Wageningen UR recently invested in optical mapping equipment for DNA analyses enabling it and its partner research institutions to map the full DNA sequence of various plants better and faster, enhancing the accuracy of crop breeding.
The acquisition of advanced equipment for the optical mapping of plant genomes will give research at Wageningen UR and other Dutch knowledge institutes a major boost, allowing breeding programmes to predict the ideal varieties for crossing and the characteristics of future mature plants from seedlings with far greater precision than before.
Precision breeding
Using the new analysis equipment, scientists can map the genome – the collection of all the hereditary properties of a living organism – more quickly and accurately than before. This information enables precision breeding as each component of the billions of building blocks in a genome can be identified. Sometimes clear differences in the characteristics of crops, such as red or yellow tomatoes, depend on subtle deviations in the genome. The genome analysis system can deal with complex genomes, including several economically important crops such as the tomato and potato. Other crops that are still waiting to be analysed are the banana, melon and lettuce.
Genome analysis is the field of Gabino Sanchez Perez, head of the Applied Bioinformatics department, which is where research into the genomes of cropsat Wageningen UR is focused. “The existing reference maps of many genomes still contain multiple uncertainties, gaps and duplications. The new equipment allows us to make high quality genome maps and, even more importantly, unravel sections of the genome that are related to valuable features, such as the content of healthy substances.” In addition, there are complex plant genomes for which standard equipment cannot provide a clear picture – this includes crops which have a lot of repetitive stretches of DNA with many variations. “The new system lets us analyse these previously ‘inaccessible’ genomes; and not just individual genomes, but entire populations.”
Wild tomato sequenced in ‘no time’
The group already has the first results of an analysis of the comprehensive DNA of a wild relative of the tomato. “This took two weeks,” reports Sanchez-Perez. “With the old technology it would have cost us two months.” Several other groups within Wageningen UR are now building up expertise with the technology, especially in the fields of bioinformatics, biosystematics and genetics.
The Irys equipment will initially be used to improve the various genome maps of the tomato. This will have an immediate positive effect on the speed of tomato breeding. It will, for example, allow tomato plants that also deliver high food yields in poor growing conditions to be developed more quickly.
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