SEARCH

SEARCH BY CITATION

References

  • Ali-Rachedi, S., Bouinot, D., Wagner, M.H., Bonnet, M., Sotta, B., Grappin, P. and Jullien, M. (2004) Changes in endogenous abscisic acid levels during dormancy release and maintenance of mature seeds: studies with the Cape Verde Islands ecotype, the dormant model of Arabidopsis thaliana. Planta, 219, 479488.
  • Amaral, P.P., Dinger, M.E., Mercer, T.R. and Mattick, J.S. (2008) The eukaryotic genome as an RNA machine. Science, 319, 17871789.
  • Baskin, C.C. and Baskin, J.M. (1998) Seeds: Ecology, Biogeography, and Evolution of Dormancy and Germination. San Diego: Academic Press.
  • Bassel, G.W., Fung, P., Chow, T.F.F., Foong, J.A., Provart, N.J. and Cutler, S.R. (2008) Elucidating the germination transcriptional program using small molecules. Plant Physiol. 147, 143155.
  • Ben Amor, B., Wirth, S., Merchan, F. et al. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res. 19, 5769.
  • Bewley, J.D. (1997) Seed germination and dormancy. Plant Cell, 9, 10551066.
  • Cadman, C.S.C., Toorop, P.E., Hilhorst, H.W.M. and Finch-Savage, W.E. (2006) Gene expression profiles of Arabidopsis Cvi seeds during dormancy cycling indicate a common underlying dormancy control mechanism. Plant J. 46, 805822.
  • Carrera, E., Holman, T., Medhurst, A., Peer, W., Schmuths, H., Footitt, S., Theodoulou, F.L. and Holdsworth, M.J. (2007) Gene expression profiling reveals defined functions of the ATP-binding cassette transporter COMATOSE late in phase II of germination. Plant Physiol. 143, 16691679.
  • Carrera, E., Holman, T., Medhurst, A., Dietrich, D., Footitt, S., Theodoulou, F.L. and Holdsworth, M.J. (2008) Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. Plant J. 53, 214224.
  • Chen, F. and Bradford, K.J. (2000) Expression of an expansin is associated with endosperm weakening during tomato seed germination. Plant Physiol. 124, 12651274.
  • Chibani, K., Ali-Rachedi, S., Job, C., Job, D., Jullien, M. and Grappin, P. (2006) Proteomic analysis of seed dormancy in Arabidopsis. Plant Physiol. 142, 14931510.
  • Dai, X.Y., Yu, J.J., Ma, J.X., Ao, G.M. and Zhao, Q. (2007) Overexpression of Zm401, an mRNA-like RNA, has distinct effects on pollen development in maize. Plant Growth Regul. 52, 229239.
  • Debeaujon, I. and Koornneef, M. (2000) Gibberellin requirement for Arabidopsis seed germination is determined both by testa characteristics and embryonic abscisic acid. Plant Physiol. 122, 415424.
  • Dubreucq, B., Berger, N., Vincent, E., Boisson, M., Pelletier, G., Caboche, M. and Lepiniec, L. (2000) The Arabidopsis AtEPR1 extensin-like gene is specifically expressed in endosperm during seed germination. Plant J. 23, 643652.
  • Finkelstein, R.R. (1994) Mutations at 2 new Arabidopsis Aba response loci are similar to the Abi3 mutations. Plant J. 5, 765771.
  • Finkelstein, R., Reeves, W., Ariizumi, T. and Steber, C. (2008) Molecular aspects of seed dormancy. Annu. Rev. Plant Biol. 59, 387415.
  • Franco-Zorrilla, J.M., Valli, A., Todesco, M., Mateos, I., Puga, M.I., Rubio-Somoza, I., Leyva, A., Weigel, D., Garcia, J.A. and Paz-Ares, J. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat. Genet. 39, 10331037.
  • González-Guzmán, M., Abia, D., Salinas, J., Serrano, R. and Rodríguez, P.L. (2004) Two new alleles of the abscisic aldehyde oxidase 3 gene reveal its role in abscisic acid biosynthesis in seeds. Plant Physiol. 135, 325333.
