Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination

Plant Physiology

Volumn 163, Issue 1, 2013, Pages 205-215

  Dekkers, Bas J W ^a,b   Pearce, Simon ^c   van Bolderen Veldkamp, R P ^a,b   Marshall, Alex ^d   Widera, Paweł ^c   Gilbert, James ^c   Drost, Hajk Georg ^e,g   Bassel, George W ^f   Müller, Kerstin ^c   King, John R ^c   Wood, Andrew T A ^c   Grosse, Ivo ^e   Quint, Marcel ^g   Krasnogor, Natalio ^c   Leubner Metzger, Gerhard ^h   Holdsworth, Michael J ^c   Bentsink, Leónie ^a,b  

^a UTRECHT UNIVERSITY   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^f UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^g LEIBNIZ INSTITUTE OF PLANT BIOCHEMISTRY   (Germany)

^h UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GERMINATION; GROWTH, DEVELOPMENT AND AGING; PLANT SEED;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENE EXPRESSION REGULATION, PLANT; GERMINATION; MODELS, BIOLOGICAL; SEEDS; TRANSCRIPTION, GENETIC; TRANSCRIPTOME;

EID: 84883230671     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.113.223511     Document Type: Article

References (39)

1. Bassel GW, Lan H, Glaab E, Gibbs DJ, Gerjets T, Krasnogor N, Bonner AJ, Holdsworth MJ, Provart NJ (2011) Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci USA 108: 9709-9714
2. Belmonte MF, Kirkbride RC, Stone SL, Pelletier JM, Bui AQ, Yeung EC, Hashimoto M, Fei J, Harada CM, Munoz MD, et al (2013) Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc Natl Acad Sci USA 110: E435-E444
3. Bethke PC, Libourel IG, Aoyama N, Chung YY, Still DW, Jones RL (2007) The Arabidopsis aleurone layer responds to nitric oxide, gibberellin, and abscisic acid and is sufficient and necessary for seed dormancy. Plant Physiol 143: 1173-1188
4. Braam J (2005) In touch: plant responses to mechanical stimuli. New Phytol 165: 373-389
5. Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, et al (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell 23: 873-894
6. Chehab EW, Yao C, Henderson Z, Kim S, Braam J (2012) Arabidopsis touch-induced morphogenesis is jasmonate mediated and protects against pests. Curr Biol 22: 701-706
7. Debeaujon I, Lepiniec L, Pourcel L, Routaboul J-M (2007) Seed coat development and dormancy. In Annual Plant Reviews, Vol 27: Seed Development, Dormancy and Germination. Blackwell Publishing, Oxford, pp 25-49
8. Domazet-Loso T, Brajkovic J, Tautz D (2007) A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23: 533-539
9. Domazet-Loso T, Tautz D (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468: 815-818
10. Endo A, Tatematsu K, Hanada K, Duermeyer L, Okamoto M, Yonekura-Sakakibara K, Saito K, Toyoda T, Kawakami N, Kamiya Y, et al (2012) Tissue-specific transcriptome analysis reveals cell wall metabolism, flavonol biosynthesis, and defense responses are activated in the endosperm of germinating Arabidopsis thaliana seeds. Plant Cell Physiol 53: 16-27
11. Farrant JM, Moore JP (2011) Programming desiccation-tolerance: from plants to seeds to resurrection plants. Curr Opin Plant Biol 14: 340-345
12. Finch-SavageWE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171: 501-523
13. Glaab E, Baudot A, Krasnogor N, Valencia A (2010) TopoGSA: network topological gene set analysis. Bioinformatics 26: 1271-1272
14. Holdsworth MJ, Bentsink L, Soppe WJ (2008a) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol 179: 33-54
15. Holdsworth MJ, Finch-Savage WE, Grappin P, Job D (2008b) Post-genomics dissection of seed dormancy and germination. Trends Plant Sci 13: 7-13
16. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264
17. Kumpf RP, Shi CL, Larrieu A, Stø IM, Butenko MA, Péret B, Riiser ES, Bennett MJ, Aalen RB (2013) Floral organ abscission peptide IDA and its HAE/HSL2 receptors control cell separation during lateral root emergence. Proc Natl Acad Sci USA 110: 5235-5240
18. Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, et al (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seedspecific transcription factors. Proc Natl Acad Sci USA 107: 8063-8070
19. Lee D, Polisensky DH, Braam J (2005) Genome-wide identification of touchand darkness-regulated Arabidopsis genes: a focus on calmodulin-like and XTH genes. New Phytol 165: 429-444
20. Lee KJD, Dekkers BJW, Steinbrecher T, Walsh CT, Bacic A, Bentsink L, Leubner-Metzger G, Knox JP (2012) Distinct cell wall architectures in seed endosperms in representatives of the Brassicaceae and Solanaceae. Plant Physiol 160: 1551-1566
21. Lee KP, Piskurewicz U, Turecková V, Strnad M, Lopez-Molina L (2010) A seed coat bedding assay shows that RGL2-dependent release of abscisic acid by the endosperm controls embryo growth in Arabidopsis dormant seeds. Proc Natl Acad Sci USA 107: 19108-19113
22. Lim PO, Kim HJ, NamHG(2007) Leaf senescence. Annu Rev Plant Biol 58: 115-136
23. Martínez-Andújar C, Pluskota WE, Bassel GW, Asahina M, Pupel P, Nguyen TT, Takeda-Kamiya N, Toubiana D, Bai B, Górecki RJ, et al (2012) Mechanisms of hormonal regulation of endosperm cap-specific gene expression in tomato seeds. Plant J 71: 575-586
24. Müller K, Tintelnot S, 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: 864-877
25. Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, 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: 697-709
26. Narsai R, Law SR, Carrie C, Xu L, Whelan J (2011) In-depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis. Plant Physiol 157: 1342-1362
27. Nonogaki H (2006) Seed germination: the biochemical and molecular mechanisms. Breed Sci 56: 93-105
28. Nonogaki H, Chen F, Bradford KJ (2007) Mechanisms and genes involved in germination sensu stricto. In Annual Plant Reviews, Vol 27: Seed Development, Dormancy and Germination. Blackwell Publishing, Oxford, pp 264-304
29. Ohto M-a, Stone SL, Harada JJ (2007) Genetic control of seed development and seed mass. In Annual Plant Reviews, Vol 27: Seed Development, Dormancy and Germination. Blackwell Publishing, Oxford, pp 1-24
30. Penfield S, Graham S, Graham IA (2005) Storage reserve mobilization in germinating oilseeds: Arabidopsis as a model system. Biochem Soc Trans 33: 380-383
31. Penfield S, Li Y, Gilday AD, Graham S, Graham IA (2006) Arabidopsis ABA INSENSITIVE4 regulates lipid mobilization in the embryo and reveals repression of seed germination by the endosperm. Plant Cell 18: 1887-1899
32. Preston J, Tatematsu K, Kanno Y, Hobo T, Kimura M, Jikumaru Y, Yano R, Kamiya Y, Nambara E (2009) Temporal expression patterns of hormone metabolism genes during imbibition of Arabidopsis thaliana seeds: a comparative study on dormant and non-dormant accessions. Plant Cell Physiol 50: 1786-1800
33. Quint M, Drost HG, Gabel A, Ullrich KK, Bönn M, Grosse I (2012) A transcriptomic hourglass in plant embryogenesis. Nature 490: 98-101
34. Rajjou L, Duval M, Gallardo K, Catusse J, Bally J, Job C, Job D (2012) Seed germination and vigor. Annu Rev Plant Biol 63: 507-533
35. Sliwinska E, Bassel GW, Bewley JD (2009) Germination of Arabidopsis thaliana seeds is not completed as a result of elongation of the radicle but of the adjacent transition zone and lower hypocotyl. J Exp Bot 60: 3587-3594
36. Stenvik GE, TandstadNM, Guo Y, Shi CL, KristiansenW, Holmgren A, Clark SE, Aalen RB, Butenko MA (2008) The EPIP peptide of INFLORESCENCE DEFICIENT IN ABSCISSION is sufficient to induce abscission in Arabidopsis through the receptor-like kinases HAESA and HAESA-LIKE2. Plant Cell 20: 1805-1817
37. Usadel B, Nagel A, Steinhauser D, Gibon Y, Bläsing OE, Redestig H, Sreenivasulu N, Krall L, HannahMA, Poree F, et al (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7: 535
38. Weitbrecht K, Müller K, Leubner-Metzger G (2011) First off the mark: early seed germination. J Exp Bot 62: 3289-3309
39. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2: e718