Comparative analysis of plant genome architecture

It is clear that there are close, family wide similarities between different crop species in both the genes (often with only allelic differences) and the gene order along chromosomes. However, there are extensive differences in both the type and organization of repetitive DNA, even between related species, which may be of importance for genome changes and the exchange of genes in both long (evolutionary) and short (plant breeding) time-scales. There is additional non-genic information in a genome, related to the methylation and coiling of sequences, and to the three-dimensional organization of these sequences in the nucleus. Highly repetitive DNA makes up the majority of most plant genomes. Some sequences, such as microsatellites, are similar in every organism, while other repeat units are specific to one species or a small group of species. Different sequences have characteristic genomic distribution, and most can be identified by their chromosomal distribution. Knowledge of the genome architecture - the organization and the nature of repetitive sequences, and the three-dimensional organization in the interphase nucleus - is likely to be helpful for applied research and plant breeding. There is little knowledge of why repetitive sequences have particular characteristic. Is the three-dimensional architecture of the nucleus important for functions? Do repetitive sequences put coding or regulatory sequences in particular nuclear position? Why are different sequences located at particular sites in the genome? A comprehensive and quantitative model is being constructed of the variable and constant parts of the plant genome. Such integrated models of large scale genome organization may be useful in learning the function of different components of the genome, and in evolutionary studies. Since repetitive DNA changes are frequent, perhaps one can learn more about which manipulations are possible in plant genomes by examining the changes already made between related species during evolution or during plant breeding programmes. (author). 36 refs