  • Grappin, P., Bouinot, D., Sotta, B., Miginiac, E. and Jullien, M. (2000) Control of seed dormancy in Nicotiana plumbaginifolia: post-imbibition abscisic acid synthesis imposes dormancy maintenance. Planta, 210, 279285.
  • Groot, S.P.C. and Karssen, C.M. (1992) Dormancy and germination of abscisic acid-deficient tomato seeds - studies with the sitiens mutant. Plant Physiol. 99, 952958.
  • Halmer, P., Bewley, J.D. and Thorpe, T.A. (1976) An enzyme to degrade lettuce endosperm cell walls. Appearance of a mannanase following phytochrome- and gibberellin-induced germination. Planta, 130, 189196.
  • Hazen, S.P., Naef, F., Quisel, T., Gendron, J.M., Chen, H.M., Ecker, J.R., Borevitz, J.O. and Kay, S.A. (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol. 10, R17.
  • Holdsworth, M.J., Bentsink, L. and Soppe, W.J.J. (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol. 179, 3354.
  • Ihaka, R. and Gentleman, R. (1996) R: a language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299314.
  • Jacobsen, J.V., Pearce, D.W., Poole, A.T., Pharis, R.P. and Mander, L.N. (2002) Abscisic acid, phaseic acid and gibberellin contents associated with dormancy and germination in barley. Physiol. Plant. 115, 428441.
  • Karssen, C.M., Brinkhorstvanderswan, D.L.C., Breekland, a.E. and Koornneef, M. (1983) Induction of dormancy during seed development by endogenous abscisic acid : studies on abscisic acid deficient genotypes of Arabidopsis thaliana (L) Heynh. Planta, 157, 158165.
  • Koornneef, M., Hanhart, C.J., Hillhorst, H.W.A. and Karssen, C.M. (1989) In vivo inhibition of seed development and reserve protein accumulation in recombinants of abscisic acid biosynthesis and responsiveness mutants in Arabidopsis thaliana. Plant Physiol. 90, 463469.
  • Kushiro, T., Okamoto, M., Nakabayashi, K., Yamagishi, K., Kitamura, S., Asami, T., Hirai, N., Koshiba, T., Kamiya, Y. and Nambara, E. (2004) The Arabidopsis cytochrome P450 CYP707A encodes ABA 8′-hydroxylases: key enzymes in ABA catabolism. EMBO J. 23, 16471656.
  • Léon-Kloosterziel, K.M., Keijzer, C.J. and Koornneef, M. (1994) A seed shape mutant of Arabidopsis that is affected in integument development. Plant Cell, 6, 385392.
  • Léon-Kloosterziel, K.M., Gil, M.A., Ruijs, G.J., Jacobsen, S.E., Olszewski, N.E., Schwartz, S.H., Zeevaart, J.A.D. and Koornneef, M. (1996) Isolation and characterization of abscisic acid-deficient Arabidopsis mutants at two new loci. Plant J. 10, 655661.
  • Li, L., Wang, X.F., Stolc, V. et al. (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat. Genet. 38, 124129.
  • de Longevialle, A.F., Meyer, E.H., Andres, C., Taylor, N.L., Lurin, C., Millar, A.H. and Small, I.D. (2007) The pentatricopeptide repeat gene OTP43 is required for trans-splicing of the mitochondrial nad1 intron 1 in Arabidopsis thaliana. Plant Cell, 19, 32563265.
  • Lurin, C., Andres, C., Aubourg, S. et al. (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell, 16, 20892103.
  • Martin, R.C., Liu, P.P. and Nonogaki, H. (2005) Simple purification of small RNAs from seeds and efficient detection of multiple microRNAs expressed in Arabidopsis thaliana and tomato (Lycopersicon esculentum) seeds. Seed Sci. Res. 15, 319328.
  • Matsui, A., Ishida, J., Morosawa, T. et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol. 49, 11351149.
  • Meyers, B.C., Tej, S.S., Vu, T.H., Haudenschild, C.D., Agrawal, V., Edberg, S.B., Ghazal, H. and Decola, S. (2004) The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res. 14, 16411653.
