The central research topic of this theme is the organization of the genome, which is studied at all levels, including the molecular structure, nuclear and cellular organisation and genetic transmission, as well as at the level of populations, phylogeny and evolution.

Introduction

The central research topic of this theme is the organization of the genome, which is studied at all levels, including the molecular structure, nuclear and cellular organisation and genetic transmission, as well as at the level of populations, phylogeny and evolution. The major disciplines involved include; Genetics, Biosystematics, Genomics and Bioinformatics. The four are closely related with numerous connections and opportunities for co-operations within Theme 4 and with research groups in the other themes. 

Genetics is essential for understanding the regulation and evolutionary development of all processes in living organisms including growth, differentiation, maintenance and reproduction. Differences in genetic composition form the basis for (interspecific) biodiversity and provide the (mostly intraspecific) basis for plant breeding. Besides, organisms employ epigenetic systems to control gene expression in relation to their developmental programs and in response to changing environmental conditions. This phenomenon involves both transcriptional and post-transcriptional events and the important role of chromatin structure in this regard is increasingly recognized. 

The genetic dissection of biological traits makes use of induced and spontaneous mutations, for example with the controlled use of transposon - and transformation technology. The versatile world of molecular tools has provided an almost endless list of marker technologies using restriction enzymes, PCR, DNA chip and high-throughput sequencing technologies. Also, the construction of genetic maps has improved considerably by the strong contributions of statistical tools and powerful software and this has tremendously facilitated the study of genetic variation. The use of these genetic analyses has become one of the pillars of basic research and they are widely employed for the projects in this and all other themes of the graduate school. 

The science of systematics takes a comparative approach to the study of biodiversity and provides a framework for the other disciplines. To foster synergy with and between these disciplines and to contribute to an increased understanding of patterns of diversity, systematics research focuses in particular on phylogenetics, species-level systematics and molecular evolution. Research will focus both on domesticated and naturally occurring species. 

EPS research on Genome Biology describes genetic variation and aims to unravel genetic and evolutionary mechanisms, also with the purpose of providing materials and tools for the other three research themes and for plant breeding in general. The approaches, outlined above, enable a quick and thorough identification of biodiversity in natural populations and accessions used in plant breeding related to QTL for disease resistance and other traits. The accumulation of knowledge from the fields of bio-informatics, molecular biology, biosystematics, genetics and cytogenetics within EPS provides an excellent basis to perform top-level research. Theme 4 also provides several lines of applications which include various cooperations and contract research projects with breeding companies and genomics initiatives. 

The Theme Genome Biology is subdivided in the three following subthemes:
 

Subtheme 4a - The Structure and Organization of Genomes and Epigenetic Patterns

This subtheme deals with structural and organizational aspects of the genome, for example in relation to genetic position of important genes/traits, chromatin structure and epigenetic modifications of gene regulation and -expression. Major programmes are the sequencing of tomato chromosome 6, financed and organized by CBSG and EU-SOL, the sequencing of the potato genome by the Potato Genome Sequencing Consortium and the participation of an EPS team in the Medicago/ Red clover genome consortium. An STW Potato Genome project delivered many new tools and upgraded many existing ones. Marker technology, recently implemented by GS pyrosequencing complements AFLP technology as the method of choice for marker analysis. The ultimate goal will be the sequencing of regions of interest in segregating populations. 

The acquired expertise in sequencing technology and bioinformatics from the tomato and potato teams provides unique opportunities for comparing DNA sequences, and genetic and chromosome maps between tomato and potato, and other Solanaceae crop species. This information will also benefit introgressive hybridization programs for plant breeders and biodiversity studies. 

As to the cytogenetics, multicolour FISH (Fluorescence in situ Hybridisation) for simultaneously mapping annotated DNA sequences (mostly BACs) on chromosomes or extended DNA fibres, are powerful technologies to connect genetic and physical maps and to direct information of genetic co-linearity between genotypes of even related species, without the use of extensive genetic mapping and large scale sequencing. This technique together with species-specific DNA probes in combination with Genomic in situ Hybridization (GISH) allows the recognition of parental and recombinant chromosomes in hybrids and backcross derivatives. 

