NetNews Usenet Archive 1992 #31

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Path: sparky!uunet!zaphod.mps.ohio-state.edu!uwm.edu!biosci!FRODO.MGH.HARVARD.EDU From: CHERRY@FRODO.MGH.HARVARD.EDU (Mike Cherry 726-5955) Newsgroups: bionet.genome.arabidopsis Subject: Mutant Gene Symbols of Arabidopsis thaliana Message-ID: <Dec.31.09.43.37.1992.23508@net.bio.net> Date: 30 Dec 92 15:54:43 GMT Sender: kristoff@net.bio.net Lines: 450 [ Note: A printed copy of the following table, created by David Meinke, was included in the recent postal mailing from the ABRC at Ohio State. This table is now electronically available from the Arabidposis Research Companion Gopher in the "Arabidopsis Genetic Maps and Tables" folder. The information contained within this table has been incorporated into the AAtDB database available via gopher and wais. The next version of the Unix AAtDB database, release 1-4, will also contain this information. Special thanks go to David Meinke for volunteering to be the Genetics Curator for Arabidopsis. Mike Cherry AAtDB Project ] Overview of Mutant Gene Symbols of Arabidopsis thaliana David W. Meinke, Curator Phone: 405-744-6549; FAX: 405-744-7673 email: btnydwm@osucc.bitnet The attached list presents a comprehensive summary of mutant gene symbols currently being used in research with Arabidopsis thaliana. This list is (hopefully) limited to mutants with viable seeds and established phenotypes that have been examined in some detail. Additional information on certain mutant phenotypes is given in parentheses. Reference laboratory refers to the individual(s) involved in the initial identification or subsequent characterization of each class of mutants. This reference is included to help locate individuals who could provide further information on specific symbols. This list does not include information on the total number of loci given the same mutant gene symbol. For example, there are 250 distinct emb loci (emb1 to emb250) and one bio locus (bio1), but each symbol is given a single line. A separate list summarizing all well-characterized mutant loci by symbol and number will need to be prepared in the future. Note that in some cases on the attached list (*) the same gene symbol has already been assigned to unrelated mutants. These conflicts will need to be resolved to avoid further confusion in the literature. Suggested Protocol for the Future: Mutants should be characterized in some detail before a formal gene symbol is chosen and published. This analysis should include (whenever possible) mapping the chromosomal location of the mutant locus. Complementation tests should be performed with mutants that map to similar regions and/or exhibit similar phenotypes to ensure that the "new" mutant has not already been identified and assigned a different name. The standard system of nomenclature for Arabidopsis should be followed: A. Mutant gene symbols should have 3 letters (underlined or italics) in lower case. B. The wild-type allele should have these letters (underlined or italics) in CAPS. C. Different genes with the same symbol are distinguished by different numbers (for example: emb25 and emb26). D. Different alleles of the same gene are distinguished with a number following a hyphen (for example: emb20-1 and emb20-2). E. When only a single allele is known, the hyphen (-1) is not needed (thus: emb33 equals emb33-1 if only a single allele is known). F. When only a single gene is given a particular symbol, the number is not needed (thus: lec equals lec1) G. The same nomenclature applies to both dominant and recessive mutants. H. Cloned wild-type genes should be in CAPS (underlined or italics) and the protein products of these genes should be in CAPS only. I. When picking a mutant gene symbol, avoid the use of symbols that might have another meaning (for example, CHS currently refers to both the wild-type allele of a chilling sensitive mutant (chs), and the cloned chalcone synthase gene). A large number of form and color mutants obtained from the Kranz collection are currently available through the Nottingham stock center. These mutants have names that do not correspond to the nomenclature described above. The best approach with this collection may be to select new symbols for mutants that have been further characterized