Finding useful genes: The search for the natural relatives of Cassava

The essence of genetic engineering is to transfer a useful gene from one organism to another. But where do they find useful genes? When scientists know what to look for — the identity of the exact gene they need — it doesn’t much matter from what kind of organism they actually extract the desired useful gene. The gene will function the same, regardless of the DNA background from which it is extracted. The novel Treasure Island is the same, no matter from which store you purchase it.

In many instances, however, scientists don’t know enough to identify exactly which genes they need to improve a particular trait. To increase yield or other useful traits, they must look to a crop’s wild relatives, and then try out candidate bits of DNA. With patience and a little luck, you fish out the DNA you need to achieve the improvement you seek.

Looking for the natural relatives of crop plants, then, can play an important role in improving crop yield and quality. A single poster at the International Botanical Congress, one of thousands, describes an instance of this sort of detective work. The poster describes a search by my colleague Washington University Professor Barbara Schaal and her graduate student Ken Olsen for the natural relatives of the tropical food crop Cassava. Their work serves as an excellent example of how we search for the natural relatives of key crops.

Cassava ranks sixth among crops in global production, and has been cultivated in tropical America for over 5,000 years. Introduced to Africa by the Portuguese before 1600, Cassava is today the primary carbohydrate source in all of Africa below the Sahara, and feeds 500 million people worldwide. The plant grows as a bush the size of a child, and is harvested for its tubers, which are fleshy underground stems (a potato is a tuber). You might be familiar with cassava as tapioca, but the vast majority of its consumers pound the tubers into flour. Because all cassava contains cyanide, the flour is typically treated with spit, introducing microbes to break down the cyanide.

To identify cassava’s natural relatives, it is necessary to know where the crop comes from, where it originated. Some researchers seeking cassava’s origins have argued that the domestic cassava used as a crop wsorldwide, Manihot esculenta, might be descended from the closely related species Manihot pruinosa. Most researchers have concluded instead that cassava originated from interbreeding among several Manihot esculenta subspecies in Mexico.

Schaal and Olsen have come to yet a different conclusion, solving the problem once and for all by bringing to bear powerful molecular approaches and by being very specific. They selected a single gene to examine closely, the gene G3pdh (encoding a key metabolic enzyme). They chose G3pdh because each cell has only one copy of this nuclear gene (Schaal is among the first to grasp the importance of this point), and these copies vary a lot from one subspecies to another. This makes it possible to decipher a unique sequence for each variety, and to uncover enough differences to tell the varieties apart. Good science is a matter of asking clear questions.

Schaal and Olsen examined G3pdh in a variety of Manihot subspecies. Olsen collected specimens of a South American wild subspecies of Manihot esculenta, with the romantic name of flabellifolia, on trips to Brazil in 1996 and 1997. Sequencing the DNA of the G3pdh gene from the different varieties of cassava over a period of two years (even with expensive computer-driven machines, it is time consuming, exacting work), Olsen was able to develop a phylogenetic tree, a sort of branching “family tree.” This is a very powerful approach, because it allows an objective assessment of just how the varieties are related to each other.

It immediately became apparent to Schaal and Olsen, looking at the DNA sequence data, that their tree ruled out a Mexican origin of cassava. The closest relative proved to be wild flabellifolia populations growing along the southern border of the Amazon basin.

These results can be expected to play an important role in the broader commercialization of cassava. Knowing where the key relatives are, both traditional breeders and bioengineers can begin to improve cassava. Bioengineers can look for DNA that might increase yield, provide resistance to the mosaic virus that threatens African cassava, improve protein content, and in other ways improve this crop, so critical to feeding much of the world’s poor.

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