Extracting DNA in an environmentally controlled laboratory where everyone wears a white coat may seem light-years away from the food crop experiments done by African farmers in their fields and around cooking fires. Yet these contrasting forms of science are now merging into an integrated process of crop improvement. While CIAT continues to promote farmer participatory research methods, it is also working to build African capacity for biotechnology research on beans and cassava.

Over the past 2 decades, nearly all of CIAT’s crop-related biotechnology for Africa has been carried out at our laboratory in Colombia or in advanced facilities in other countries. But since 1999 these arrangements have been evolving. Center scientists now conduct biotechnology research and training in a new laboratory at Uganda’s Kawanda Agricultural Research Institute.

In the past lack of equipment and training in sub-Saharan African and other regions of the developing world meant that microorganisms and plant tissues had to be shipped abroad for DNA extraction and analysis. This was slow and cumbersome, in part because of quarantine rules designed to prevent disease transmission. DNA itself, though, is not bulky and shipping it poses little or no biohazard.

CIAT and collaborating national scientists recently designed and tested a simple, inexpensive method for DNA extraction that gets around technical and financial hurdles involved in conventional procedures. In particular, it eliminates the use of two toxic organic compounds, phenol and chloroform, which African laboratories are generally not equipped to handle.

The new method, which is suitable for a range of organisms, including bacteria, fungi, and plants, allows for processing of more than 40 samples per day. Experiments have demonstrated that the resulting DNA is pure enough for most kinds of genetic analysis based on polymerase chain reaction (PCR), the standard means of DNA amplification.

Problem-solving Applications

One of the main activities at the Kawanda biotech lab has been DNA extraction from bean plants and from the Pythium spp. fungi that cause bean root rots. Genetic characterization of these fungi is of special importance to Africa. Beans are highly susceptible to attack a week or two after germination, especially when soil moisture is high. In parts of Western Kenya, root rots were such a big problem several years ago that farmers stopped growing beans.

Control of bean root rots depends, among other things, on correct diagnosis of the disease agent. Of the 100 or so species of Pythium, only nine—what CIAT plant pathologist Robin Buruchara calls the “bad guys”—have to date been confirmed as pathogenic.

Conventional genotyping of fungi is difficult because of the presence of many different organisms in soil samples. CIAT scientists have thus adopted DNA profiling to distinguish between species of Pythium. During 2001 and 2002, this allowed them to organize hundreds of samples (“isolates”) of the fungi from Kenya, Uganda, and Rwanda into 24 clusters. Isolates representing major groups are now being selected for DNA sequencing. Once easy-to-use diagnostic tests are developed for the worst offenders, bean breeders can use them to target research on host plant resistance.

CIAT scientists recently identified molecular markers that can assist in the fight against another major bean disease—angular leaf spot, caused by the fungus Phaeoisariopsis griseola. The markers distinguish between virulent and nonvirulent strains, as well as between Latin American and African strains. The biotechnology laboratory in Uganda has helped to validate the utility of these molecular tools under African conditions.

There has also been progress in combating cassava mosaic disease (CMD), the most damaging disease of the crop in Africa. CMD2 is a resistance gene in cassava that was identified 3 years ago by CIAT molecular geneticist Martin Fregene. Molecular markers for the gene have since been used to systematically screen crosses of resistant and susceptible cassava varieties. This has paved the way for major projects in which African producers and scientists will evaluate and improve resistant genotypes.

In Tanzania, for example, CIAT will work on a 6-year project with the agriculture ministry’s Department for Research and Development, the International Institute of Tropical Agriculture (IITA), and farmer groups. With funding from the Rockefeller Foundation, researchers will cross germplasm resistant to CMD, cassava bacterial blight, and green mite with preferred local varieties adapted to specific ecological niches. Training of national scientists in biotechnology and participatory methods will figure prominently in the project.

Given the large number of parent plants involved, the breeders will use molecular markers to quickly pare down candidate progeny to a workable, but still sizable number. These will then be evaluated in the appropriate ecological zones by scientists and cassava producers. “It’s a disservice to farmers not to give them a wide range of choices in view of the high risks they face,” says Fregene.

If all goes well, this project will showcase the rapid convergence of biotechnology and participatory methods in the concerted push for greater food security and rural incomes. For Fregene, improved cassava has enormous commercial potential for his native Africa. “I’m really excited about all this,” he says. “I always come to work with a spring in my step.”