Dissecting the seed-to-seedling transition in Arabidopsis thaliana by gene co-expression networks

A.T. Silva

Research output: Thesisinternal PhD, WU


One of the most important developmental processes in the life-cycle of higher plants is the transition from a seed to a plant and from a generative to a vegetative developmental program. The major hallmark or end-point of the transition from seed to plant is the onset of photosynthesis and the concomitant shift from a heterotrophic to an autotrophic organism. It is advantageous for a species to keep the period of seedling establishment as short as possible since young seedlings are highly sensitive to biotic and abiotic stresses. This implies that the extreme stress tolerance of seeds to i.e. desiccation is lost upon germination. If the regulatory principles of the seed-to-seedling transition are better understood it may become feasible to maintain the seed’s stress tolerance well into the seedling stage.

Despite the profound impact of seedling performance on crop establishment and yield, the seed-to-seedling transition has hardly been studied at the molecular level. This thesis aims at deciphering and understanding the molecular processes that govern this transition in Arabidopsis thaliana. A high-resolution study of the molecular events that occur during these successive transitional stages may provide clues as to the regulatory principles that drive this transition. It may also yield information about the factors that determine the (in)ability to revert to a developmental mode and which features are critical for the maintenance and loss of desiccation tolerance and other stress responses.

In Chapter 1 important processes such as abscisic acid and their regulation are described and it is discussed in what way the seed-to-seedling transition may have links to a trait such as desiccation tolerance. An overview is presented of the current knowledge of the seed-to-seedling phase transition and the existence of a temporal developmental block that can be manipulated by osmotic treatment, the carbon/nitrogen balance and by abscisic acid which results in the re-establishment of desiccation tolerance.

Chapter 2 focuses on comprehensive gene regulation by a detailed transcriptional analysis across seven developmental stages of the seed-to-seedling transition. It describes the inference of a gene co-expression network and several transcriptional modules. I show that such an approach highlights important molecular processes during seedling development, which would not likely be derived from comparative transcript profiling. Moreover, I show that a putative key regulator in one of the transcriptional modules affects late seedling establishment.

In Chapter 3 it is shown how this phase transition is expressed in the primary metabolite profiles in correlation with gene expression. A metabolite-metabolite correlation analysis suggested two profiles, which point at the metabolic preparation of seed germination and of vigorous seedling establishment. Furthermore, a linear correlation between metabolite contents and transcript abundance (Chapter 2) provides a global view of the transcriptional and metabolic changes during the seed-to-seedling transition. It creates new perspectives of the regulatory complexes underlying the seed-to-seedling transition.

Chapter 4 describes the development of a novel method to re-establish desiccation tolerance during the seed-to-seedling transition without adverse effects such as those caused by an osmotic treatment with polyethylene glycol. By using this method, named ‘Mild Air Drying Treatment’ (MADT), I show that the re-establishment of desiccation tolerance is not linked to a reduced ability to accumulate ABA in the desiccation sensitive seeds (germinated seeds at root hair stage). I also present a genetic  interaction study of ABSCISIC ACID INSENSITIVE (ABI) genes in their germination response to ABA, and their response to the re-establishment of desiccation tolerance using the MADT. The interaction between ABI3 and ABI4, and between ABI4 and ABI5 act synergistically in the re-establishment of DT, as well as in the germination response to ABA.

In a more in depth study in Chapter 5 I carried out an extensive transcript analysis to infer possible mechanisms of the re-establishment of desiccation tolerance using the MADT protocol. Possible mechanisms underlying the re-establishment of desiccation tolerance were inferred by employing a time-series comparison of germinated desiccation tolerant and -sensitive seeds. Early-response genes of the re-establishment of desiccation tolerance may play a role in events that promote the initial protection to dehydration stress, whereas the late-response genes may play a role in events that help seed to respond to the changes in water dynamics. Moreover, using a gene co-expression network and transcriptional module I concluded that a crosstalk between ABA-dependent and ABA-independent transcription factors regulate the re-establishment of desiccation tolerance.

In Chapter 6 I discuss how the results presented in this thesis contribute to our knowledge of the molecular basis of the seed-to-seedling transition and the re-establishment of desiccation tolerance during its phase changes. Finally, new possibilities for further research are discussed, as well as the further use of the data sets to delineate the mechanisms underlying the seed-to-seedling transition and desiccation tolerance. Possible applications of the results for crop improvement are addressed. Thus, the generation of genetically modified plants that produce seeds with a stress tolerance that extends well into seedling stage may be feasible.




Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Bouwmeester, Harro, Promotor
  • Hilhorst, Henk, Co-promotor
  • Ligterink, Wilco, Co-promotor
Award date9 Dec 2015
Place of PublicationWageningen
Print ISBNs9789462575929
Publication statusPublished - 2015


  • arabidopsis thaliana
  • seeds
  • seed germination
  • seedlings
  • gene expression
  • desiccation tolerance

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  • Projects

    The transition from seed to seedling and implications for stress resistance

    Bouwmeester, H., Hilhorst, H. & Ligterink, W.


    Project: PhD

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