Sequencing and annotation of the evergrowing locus in peach [Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation
Tóm tắt
Từ khóa
Tài liệu tham khảo
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Alvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C, Ditta GS, Vergara-Silva F, Yanofsky MF (2000) MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J 24:457–466
Anderson JV, Chao WS, Horvath DP (2001) A current review on the regulation of dormancy in vegetative buds. Weed Sci 49:581–589
Anderson JV, Gesch RW, Jia Y, Chao WS, Horvath DP (2005) Seasonal shifts in dormancy status, carbohydrate metabolism, and related gene expression in crown buds of leafy spurge. Plant Cell Environ 28:1567–1578
Aranzana MJ, Garcia-Mas J, Carbo J, Arus P (2002) Development and variability analysis of microsatellite markers in peach. Plant Breed 121:87–92
Aswath CR, Mo SY, Kim SH, Kim DH (2004) IbMADS4 regulates the vegetative shoot development in transgenic chrysanthemum (Dendrathema grandiflora (Ramat.) Kitamura). Plant Sci 166:847–854
Barak S, Tobin EM, Andronis C, Sugano S, Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends Plant Sci 5:517–522
Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454
Bielenberg DG, Wang Y, Fan S, Reighard GL, Scorza R, Abbott AG (2004) A deletion affecting several gene candidates is present in the Evergrowing peach mutant. J Heredity 95:436–444
Bohlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O (2006) CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312:1040–1043
Brill EM, Watson JM (2004) Ectopic expression of a Eucalyptus grandis SVP orthologue alters the flowering time of Arabidopsis thaliana. Funct Plant Biol 3::217–224
Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78–94
Cantini C, Iezzoni AF, Lamboy WF, Boritzki M, Struss D (2001) DNA fingerprinting of tetraploid cherry germplasm using simple sequence repeats. J Am Soc Hortic Sci 126:205–209
Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L) Batsch]: isolation, characterisation and cross-species amplification in Prunus. Theor Appl Genet 99:65–72
Dennis FG (1996) A physiological compasion of seed and bud dormancy. In: Lang GA (ed) Plant Dormancy: Physiology, Biochemistry, and Molecular Biology. CAB, New York, pp 47–56
Dirlewanger E, Cosson P, Tavaud M, Aranzana MJ, Poizat C, Zanetto A, Arus P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105:127–138
Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Nat Acad Sci USA 101:9891–9896
Duarte JM, Cui LY, Wall PK, Zhang Q, Zhang XH, Leebens-Mack J, Ma H, Altman N, dePamphilis CW (2006) Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol Biol Evol 23:469–478
Faust M, Erez A, Rowland LJ, Wang SY, Norman HA (1997) Bud dormancy in perennial fruit trees: physiological basis for dormancy induction, maintenance, and release. Hortscience 32:623–629
Fuchigami LH, Wisniewski M (1997) Quantifying bud dormancy: physiological approaches. Hortscience 32:618–623
Garcia-Maroto F, Carmona MJ, Garrido JA, Vilches-Ferron M, Rodriguez-Ruiz J, Alonso DL (2003) New roles for MADS-box genes in higher plants. Biologia Plantarum 46:321–330
Georgi LL, Wang Y, Yvergniaux D, Ormsbee T, Inigo M, Reighard G, Abbott AG (2002) Construction of a BAC library and its application to the identification of simple sequence repeats in peach Prunus persica (L.) Batsch. Theor Appl Genet 105:1151–1158
Gevaudant F, Samson I, Guilliot A, Petel G (1999) An improved method for isolating polyphenol-free RNA from woody plant tissues. J Trace Microprobe Tech 17:445–450
Gevaudant F, Petel G, Guilliot A (2001) Differential expression of four members of the H + -ATPase gene family during dormancy of vegetative buds of peach trees. Planta 212:619–626
Gish W, States DJ (1993) Identification of protein coding regions by database similarity search. Nature Genet 3:266–272
Horn R (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419–1428
Horvath DP, Anderson JV (2002) A molecular approach to understanding root bud dormancy in leafy spurge. Weed Sci 50:227–231
Horvath DP, Anderson JV, Chao WS, Foley ME (2003) Knowing when to grow: signals regulating bud dormancy. Trends Plant Sci 8:534–540
Joobeur T, Viruel MA, de Vicente MC, Jauregui B, Ballester J, Dettori MT, Verde I, Truco MJ, Messeguer R, Batlle I, Quarta R, Dirlewanger E, Arus P (1998) Construction of a saturated linkage map for Prunus using an almond x peach F-2 progeny. Theor Appl Genet 97:1034–1041
Jung S, Jesudurai C, Staton M, Du ZD, Ficklin S, Cho IH, Abbott A, Tomkins J, Main D (2004) GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 5: Art. No. 130
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110::462–467
Klee H, Estelle M (1991) Molecular genetic approaches to plant hormone biology. Ann Rev Plant Physiol Plant Mol Biol 42:529–551
Koornneef M, Bentsink L, Hilhorst H (2002) Seed dormancy and germination. Curr Opin Plant Biol 5:33–36