  • Millar, A.A., Jacobsen, J.V., Ross, J.J., Helliwell, C.A., Poole, A.T., Scofield, G., Reid, J.B. and Gubler, F. (2006) Seed dormancy and ABA metabolism in Arabidopsis and barley: the role of ABA 8′-hydroxylase. Plant J. 45, 942954.
  • Muller, K., Tintelnot, S. and Leubner-Metzger, G. (2006) Endosperm-limited Brassicaceae seed germination: abscisic acid inhibits embryo-induced endosperm weakening of Lepidium sativum (cress) and endosperm rupture of cress and Arabidopsis thaliana. Plant Cell Physiol. 47, 864877.
  • Nakabayashi, K., Okamoto, M., Koshiba, T., Kamiya, Y. and Nambara, E. (2005) Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J. 41, 697709.
  • Nakashima, K., Fujita, Y., Kanamori, N. et al. (2009) Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. Plant Cell Physiol. 50, 13451363.
  • Nambara, E. and Marion-Poll, A. (2005) Abscisic acid biosynthesis and catabolism. Annu. Rev. Plant. Biol. 56, 165185.
  • Nonogaki, H., Gee, O.H. and Bradford, K.J. (2000) A germination-specific endo-beta-mannanase gene is expressed in the micropylar endosperm cap of tomato seeds. Plant Physiol. 123, 12351245.
  • Ogawa, M., Hanada, A., Yamauchi, Y., Kuwahara, A., Kamiya, Y. and Yamaguchi, S. (2003) Gibberellin biosynthesis and response during Arabidopsis seed germination. Plant Cell, 15, 15911604.
  • Okamoto, M., Kuwahara, A., Seo, M., Kushiro, T., Asami, T., Hirai, N., Kamiya, Y., Koshiba, T. and Nambara, E. (2006) CYP707A1 and CYP707A2, which encode abscisic acid 8 ‘-hydroxylases, are indispensable for proper control of seed dormancy and germination in Arabidopsis. Plant Physiol. 141, 97107.
  • Penfield, S., Rylott, E.L., Gilday, A.D., Graham, S., Larson, T.R. and Graham, I.A. (2004) Reserve mobilization in the Arabidopsis endosperm fuels hypocotyl elongation in the dark, is independent of abscisic acid, and requires PHOSPHOENOLPYRUVATE CARBOXYKINASE1. Plant Cell, 16, 27052718.
  • Penfield, S., Li, Y., Gilday, A.D., Graham, S. and Graham, I.A. (2006) Arabidopsis ABA INSENSITIVE4 regulates lipid mobilization in the embryo and reveals repression of seed germination by the endosperm. Plant Cell, 18, 18871899.
  • Pérez-Flores, L., Carrari, F., Osuna-Fernández, R., Rodríguez, M.V., Enciso, S., Stanelloni, R., Sanchez, R.A., Bottini, R., Iusem, N.D. and Benech-Arnold, R.L. (2003) Expression analysis of a GA 20-oxidase in embryos from two sorghum lines with contrasting dormancy: possible participation of this gene in the hormonal control of germination. J. Exp. Bot. 54, 20712079.
  • Piskurewicz, U., Jikumaru, Y., Kinoshita, N., Nambara, E., Kamiya, Y. and Lopez-Molina, L. (2008) The gibberellic acid signaling repressor RGL2 inhibits arabidopsis seed germination by stimulating abscisic acid synthesis and ABI5 activity. Plant Cell, 20, 27292745.
  • Pritchard, S.L., Charlton, W.L., Baker, A. and Graham, I.A. (2002) Germination and storage reserve mobilization are regulated independently in Arabidopsis. Plant J. 31, 639647.
  • Rymarquis, L.A., Kastenmayer, J.P., Huttenhofer, A.G. and Green, P.J. (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci. 13, 329334.
  • Saika, H., Okamoto, M., Miyoshi, K. et al. (2007) Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that encodes ABA 8 ‘-hydroxylase in rice. Plant Cell Physiol. 48, 287298.
