DNA technique measures suitability of soil for onion crops

Nematodes, such as the stem nematode, and fungi, such as white rot, are particularly harmful for onion crops in the Netherlands: they cause rot. Soil samples are investigated to detect this; a labour-intensive and expensive operation. Together with the Laboratory for Nematology (University of Wageningen) the company Blgg has developed a molecular technique to detect the stem nematode and white rot in soil samples.

Agricultural laboratory Blgg will start using the new system in November 2005. The system quickly and accurately measures soil samples at the molecular level. In a series of comparative trials, the molecular test had a higher detection rate than the traditional microscopic investigation for both the stem nematode and onion white rot.

Each year thousands of soil samples are investigated for their suitability for onion crops. They are examined for the presence of the nematode Ditylenchus dipsaci (the stem nematode) and the fungus Sclerotium cepivorum (onion white rot). For years this has been done visually under the microscope; a specialised and labour-intensive process.

Blgg director Henri Hekman had been looking for a more accurate, faster and cheaper method for some time. He came into contact with Wageningen researcher Hans Helder who, with funding from Technology Foundation STW, was compiling a DNA database of all nematode species in the Netherlands. This database, together with a method for the easy extraction of DNA from nematodes, forms the basis for the technique developed to detect harmful nematodes. The Technology Foundation STW filed a patent for this technology, and this patent was recently transferred to Blgg.

In close cooperation with the Laboratory for Nematology, Blgg managed to successfully combine the fundamental knowledge from the patent with state-of-the-art laboratory practice. The result is a practical test that conclusively demonstrates the presence of both the stem nematode and onion white rot.

Both parties are continuing to work on the development of molecular tests to detect other plant pathogenic nematode species in the soil. With this new method, the analysis of soil samples under the microscope will be made superfluous. It will soon be possible to detect nematodes extracted from the soil samples according to their individual DNA ’barcode’. The grower can then decide whether or not he wants to grow onions on the plot of land tested.