Kovarík A, Matzke MA, Matzke AJM, Koukalová B (2001) Transposition of IS10 from the host Escherichia coli genome to a plasmid may lead to cloning artefacts. Mol Genet Genom 266:216–222
Kozlowski TT, Pallardy SG (1997) In: Physiology of woody plants. 2nd edn. Academic, San Diego
Lawton-Rauh A (2003) Evolutionary dynamics of duplicated genes in plants. Mol Phylogenet Evol 29:396–409
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878–2879
Messina R, Lain O, Marrazzo MT, Cipriani G, Testolin R (2004) New set of microsatellite loci isolated in apricot. Mol Ecol Notes 4:432–434
Michaels SD, Amasino RM (2000) Memories of winter: vernalization and the competence to flower. Plant Cell Environ 23:1145–1153
Molmann JA, Berhanu AT, Stormo SK, Ernstsen A, Junttila O, Olsen JE (2003) Metabolism of gibberellin A(19) is under photoperiodic control in Populus, Salix and Betula, but not in daylength-insensitive Populus overexpressing phytochrome A. Physiologia Plantarum 119:278–286
Molmann JA, Asante DKA, Jensen JB, Krane MN, Ernstsen A, Junttila O, Olsen JE (2005) Low night temperature and inhibition of gibberellin biosynthesis override phytochrome action and induce bud set and cold acclimation, but not dormancy in PHYA overexpressors and wild-type of hybrid aspen. Plant Cell Environ 28:1579–1588
Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8:122–128
Moore RC, Grant SR, Purugganan MD (2005) Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana. Mol Biol Evol 22:91–103
Olsen JE (2003) Molecular and Physiological Mechanisms of Bud Dormancy Regulation. In: Tanino KK et al (ed) XXVI International Horticultural Congress-Environmental Stress, Vol 618. ISHS, Leuven, pp 437–453
Parenicova L, de Folter S, Kieffer M, Horner DS, Favalli C, Busscher J, Cook HE, Ingram RM, Kater MM, Davies B, Angenent GC, Colombo L (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15:1538–1551
Peace CP, Crisosto CH, Gradziel TM (2005) Endopolygalacturonase: a candidate gene for freestone and melting flesh in peach. Mol Breed 16:21–31
Prakash AP, Kumar PP (2002) PkMADS1 is a novel MADS box gene regulating adventitious shoot induction and vegetative shoot development in Paulownia kawakamii. Plant J 29:141–151
Rai M (2006) Refinement of the Citrus tristeza virus resistance gene (Ctv) positional map in Poncirus trifoliata and generation of transgenic grapefruit (Citrus paradisi) plant lines with candidate resistance genes in this region. Plant Mol Biol 61:399–414
Ratcliffe OJ, Kumimoto RW, Wong BJ, Riechmann JL (2003) Analysis of the Arabidopsis MADS affecting flowering gene family: MAF2 prevents vernalization by short periods of cold. Plant Cell 15:1159–1169
Rodriguez J, Sherman WB, Scorza R, Wisniewski M, Okie WR (1994) Evergreen peach, its inheritance and dormant behavior. J Am Soc Hortic Sci 119:789–792
Rohde A, Howe GT, Olsen JE, Moritz T, Van Montagu M, Junttila O, Boerjan W (2000) Molecular aspects of bud dormancy in trees. In: Jain SM, Minocha SC (eds) Molecular Biology of Woody Plants, Vol 1. Kluwer, Dordrecht, pp 89–134
Rowland LJ, Ogden EL, Arora R, Lim CC, Lehman JS, Levi A, Panta GR (1999) Use of blueberry to study genetic control of chilling requirement and cold hardiness in woody perennials. Hortscience 34:1185–1191
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana, Totowa, pp 365–386
Ruonala R, Rinne PLH, Baghour M, Moritz T, Tuominen H, Kangasjarvi J (2006) Transitions in the functioning of the shoot apical meristem in birch (Betula pendula) involve ethylene. Plant J 46:628–640
Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522
Sambrook J, Russell DW (2002) In: Molecular cloning: a laboratory manual Vol 2. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
Scorza R, Sherman WB (1996) Peaches. In: Janick J, Moore JN (eds) Fruit Breeding, Vol 1 Tree and tropical fruits. Wiley, New York, pp 325–440
Theissen G, Strater T, Fischer A, Saedler H (1995) Structural characterization, chromosomal localization and phylogenetic evaluation of two pairs of agamous-like MADS-box genes from maize. Gene 156:155–166
Thompson MM, Smith DC, Burgess JE (1985) Non-dormant mutants in a temperate tree species, Corylus avellana L. Theor Appl Genet 70:687–692
van der Linden CG, Vosman B, Smulders MJM (2002) Cloning and characterization of four apple MADS-box genes isolated from vegetative tissue. J Exp Bot 53:1025–1036
Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research, Wageningen
Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (Rin) locus. Science 296:343–346
Wang Y, Georgi LL, Reighard GL, Scorza R, Abbott AG (2002a) Genetic mapping of the evergrowing gene in peach Prunus persica (L.) Batsch. J Heredity 93:352–358
Wang Y, Georgi LL, Zhebentyayeva TN, Reighard GL, Scorza R, Abbott AG (2002b) High-throughput targeted SSR marker development in peach (Prunus persica). Genome 45:319–328
Werner DJ, Okie WR (1998) A history and description of the Prunus persica plant introduction collection. Hortscience 33:787–793