Search

When plants colonized land they developed a wide range of adaptations to cope with life in a drier environment. One key adaptation was desiccation tolerance (DT) which is the ability to survive the removal of almost all cellular water without irreparable damage. DT is recurrent in orthodox seeds and in the vegetative body of species commonly known as ‘resurrection plants’. In this thesis a multilevel approach, combining genomics, transcriptomics, gene family evolution, protein structural and functional analysis, and seed physiology was employed in order to tackle curiosity-driven fundamental questions about the major mechanisms governing DT. Several mechanisms were found to be important for DT, including the coordinated activation of cell protection through Late Embryogenesis Abundant (LEA) proteins, which were shown to be common amongst resurrection plants and orthodox seeds. These findings aid to the comprehension of the complexity of DT in plants, and may provide transferrable knowledge to design more water-stress tolerant crops.

Quality of seeds is strongly affected by their genetic make-up, the environment during seed development and maturation and also the interaction between the genome and the environment. In this thesis, I tried to dissect the genetic basis of tomato seed quality by a combined study of physiology, genetics and genomics in relation to the maternal environment. Chapter 1 of the thesis (General introduction) describes the definition and different aspects of seed and seedling quality and the factors influencing them, with the emphasis on the maternal environment. Additionally background on the used genetic tools with emphasis on the generalized genetical genomics (GGG) approach is provided. Finally, integration of large ‘omics’ technology driven datasets is suggested as an approach to assist in the identification of the genes underlying QTLs. Seed performance traits, such as seed dormancy and germinability, can be influenced by different maternal nutritional environmental conditions. In Chapter 2 I investigated the effect of different maternal nutritional environments on the quality of seeds from two tomato species (S. lycopersicum and S. pimpinellifolium). I showed that different phosphate and nitrate levels available for mother plants influences seed and seedling quality traits especially in stressful germination environments. Correlation analysis was done between physiological traits and metabolic changes caused by the different maternal environments in tomato and interesting positive and negative correlations were identified which shed light on the molecular regulation of seed quality in different maternal environments. High quality seed is defined by high levels of seed germination and seedling establishment, especially under sub-optimal conditions. Seed quality however, is acquired during seed maturation and therefore in addition to the mother plant’s genetic background can be strongly influenced by the maternal environment in which the seeds develop. Chapter 3 of the

The environmental conditions under which plants grow affect the quality of seeds produced in a genotype-dependent manner. In nature, genotype-by-environment interactions are often observed however little is known about the underlying mechanisms. The combined use of genetic tools and omics data can help to explore the influence of the environment on the genetic control of seed performance. The research presented in this thesis explores genotype-by-environment interaction at the phenotypic with an effort to connect phenotypic changes to changes observed at the metabolome and transcriptome in a systems genetics approach. For this purpose, an Arabidopsis thaliana recombinant inbred lines population derived from the cross between the parental lines Bay-0 and Sha was grown under different conditions, namely standard, high light, high temperature and low phosphate conditions from flowering until seed harvest. The germination properties of the seeds produced under the different environments were investigated and the seed germination QTLs identified displayed large QTL-by-environment interaction. Quantitative changes in primary metabolites in response to the maternal environment were investigated by GC-TOF-MS. Further, mQTLs under the different environments were identified. RNA-seq of the same lines enabled to explore changes in gene expression across genotypes and environments as well as differences in the eQTL landscape under the different maternal environment. The findings of this research show that seed quality is largely influenced by genotype-by-environment interactions which result in large changes at the molecular level. The data generated provide many opportunities to further study.

Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth × Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.

Plants are exposed to a wide variety of extracellular stimuli and employ a broad set of signaling pathways to give the appropriate response. M itogen a ctivated p rotein k inases (MAPKs) play an important role in the signal transduction of yeast and animals and increasing evidence suggests a similar role of MAPKs in the signal transduction of plants. MAPKs employ their function as part of protein kinase cascades, composed of a MAPK, a M AP Kk inase (MKK), and a M AP Kk inase k inase (MKKK). MKKKs activate MKKs by phosphorylation of conserved threonine or serine residues, and subsequently MKKs activate the MAPKs by phosphorylation of highly conserved tyrosine and threonine residues.The introduction gives a brief overview of the MAPK cascades employed by yeast and animals and a more extensive overview of our current knowledge about the function of MAPK cascades in plants. To get an overview of the plant MAPKs and their functions the known plant MAPKs were classified and the analyses of all isolated full-length plant MAPK sequences reveals that they can be divided into at least five distinct subfamilies (Chapter 2). For some of these groups it could be shown that MAPKs with similar sequences also perform similar functions. In addition, analysis of e xpressed s equence t ags (ESTs) and partial cDNAs coding for MAPKs revealed the existence of a new plant MAPK subfamily.The goal of the research described in this thesis was to provide insight in the role of several plant MAPKs in stress responses of plants. One of the most severe environmental stresses to which plants can be exposed is wounding. It can be the result of physical injury, herbivore or pathogen attack and induces a wide range of responses, in general involving the induction of genes active in healing and defense processes. In chapter 3 the involvement of a MAPK in the wound response of alfalfa is discussed. It could be shown that wounding activates the alfalfa s tress a ctivated M AP K (SAMK) both at the post