in preparation for publication. In Order to Minimize Duplication of Gene Symbols: The attached list of mutant gene symbols will be added immediately to AIMS, AAtDB, and stock center catalogs, and will be periodically updated. Check this list before you choose a new gene symbol. Then contact the current curator of gene symbols (David Meinke: phone 405-744-6549; FAX 405-744-7673; email btnydwm@osucc.bitnet) to reserve your new symbol prior to publication and ensure that someone else was not also planning to use the same symbol. This protocol must be followed in order to minimize problems in the future. Symbols can be reserved without details on mutant phenotype if there is concern about providing too much information prior to publication. Editors of journals will be informed of this policy to minimize the chances of publishing a paper with a duplicate symbol. Please report any mistakes or changes to the attached list to the curator as soon as possible. Comments regarding this new system are also welcome. Contact David Meinke, Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA. Overview of Mutant Gene Symbols for Arabidopsis thaliana This List Excludes Gene Symbols for Cloned Sequences (*) = Change Suggested; (**) = No Longer Used Updated December 15, 1992; David W. Meinke ___________________________________________________________________________ Mutant Symbol Full Descriptive Name for Gene Symbol Reference Laboratory ___________________________________________________________________________ aba ABA deficient Koornneef abi ABA insensitive Koornneef aca azetidine-2-carboxylic acid resistant Lehle and Khan acd accelerated cell death Ausubel; Dangl acf suppressor of fca Dean act chloroplast glycerol-3-phosphate Kunst and Somerville acyltransferase deficient adg ADP glucose pyrophosphorylase deficient Caspar adh Alcohol dehydrogenase deficient Jacobs ag agamous (floral defective) Koornneef agr agravitropic Maher ain ethylene insensitive Van der Straeten alb albina (white embryo and seedling) Van der Veen; Relichova ali alien (abnormal trichomes) Jurgens amt a-methyl tryptophan resistant (see mtr) Town an angustifolia (narrow leaf) Redei ap apetala (floral defective) Koornneef apt adenine phosphoribosyl transferase Moffatt and Somerville ara arabinose sensitive Cobbett arc accumulation and replication of Pyke and Leech chloroplasts as asymmetric leaves Redei aux auxin-resistant Maher axr auxin-resistant Estelle bel bell-shaped ovules, female sterile Pruitt and Gasser bic bacterial induced chlorosis Dangl bio biotin auxotroph Meinke blu blue light response defective Hangarter bp brevipedicellus (downward siliques) Koornneef ca caespitosa (short stems; bushy plants) McKelvie; Redei cad cadmium sensitive Cobbett cal cauliflower (defective inflorescence) Bowman and Meyerowitz cdo chardonnay (abnormal trichomes) Jurgens cer eceriferum (shiny stems; reduced wax) Dellaert; Koornneef ch chlorina (yellow green) Redei; Relichova cha chablis (abnormal trichomes) Jurgens chl chlorate-resistant Feenstra; Crawford chm chloroplast mutator Redei chm* chlorominuta (light green) Relichova chp chlorophyll mutant Koornneef chs chilling sensititve Hugly and Somerville ckr cytokinin resistant Howell clv clavata (extra carpels) McKelvie; Koornneef cn convoluta (leaf shape; twisted stem) Relichova cnx chlorate resistant (NR cofactor) Braaksma and Feenstra co late flowering (replaces fg) Redei cob cobra (root) Benfey cop constitutive photomorphogenic Deng (light response in dark) cp compacta (semi dwarf) Koornneef cp* cupuliformis (leaf shape) Relichova crc crabs claw (floral defective) Smyth crk crooked (abnormal trichomes) Jurgens crl curly (defective cotyledons and leaves) Medford csi cesium resistant Sussman csr acetolactate synthetase; Haughn and Somerville imidazolinone resistant ctr constitutive triple response Ecker dct dicarboxylate transport defective Somerville and Ogren det de-etiolated (light response in dark) Chory dip disrupted (defective leaves, meristem) Medford dis distorted trichomes Feenstra dn dentata (broad leaves, late flowering) Relichova doc dark over-expression of cab Chory dwf dwarf Koornneef; Feldmann dwf auxin-resistant dwarf Mizra; Olsen ein ethylene insensitive Ecker eir ethylene insensitive root Ecker ela enhanced linolenate