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Plant Dormancy Transcriptomes and Epigenetic Control

Physiological seed dormancy and bud dormancy are compared in different species to understand the shared molecular pathways that are essential for plant dormancy in general and seed dormancy specifically.
Relative gene expression of CsHUB2 and CsGCN5L follows a transient increase corresponding with the induction of and release from dormancy in Castanea sativa buds, assessed by real-time RT-PCR.

Dormancy in seeds is defined as the “failure of a viable intact seed to complete germination under favourable conditions” (Bewley, 1997). However, seeds are not the only plant structures displaying dormancy; bulbs, cambium, and buds also display dormancy. Generally, dormancy is a tool for the plant to suspend and resume growth recurrently in response to environmental or seasonal conditions. Like seeds from many species that display physiological dormancy, buds in perennials have the capacity for release and recurrent induction of dormancy if growth is otherwise inhibited. Moreover, buds and seeds with physiological dormancy often require cold stratification for release of dormancy. These similarities make it likely that underlying molecular pathways for dormancy are shared between buds and seeds.

We studied gene expression in Arabidopsis thaliana seeds using Affymetrix and CATMA microarrays. Gene expression patterns were identified using seeds of Arabidopsis thaliana ecotype Cvi and then compared with other species with somewhat different dormancy behaviour (e.g. Sisymbrium officinale, Brassica oleracea). Fundamental questions were addressed: 1) how do temperature, light, and nitrate influence gene expression in relation to dormancy status? 2) Are seeds that cycle through dormancy identical in gene expression patterns? 3) The environmental cues and physiological mechanisms that control dormancy status may differ between species, but are the same genes involved? Following studies on A. thaliana ecotype Cvi comparisons were made more widely within the Brassicaceae to generalise the findings. Thus, the objective of this project was to explain germination and dormancy in terms of gene expression; to identify a comprehensive set of genes that are suitable as indicators of physiological states. The purpose was to generate a better understanding of dormancy, which can be used to understand the behaviour of banked seeds. The project may lead to the development of a diagnostics test to assess dormancy and germination capacity in any accession of the MSB, as demonstrated for two markers in Brassica oleracea.

Comparison of described transcriptomes of different systems with shared characteristics allows the extraction of these shared molecular pathways. With the description of the transcriptomes for seed dormancy in Arabidopsis thaliana and for bud dormancy induction in Populus tremula x P. alba, the work on Castanea sativa aimed to describe the transcriptome of bud dormancy and seed dormancy in this species, and compare the two types of dormancy within the species. Furthermore, these transcriptomes were then compared with the published transcriptomes for aforementioned species, to understand the essence of dormancy. Both the control of transcription and response to the environment is often controlled epigenetically, which formed a focal point in this study.

The results for seed dormancy studies have identified subsets of dormancy- and germination-associated genes in distinct functional groups. Environmental factors controlled distinct subsets of genes, mediated by abscisic acid signal transduction. Similarities were found between three species for smaller gene-sets. In buds subsets of dormancy- associated genes are identified in distinct functional groups that differed from those associated with non-dormancy. There were strong indications for epigenetic control that was different for dormancy and non-dormancy. The comparison of dormancy transcriptomes in the various species indicated shared pathways for stress response (dormancy) and biogenesis of cellular components (non-dormancy). Epigenetic control of dormancy is the topic of continuing investigation.

Project partners and collaborators


University of Oviedo

The Netherlands

Wageningen University


University of Warwick

Annex material

Key papers published since 2006:
Santamaría, M.E., Rodríguez, R., Cañal, M.J. & Toorop, P.E. (2011) Transcriptome analysis of chestnut (Castanea sativa Mill.) tree buds suggests a putative role for epigenetic control of bud dormancy. Annals of Botany 108: 485–498 (IF 3.388).

Santamaría, M.E., Toorop, P.E., Rodríguez, R. & Cañal, M.J. (2010) Dormant and non-dormant Castanea sativa Mill. buds require different polyvinylpyrrolidone concentrations for optimal RNA isolation. Plant Science 178: 55–60. (IF 2.481).

Santamaría, M.E., Hasbún, R., José Valera, M., Meijón, M., Valledor, L., Rodríguez, J.L., Toorop, P.E., Jesús Cañal, M. & Rodríguez, R. (2009) Acetylated H4 histone and genomic DNA methylation patterns during bud set and bud burst in Castanea sativa. Journal of Plant Physiology 166: 1360–1369 (IF 2.677; times cited 2).

Finch-Savage, W.E., Cadman, C.S.C., Toorop, P.E., Lynn, J.R. & Hilhorst, H.W.M. (2007) Seed dormancy release in Arabidopsis Cvi by dry after-ripening, low temperature, nitrate and light shows common quantitative patterns of gene expression directed by environmentally specific sensing. The Plant Journal 51: 60–78 (IF 6.948; times cited 67).

Cadman, C.S.C., Toorop, P.E., Hilhorst, H.W.M. & Finch-Savage, W.E. (2006) Gene expression profiles of Arabidopsis Cvi seeds during cycling through dormant and non-dormant states indicate a common underlying dormancy control mechanism. The Plant Journal 46: 805–822 (IF 6.948; times cited 100).

Conferences and workshops:
2009, 4th International Symposium on Plant Dormancy, Fargo
2008, Workshop: dormancy and resistance in harsh environments, Berlin
2005, 8th International Workshop on Seeds, Brisbane
2004, Workshop on Molecular Aspects of Seed Germination and Dormancy, Wageningen

Project team

Seed Conservation Department

Dr Peter Toorop