  • Salaita, L., Kar, R.K., Majee, M. and Downie, A.B. (2005) Identification and characterization of mutants capable of rapid seed germination at 10 degrees C from activation-tagged lines of Arabidopsis thaliana. J. Exp. Bot. 56, 20592069.
  • Schmid, M., Davison, T.S., Henz, S.R., Pape, U.J., Demar, M., Vingron, M., Scholkopf, B., Weigel, D. and Lohmann, J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nat. Genet. 37, 501506.
  • Schmitz-Linneweber, C. and Small, I. (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci. 13, 663670.
  • Schopfer, P. and Plachy, C. (1985) Control of Seed Germination by Abscisic-Acid. III. Effect on Embryo Growth Potential (Minimum Turgor Pressure) and Growth Coefficient (Cell Wall Extensibility) in Brassica napus L. Plant Physiol. 77, 676686.
  • Seki, M., Narusaka, M., Kamiya, A. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141145.
  • Seo, M., Hanada, A., Kuwahara, A. et al. (2006) Regulation of hormone metabolism in Arabidopsis seeds: phytochrome regulation of abscisic acid metabolism and abscisic acid regulation of gibberellin metabolism. Plant J. 48, 354366.
  • Shen, Q.X. and Ho, T.H.D. (1995) Functional dissection of an abscisic-acid (Aba)-inducible gene reveals 2 independent Aba-responsive complexes each containing a G-Box and a novel cis-acting element. Plant Cell, 7, 295307.
  • da Silva, E.A.A., Toorop, P.E., van Aelst, A.C. and Hillhorst, H.W.A. (2004) Abscisic acid controls embryonic growth potential and endosperm cap weakening during coffee (Coffea Arabica cv. Rubi) seed germination. Planta, 220, 251261.
  • Stolc, V., Samanta, M.P., Tongprasit, W. et al. (2005) Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl Acad. Sci. USA, 102, 44534458.
  • Storey, J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. Series B Stat. Methodol. 64, 479498.
  • Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 94409445.
  • Tamura, N., Yoshida, T., Tanaka, A., Sasaki, R., Bando, A., Toh, S., Lepiniec, L. and Kawakami, N. (2006) Isolation and characterization of high temperature-resistant germination mutants of Arabidopsis thaliana. Plant Cell Physiol. 47, 10811094.
  • Tatematsu, K., Kamiya, Y. and Nambara, E. (2008) Co-regulation of ribosomal protein genes as an indicator of growth status: comparative transcriptome analysis on axillary shoots and seeds in Arabidopsis. Plant Signal. Behav. 3, 450452.
  • Toh, S., Imamura, A., Watanabe, A. et al. (2008) High temperature-induced abscisic acid biosynthesis and its role in the inhibition of gibberellin action in Arabidopsis seeds. Plant Physiol. 146, 13681385.
  • Toyoda, T. and Shinozaki, K. (2005) Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. Plant J. 43, 611621.
  • Winter, D., Vinegar, B., Nahal, H., Ammar, R., Wilson, G.V. and Provart, N.J. (2007) An “electronic fluorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS ONE, 2, e718.
  • Wu, C.T., Leubner-Metzger, G., Meins, F. and Bradford, K.J. (2001) Class I beta-1,3-glucanase and chitinase are expressed in the micropylar endosperm of tomato seeds prior to radicle emergence. Plant Physiol. 126, 12991313.
  • Yamada, K., Lim, J., Dale, J.M. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842846.
  • Yamagishi, K., Tatematsu, K., Yano, R., Preston, J., Kitamura, S., Takahashi, H., McCourt, P., Kamiya, Y. and Nambara, E. (2009) CHOTTO1, a double AP2 domain protein of Arabidopsis thaliana, regulates germination and seedling growth under excess supply of glucose and nitrate. Plant Cell Physiol. 50, 330340.
  • Zeller, G., Henz, S.R., Widmer, C.K., Sachsenberg, T., Ratsch, G., Weigel, D. and Laubinger, S. (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J. 58, 10681082.
  • Zhang, X.Y., Yazaki, J., Sundaresan, A. et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126, 11891201.