andMeyerowitz, E.M. and Somerville, C.R. (eds) (1994) Arabidopsis.random amplified polymorphic DNAs. Proc. Natl Acad. Sci.Cold Spring Harbor, New York: Cold Spring Harbor LaboratoryUSA, 89, 1477–1481.Press.Robinson-Beers, K., Pruitt, R.E. and Gasser, C.S. (1992) OvuleNagatani, A., Reed, J.W. and Chory, J. (1993) Isolation and initialdevelopment in wild-type Arabidopsis and two female-sterilecharacterization of Arabidopsis mutants that are deficient inmutants. Plant Cell, 4, 1237–1249.phytochrome A. Plant Physiol. 102, 269–277.Su, W. and Howell, S.H. (1992) A single genetic locus, Ckr1, definesNam, H.G., Giraudat, J., den Boer, B., Moonan, F., Loos, W.D.B.,Arabidopsis mutants in which root growth is resistant to lowHauge, B.M. and Goodman, H.M. (1989) Restriction fragmentconcentrations of cytokinin. Plant Physiol. 99, 1569–1574.length polymorphism linkage map of Arabidopsis thaliana. Plant Vizir, I., Thorlby, G., Briarty, G. and Mulligan, B. (1995) PositionalCell, 1, 699–705.cloning of the PRIMORDIA TIMING gene in Arabidopsis. 6th Int.Patton, D.A., Franzmann, L.H. and Meinke, D.W. (1991) MappingConf. on Arabidopsis Research. Abstract 128.genes essential for embryo development in Arabidopsis Vos, P., Hogers, R., Bleeker, M., et al. (1995) AFLP: a new conceptthaliana. Mol. Gen. Genet. 227, 337–347.for DNA fingerprinting. Nucl. Acids Res. 23, 4407–4414.Parks, B.M. and Quail, P.H. (1993) hy8, a new class of Arabidopsis Wei, N. and Deng, X.-W. (1996) The role of the COP/DET/FUSmutants deficient in functional phytochrome A. Plant Cell, 5,genes in light control of Arabidopsis seedling development.39–48.Plant Physiol. 112, 871–878.Pepper, A., Delaney, T., Washburn, T., Poole, D. and Chory, J. Whitelam, G.C., Johnson, E., Peng, J., Carol, P., Anderson, M.L.,(1994) DET1, a negative regulator of light-mediated developmentCowl, J.S. and Harberd, N.P. (1993) Phytochrome A null mutantsand gene expression in Arabidopsis, encodes a novel nuclear-of Arabidopsis display a wild-type phenotype in white light.Plant Cell, 5, 757–768.localized protein. Cell, 78, 109–116.