Theme 4: Genome Plasticity
Genetic information plays a pivotal role in the growth and development of all organisms, including plants. Differences in genetic composition lead to bio-diversity in nature, and provide the basis for plant breeding. Genetic variation is present at the level of individual genes and at the level of the organization of genes in chromosomal domains or whole chromosomes. Genetic variation not only affects the properties of the gene products, but also the regulation of genes.
Molecular genetic techniques have facilitated the study of genetic variation tremendously, and have allowed the construction of detailed genetic maps of many plant species. The transmission of genetic information by sexual and asexual mechanisms provided the basis for the genetic dissection of biological phenomena in basic and applied research, including the phenomena studied in Themes 1 to 3. Detailed knowledge on the genetic transmission processes is therefore essential. Furthermore, such knowledge is required for the deliberate modification of these processes in several applications, including plant breeding strategies. The study of meiosis therefore takes a central place in this theme. The application of genetic transformation as a tool to analyse gene-function and as a way to modify the genetic composition of plants has made transformation technology an important technique for which more basic information on the mechanism of DNA integration and stability of the transgenes is required.
Since single gene controlled properties are accessible for molecular cloning when their genetic identity has been established, it is important to know the position of loci involved in qualitative and quantitative traits on the genetic map. The identification of genetic markers linked to important traits can also be used to optimise the selection for such traits. The full exploitation of genetic data requires an efficient use and development of mapping software and data bases embedded in international collaborations. Genetic instability generated by transposable elements can be used to isolate specific genes.
Bio-diversity research integrates taxonomic and genetic tools which are available within EPS and is applied on relatives of important crop plants such as potato.
EPS research on genome plasticity describes genetic variation and unravels genetic mechanisms with the purpose to provide materials and tools for the other three research themes and plant breeding. The availability of specialists on molecular -, mathematical - and cyto-genetics within EPS provides the basis to perform this research at an excellent level.
The three subthemes that can be distinguished are related and make use of similar technical approaches.
Subtheme 4a:
The Structure and Organisation of Genomes
Genetic information is assembled into chromosomes, which consist of structural elements such as centromeres and telomeres together with repetitive non-coding sequences. The amount of this non-coding DNA shows a large variation between plant species. The consequences of the position of genes and repetitive sequences is not well understood. The study of the way genetic information is physically located and assembled within the chromosomes and the behaviour of chromosomes has been strongly promoted by the combination of molecular techniques with cytogenetics. The integrated molecular-cytogenetic approach to study the structure and organisation of chromosomes and chromosomal differences between related species (witin the genera Alstroemeria, Solanum and Lycopersicon) is an important EPS research issue. By using FISH (Fluorescence In Situ Hybridisation) applied on pachytene chromosomes or on extended DNA fibers, relatively small DNA fragments, such as TDNA insertions, can be recognised on chromosomes. Species specific DNA probes, in combination with Genomic In Situ Hybridisation (GISH) allows the recognition of parental and recombinant chromosomes in hybrids and introgression lines. Molecular markers are widely used to locate genes and to analyse 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.
Subtheme 4b:
Meiotic Recombination
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 of the next generation. The successive steps of meiosis are studied by various complementary techniques. Genes involved in meiosis are identified and characterized by three approaches:
- a reverse genetics approach is followed by which subcellular structures that mediate meiotic chromosome pairing and recombination are isolated and analysed with respect to their protein composition; antibodies against these components are then used to isolate the genes involved
- the strong evolutionary conservation of the meiotic process allows isolation of meiotic genes of plants through genes of model organisms such as yeast, fungi and mammals
- new techniques such as cDNA/AFLP fingerprinting allows detection and isolation of RNA sequences coding for genes involved in the meiotic process during different developmental stages of pollen mother cells into microspores.
The detailed analysis of the regulation and function of meiotic genes requires a combination of molecular genetic, biochemical and immunocytochemical techniques. How the various meiotic events at the DNA-, chromosomal and cellular level, such as the recognition of homology of DNA-sequences and chromosomes (homologous vs. homoeologous chromosomes) and the initiation and completion of chromosome pairing and recombination, are accomplished and coordinated are important scientific questions to answer. 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. Naturally occurring mutants with a disturbed first and second meiotic cell division provide a mechanism to generate unreduced gametes, which are applied in half tetrad analysis and sexual polyploidisation in plant breeding.
Subtheme 4c:
Genetic Modification
The combination or introduction of genetic information in plants of two parents was until recently only possible when the two parents were related. This situation has been changed by:
- The use of flower biology and cell genetics (e.g. protoplast fusion and ovule culture) by which the range of species from which genetic information could be combined has been extended.
- The asexual introduction of cloned genes isolated from all kind of organisms using genetic modification.
Through interspecies hybrids obtained with the first mentioned techniques important agricultural traits can be introduced into cultivated plants. Phenomena such as chromosomal instability, the fate of alien chromosomes and the introduction of alien traits can be followed with cytogenetics and molecular marker techniques. Species such as in Alstroemeria, potato and tomato have been shown to be useful models for this research.
Using transformation techniques specific cloned genes can be added to selected genotypes. The transformation of socalled recalcitrant crop species is very important for fundamental research and for plant breeding. In addition to the improvement of transformation technology, the mode of transfer, the targetting and tagging of genes, manipulation of expression levels and the stability of the transgenes in plants and their sexual offspring is studied. More knowledge about these different aspects related to genetic transformation is needed to improve its application in fundamental and applied research at the different organisation levels of the plant. The detailed study of the gene delivery apparatus of Agrobacterium, which is currently the most popular and versatile plant vector and its use for gene targetting is envisaged.
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