Molecular markers are widely used to locate genes on genetic maps and to analyze genetic diversity. The rapid developments in plant genome projects (Arabidopsis, rice, potato and tomato), comparative mapping and the dissection of complex traits using QTL (quantitative trait loci) mapping are studied and applied within EPS for intrinsic scientific reasons and as an aid to the projects as carried out in all (other) themes.

Traits can be added to plants by genetic modification. However, the current technology suffers from a lack of precision as transgenes integrate at random positions in the genome resulting in (epi)-genetic changes that may induce so-called position effects that can modulate the expression of transgenes. The development of homologous recombination strategies could improve this technology. Epigenetic research focuses on the relation between gene expression patterns and how they are influenced and controlled by packaging of genetic regions into chromatin units and modification of chromatin conformation (transcriptional regulation) and by selective degradation of specific transcripts (post-transcriptional regulation). This includes research on non-coding RNA and double-stranded RNA, which has recently been shown to be implicated in these processes. For understanding mechanisms of gene silencing in plants much can be learned from the mechanisms employed by plant viruses to suppress virus-induced gene silencing. 

Contributors to Subtheme 4a:

  • Dr. C.W. Bachem, Dr. H.J. van Eck, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Genetic and Physical mapping of the Potato Genome.
  • Prof. dr. J.H. de Jong (Genetics, WU): Cytogenetics, Chromosome Biology.
  • Prof.dr. T. Bisseling, Prof.dr. B.M. Mulder, Dr. J. Wellink, Dr. J.H. de Jong (Molecular Biology and Genetics, WU and AMOLF): Higher order organisation of chromatin and its function in development.
  • Dr. J.M. Kooter (Genetics, VU): RNA directed DNA methylation.
  • Prof.dr. J.A.M. Leunissen, Dr. R.C.H.J. van Ham (Bioinformatics, WU), Dr. A.D.J. van Dijk (Bioscience, PRI, WUR): Tools for efficient and reliable identification of single nucleotide polymorphisms (SNPs) in polyploid species, QualitySNP, HaploSNPer and Primer3Plus.
  • Dr. R.J.M. van der Ham (Bioinformatics, WU): Functional annotation and analysis of the tomato genome and Alternative Splicing (AS) in plants.
  • Dr. P. Fransz, Dr. M.E. Stam (Nuclear Organization, UvA): Regulation of the chromatin structure in Arabidopsis and maize.
  • Dr. E. van de Weg, Dr. P. Arens, Dr. C. Maliepaard (Plant Breeding, WUR): Crop genomics.

 

Subtheme 4b - Homologous Recombination

The research field of homologous recombination gains more and more interest in the plant biology community. The focus in the graduate school is on the processes of homologous recombination of transgenes introduced into the host plant by transformation, and the control of crossover recombination in meiotic prophase for heterozygosity, manipulation of crossover numbers and distributions, and the control of homeologous recombation. As to the former, the Leiden team (Hooijkaas and van der Zaal) studies how genes can be inserted most efficiently and precisely into the genome of plants. To this end the process of trans-kingdom DNA transfer from the bacterium Agrobacterium tumefaciens is studied in detail. It is known that genes that are introduced, integrate into the chromosome at a random position by a process of non-homologous recombination. The group also studies the process of gene targeting, whereby transgenes integrate at a position of choice in the genome by homologous recombination. To this end the factors which control non-homologous and homologous DNA-integration are determined, in order to be able to stimulate homologous and prevent non-homologous integration. In the future the group thus hopes not only to be able to insert transgenes at a preferred position in the genome of the plant, but also to be able to create specific mutations in the host genes of choice. 

Meiosis plays a central role in the transmission genetics of higher organisms. The behaviour of chromosomes during the two successive meiotic divisions determines the genetic composition of gametes, and thus that of the offspring individuals. The research teams of Nijmegen (Gerats) and Wageningen (de Jong) supported by research initiatives of Rijk Zwaan Breeding company analyze the genes involved in meiosis; such genes are identified and characterized by a combination of genetics and transcriptome analysis. Cloned (plant) meiotic genes can be used to modify meiosis in order to unravel their function and in doing so to alter the transmission genetics in (cultivated) plants. Mutants with a disturbed first or second meiotic cell division may produce unreduced gametes, which are applied in half tetrad analysis and sexual polyploidisation in plant breeding. The production of seeds without fertilization (apomixis) can occur due to genetic changes in meiosis and is studied because of its fundamental and applied aspects. 