accumulation Browse and Somerville elf early flowering Meeks-Wagner emb embryo-defective; includes lethals, Meinke defectives, and pigment mutants emf embryonic flower Sung er erecta (short, upright stems) Redei esd early flowering in short days Coupland eto ethylene overproducer Ecker etr ethylene-insensitive Bleeker ett ettin (floral defective) Roe and Zambryski fab fatty acid biosynthesis defective James and Dooner fad fatty acid desaturase deficient Somerville fae fatty acid elongation defective Kunst; Browse/Somerville fas fasciated (like clavata) Furner fb** (now gi) Koornneef fca late flowering Koornneef fd late flowering Koornneef fdh fiddlehead (organ fusion) Lolle and Sussex fdi factor differentiation instability Vizir fe late flowering Koornneef fey forever young (altered shoot apex) Medford fg** (now co) Koornneef fha late flowering Koornneef fk fackel (embryo defective) Jurgens fl folliculiformis (like clavata) Relichova fla late flowering Amasino flo floral defective Haughn and Somerville fmc late flowering (extreme) McKelvie; Koornneef fpa late flowering Koornneef fri frigida (late flowering) Napp Zinn; Dean fs fass (embryo defective) Jurgens ft late flowering Koornneef fuf fully fasciated (altered stem, apex) Medford fus fusca (anthocyanin in cotyledons) Muller; Jurgens; Meinke fus* fucose deficient (new name pending) Reiter and Somerville fve late flowering Koornneef fwa late flowering Koornneef fy late flowering Koornneef ga GA deficient Koornneef, Van der Veen gai GA insensitive Koornneef gar GA responder (suppressor of gai) Wilson and Somerville gas GA superresponder Wilson and Somerville gf female gametophytic factor Redei gh gelbherzig (yellow center of plant) Redei gi gigantea; late flowering (replaces fb) Redei gk gurke (embryo defective) Jurgens gl glabra (reduced trichomes) Lee-Chen; Koornneef gld glycine decarboxylase deficient Somerville and Ogren gls glutamate synthase deficient Somerville and Ogren gn gnom (embryo defective) Jurgens gr grisea (gray-green leaf color) Relichova grl gnarled (abnormal trichomes) Jurgens gun genomes uncoupled (cab expression in Chory absence of functional chloroplasts) han hanaba taranu (floral defective) Sakai and Meyerowitz hcf high chlorophyll fluorescent Green and Dinkins hcr high CO2 requiring Artus and Somerville hcs CO2 sensitive Artus and Somerville hex hexose analog resistant Cobbett hls hookless (ethylene response) Ecker hy elongated hypocotyl in light Redei; Koornneef; Chory hyg* hygromcyin resistant (T-DNA insert) van Lijsebettens im immutans (variegated) Redei; Robbelen inv* involute leaf Comai inv* increased variegation Dean iv involuta (leaf shape, early flowering) Relichova ivr invasive root Sung ixr isoxaben resistance Heim and Larrinua kak kaktus (abnormal trichomes) Jurgens keu keule (embryo defective) Jurgens klk klunker (embryo defective) Jurgens kmy* kanamycin resistant (T-DNA insert) van Lijsebettens kn knolle (embryo defective) Jurgens knf knopf (embryo defective) Jurgens kno knotty root Sung lan lanceolate (narrow leaves) Koornneef lc lucida (light green) Relichova ld luminidependans (late flowering) Redei le lepida (dwarf; see pa) McKelvie lec leafy cotyledon; mature seeds lethal Meinke lit lion's tail (root) Benfey lfy leafy (floral defective) Meyerowitz; Haughn and Somerville lrd light regulatory dwarf Feldmann lu lutescens (yellow-green) Lee-Chen, Steinitz-Sears ly lycopodioformia (light green; Relichova terminally forked inflorescence) mat* defective seed coat and root Valvekens mic mickey (embryo defective) Jurgens min miniature (semi-dwarf) Koornneef mp monopteros (embryo defective) Jurgens ms male sterile Koornneef mtr methyl tryptophan resistant (see amt) Koornneef mur cell wall mutant Reiter, Chapple and Somerville nia nitrate reductase Crawford; Cheng orn ornata (stem morphology) van de Loo and Somerville pa dwarf (see le) Kranz, Scheidemann pan extra perianth organs Running and Meyerowitz pco phosphoglycolate phosphatase deficient Somerville and Ogren pfl pointed first leaf van Lijsebettens pgm phosphoglucomutase deficient Caspar pho low inorganic phosphate Poirier and Somerville pi pistillata (floral defective) Koornneef pid pinoid (meristem defective) Smyth pin pin-formed (floral defective) Goto; Kranz; Okada psv pseudoverticillata ( ) Relichova pt primordia timing Vizir py pyrimidine requiring Redei; Feenstra rac resistant to Albugo candida Benyon rca regulation of caroxylase activation Somerville rcx reaction to Xanthomonas campestris Tsuji and Somerville rd rotundata (leaf shape) Relichova re reticulata (dark veins) Redei; Koornneef reb root epidermal bulger Williamson rev revolute leaf Comai rgn chlorate resistant Feenstra rhd root hair defective Schiefelbein rod reduced oleate desaturation Browse and Somerville rp proline resistant van Montagu (?) (perhaps allelic to aca) rpm resistant to Pseudomonas syringae Dangl pv. maculata rpp resistant to Peronospora parasitica Benyon rps resistant to Pseudomonas syringae Staskawicz; Ausubel rsw radially swollen (root) Williamson rts retsina (abnormal trichomes) Jurgens rxa resistant to Xanthomonas campestris Lazo pv. amoraciae race sab sabre (root) Benfey sar suppressor of auxin resistance Estelle sad salt (NaCl) addiction Lehle and Khan sat serine-glyoxylate aminotransferase Somerville and Ogren deficient sch starch accumulating root Sung sex starch excess (formerly sop) Caspar shl shootless Barton and Poethig shr* short root Benfey shr* short tap and lateral root Sung sht short tap, long lateral root Sung shz schizoid (vegetative shoot apex) Medford sin short integuments Pruitt and Gasser sin* sinapic acid biosynthesis (new name Chapple and Somerville is pending) sis sucrose insensitive Gibson and Somerville sop** (now sex) Caspar spi spirrig (abnormal trichomes) Jurgens spt spatula (floral defective) Smyth spy suppressor of gibberellin deficiency Olszewski sta stachel (abnormal trichomes) Jurgens sti stichel (unbranced trichomes) Jurgens stm serine transhydroxymethylase deficient Somerville and Ogren stp stunted plant Williamson str stunted root Sung su suppressor of nitrate reductase Braaksma and Feenstra sul sulfurata (bright yellow-green) Redei (seed available ?) sup superman (floral defective) Bowman and Meyerowitz sur super rooter van Lijsebettens ted suppressor of det Chory tfl terminal flower Meeks Wagner; Smyth th thiamine requiring Li and Redei; Langridge tom tobacco mosaic virus response Ishikawa trp tryptophan auxotroph Last and Fink tsl tousled (floral defective) Roe and Zambryski tso tso (floral defective) Liu and Meyerowitz tt transparent testa (mature seeds yellow) Koornneef ttg transparent testa; glabrous Koornneef twl twisted leaves van Lijsebettens tz thiazole requiring Redei; Feenstra ufo unusual floral organs Haughn; Meyerowitz uhv ultraviolet hypersensitive Mount var variegated Martinez Zapater vi viridis (dark green, round leaves) Redei vr virescens Redei vrn reduced vernalization response Dean wav wavy roots Okada wrm wurm (abnormal trichomes) Jurgens xav xantha variegation (pigment) Mednik and Usmanov xtc extra cotyledon (leaf morphology) Conway and Poethig xv xantha-viridis (yellow cotyledons Redei and leaf margins) yi yellow inflorescence Koornneef zwi zwichel (abnormal trichomes) Jurgens ______________________________________________________________________________ Preliminary List of Alleles with Different Symbols Prepared December 15, 1992 David W. Meinke ______________________________________________________________________________ Mutant Laboratory = Mutant Laboratory ______________________________________________________________________________ agr 1 Maher = wav 6 Okada and Shimura aux 1 Maher = wav 5 Okada and Shimura cop 1 Deng and Quail = emb 168 Meinke cop 1 Deng and Quail = fus 1 Jurgens/Muller emb 30 Meinke = gn Jurgens emb 78 Castle and Meinke = fus 6 Jurgens/Muller emb 168 Meinke = cop 1 Deng and Quail emb 168 Meinke = fus 1 Jurgens/Muller flo 10 Haughn = sup Bowman and Meyerowitz fus 1 Jurgens/Muller = cop 1 Deng and Quail fus 1 Jurgens/Muller = emb 168 Meinke fus 6 Jurgens/Muller = emb 78 Castle and Meinke gn Jurgens = emb 30 Meinke sup Bowman and Meyerowitz = flo 10 Haughn wav 5 Okada and Shimura = aux 1 Maher wav 6 Okada and Shimura = agr 1 Maher ______________________________________________________________________________ Other Synonyms: __________________ chl 4 = rgn chl 6 = cnx cnx = chl 6 csr 1 = imr fad 4 = fad A fad 5 = fad B fad 6 = fad C fad 7 = fad D imr = csr 1 rgn = chl 4 _____________________________________________________________________________