The main objective is to clone genes that have been identified by mutational analysis. The combined efforts of many laboratories have resulted in a completed outline map of the A. thaliana genome. Detailed maps of morphological and biochemical markers such as RFLPs and RAPDs are available for much of the genome. Approximately 90% of the total A. thaliana genome lies within 0.8 Mbp of an RFLP marker and 50% is within 0.27 Mbp of an RAPD marker.
The genome of A. thaliana lacks much of the repetitive DNA that riddles the genomes of other angiosperms. It does, however, contain a complete set of genes controlling developmental patterns, metabolism, reactions to differing environmental cues and resistance to pests and pathogens.
Arabidopsis thaliana was the first angiospem for which the entire genome was sequenced (The Arabidopsis Genome Initiative, 2000). This achievement now presents unlimited opportunities to mine new knowledge for functional and metabolic processes controlled by the 25,000 genes present in A. thaliana (The Arabidopsis Genome Initiative, 2000; http://www.nature.com/genomics).
Information from the analysis of this genome is being entered into a publicly accessible database along with details of the proteins that are coded for further along the chain of nuclear and cellular processes (The Arabidopsis 2010 Project; http://nasc.nott.ac.uk/garnet/2010.html). Similarities between plant and animal biology are highlighted by the information obtained from the Arabidopsis projects (Leitch and Bennett, 2003). The boundaries between these sectors of biology largely disappear, and there are distinct possibilities that knowledge obtained from Arabidopsis can be applied to the study of animal and human genomes and to understanding their nuclear and cellular processes in health and disease (Sanderfoot and Raikel, 2001).
Major efforts are underway to complete physical maps of the A. thaliana genome consisting of the overlapping sets of cosmids and yeast artificial chromosomes (YACs). Two powerful tools have resulted from the analysis of mutants in A. thaliana and these complement map-based cloning methods. The first, T-DNA tagging, relies on using 'seed transformation' or the transformation of zygotic embryos with Agrobacterium which allows T-DNA to be used as a mutagen. This method has been used successfully in the isolation of several genes. It becomes of greater value as larger populations of transformed plants with low levels of somaclonal variation become available. The second approach is a method of genomic subtraction which is used to clone genes that correspond to deletion mutants. It has, for example, been used to clone the A. thaliana ga-1 locus.
The research knowledge obtained using A. thaliana can be of the 'pure-blue skies' nature on the one hand and very applied near market on the other. In an example of the former, Lolle et al. (2005) suggest that genetic information may be stored outside the chromosomal DNA as ancestral RNA sequence caches. Such a process would question a generally accepted and fundamental tenet of Mendelian genetics. At the other end of science, Montgomery et al. (2004) applied mechanical brushing techniques to A. thaliana plants in order to induce stress and consequent dwarfing. The successful development of mechanical dwarfing techniques offers opportunities to improve the robustness of seedling propagation in businesses raising transplants (Chapter 3), allowing greater probability of success when the plants reach their final field stations.
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