Alternative approaches of fixing superior heterozygous hybrids by reducing meiotic variability are being worked out in reverse breeding technologies, which are based on post-transcriptional silencing of genes essential in crossover recombination. Both Arabidopsis as well as crop species are being tested for optimizing this technology for plant breeding. 

Contributors to Subtheme 4b:

  • Prof.dr. T. Gerats, Dr. J.L. Peters (Plant Genetics, RU): Genes involved in meiotic recombination.
  • Dr. B.J. van der Zaal, Prof.dr. P.J.J. Hooykaas (Molecular and Developmental Genetics, LU): Novel tools for plant molecular genetics.
  • Prof. dr. J.H. de Jong: manipulating meiotic genes for reverse breeding and homoeologous technologies in crop plants.

 

Subtheme 4c - Biosystematics and Biodiversity

Biodiversity is being described, analyzed and explained by reconstructing the patterns of evolutionary relationships and by studying the evolutionary processes that cause these patterns. Genome plasticity is basal to evolution and to biodiversity in nature. In plant breeding only a fraction of naturally occurring biodiversity has been exploited so far. The use of molecular genetic tools, applying both neutral and non-neutral markers, allows gaining a much better insight into the variation and genetic relationships within and between both wild and cultivated species as well as in evolutionary processes in general. New technologies allow the application of molecular genetic techniques to both living and dried (herbarium) material of plants and microorganisms, which significantly expands the possibilities for biosystematic research. 

Within EPS biosystematic research serves the following needs:

1.   Getting insight into taxonomic and genetic diversity among crop plants and their wild relatives as well as other plant groups of special evolutionary or systematic interest, allowing a better understanding of evolutionary processes creating biodiversity and the value and potential use of biodiversity, and a more efficient management of this diversity both in collections and in situ. The same approach is applied to understanding the adaptation of plant pathogens from wild hosts to agricultural crops and to understand the co-evolution of plants and associated insects. This evolutionary phenomenon is central to understanding host specificity and specialization in plant pathogenic fungi, as well as processes of co-evolution.

2.   Exploiting phylogenetic relationships and natural biodiversity among relatives of crop plants for breeding towards valuable traits such as disease resistance and plant quality. Phylogenetic analysis of multi-allelic DNA data also may reveal clusters of organisms that are likely candidates for bio-exploitation.

3.   Exploiting the natural biodiversity of plant-related (micro)-organisms to enable development of sustainable crop protection with beneficial (micro)-organisms.

4.   Development of new research tools and technologies to select efficient species identifiers (DNA level) and to study the origin of genome plasticity in crop plants and their wild relatives, as well as in other plant groups of evolutionary or biosystematic interest and in microorganisms. These data have proven valuable for the development of identification kits for specific species, populations or cultivars. This line of research is also central to the development of early detection disease protocols, and for managing free international trade of agricultural produce via qualified quarantine decisions. 

Obtaining a deeper insight in evolutionary patterns and biodiversity of the starting material for breeding and basic research related to the other themes is of enormous importance. The availability of a wealth of dried plant material in the Wageningen branch of the National Herbarium of the Netherlands (which will become part of the National Centre for Biodiversity) offers new opportunities to expand the frontiers of Genome Biology research. This is further complemented by the availability of the very rich genebank collections of the WUR Centre for Genetic Resources, the Netherlands, including the mutually complementary Solanaceae collections in Nijmegen and Wageningen. A collaboration with the CBS Fungal Biodiversity Centre in Utrecht, which hosts one of the largest living filamentous fungal and yeast microorganism collections in the world, also creates exciting and unique possibilities in biosystematics and biodiversity research. 

Contributors to Subtheme 4c:

 

  • Prof. dr. E. Schranz,  Dr. R.G. van den Berg, Dr. L.W. Chatrou, DR. F.T. Bakker (Biosystematics, WU): The evolutionary history (phylogeny) of polyploid plants and their diploid relatives .
  • Dr. F.A. Krens, Dr. J.M. van Tuyl, Prof.dr. E. Jacobsen, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Exploiting genetic modification to enlarge genetic variation in crop plants.
  • Prof.dr. P.W. Crous (Phytopathology, WU): Host specificity and speciation in the Dothideomycetes. 

      

Graduate School Experimental Plant Sciences