Where the wild beans grow

Team uncover species rich in genetic diversity

If you think genetics is staid, spend 30 minutes with Professor Paul Gepts. His love of beans, crop evolution and structural genomics is so contagious, you, too, will be wild beanspouring over the wild and domesticated beans spread across his desk like gems.

“See, now this one is a wild species,” he says, holding a bean no bigger than a freckle in the palm of his hand. “They’re much smaller than the domesticated variety.”

Small, yes, but don’t be fooled by size. The wild species Gepts and his colleagues gather from all corners of the world hold the key to cultivating crops that can feed an expanding population in the face of accelerating changes in climate and pathogens: genetic diversity.

Why? Let’s take a quick historical look at agriculture.

Domestication is a genetic selection process exerted by humans to adapt wild plants and animals to cultivation and herding. Scholars   debate whether humans did it accidentally or on purpose, but on one matter most all agree: Domestication and the agriculture that followed  changed the course of human history.

Starting some 10,000 years ago, domestication gave us major crops that were easier to cultivate and more appealing to eat. Over several hundreds of years, for example, teosinte – the wild precursor to maize – evolved from bushy, branched plants of hard, tiny spikes with just two rows of kernels to taller, straighter stalks bearing cobs with several rows of plump kernels. While we learned to plant and harvest and herd our food, we turned from hunters and gatherers to more sedentary folks in villages and cities. With the surplus of food resulting from agriculture, we took on other endeavors like making pottery and organizing governments and waging war.

Thousands of years of cultivation produced many changes to our crops, many of them improvements. Our beans are bigger, our maize is sweeter, our wheat is plentiful and nutritious. But in one important area, modern crops are vastly impoverished compared to their wild kin - genetic diversity. There are several reasons for this – from the domestication process itself to the narrowing of the gene pool as breeders select for the finest traits.

The consequences of genetic uniformity can be dire. The most famous example was the potato famine in Ireland in mid-19th century. Ireland’s potato crop was genetically uniform (and a diet staple), so when a fungal disease took hold it destroyed nine-tenth of the country’s potatoes and one million people died of starvation. It happened with coffee in southern Asia in the nineteenth century and maize in the America in the 1970s.

What’s the antidote? Genetic diversity of germplasm, the raw ingredient breeders need to develop high quality crops that can resist constantly evolving pests, diseases and environmental stresses.

Germplasm is living tissue from which new plants can be grown. It can be a seed or another plant part – a leaf, a piece of stem, pollen or even just a few cells that can be turned into a whole plant. Germplasm contains the information for a species’ genetic makeup, a valuable natural resource of plant diversity. Sexually compatible wild species and landraces – ancestral varieties of crop species - are the key to genetic diversity, but the amount of land where plants grow wild continues to shrink and many plant species and varieties are disappearing. That’s why the plant sciences community has developed conservation programs to gather, preserve, evaluate, catalogue and distribute germplasm for people all over the world to use.

That brings us back to Gepts and the beans here in the palm of his hand.

Two Domestications

Gepts has emptied a jar of assorted dried beans on his desk so a visitor can take a closer look at their diversity - round ones, skinny ones, black ones, green ones. Some are so brightly colored, they look more like marbles than a protein-packed food.

“In Bolivia, they use this bean for just that purpose – as a toy marble,” says Gepts, holding up a mottled purple beauty.

This collection of beans is so varied, it’s hard to believe they all came from the same source. Recent discoveries from the Gepts lab are proving that, in fact, they did not.

“We’ve learned there were at least two bean domestications,” Gepts explains.

That’s big news for plant breeders because making crosses with beans that share the same ancestor achieves faster, better results. Gepts is now able to tell breeders which beans come from which common ancestor.

“Beans domesticated in the Andean region are elongated, like these,” he says, selecting a few kidney beans from the assortment. “These navy, black and pinto beans are examples of beans domesticated in Mexico.”

How does Gepts make those determinations? It takes work in both the field and the lab. First, he and his colleagues comb the countryside of South and Central America and Mexico, gathering wild species of beans. Back in the lab, Gepts examines the wild populations of beans looking for DNA sequences or seed proteins found in domesticated  beans. By looking for those same markers in wild beans, he is able to tell which populations of beans share an ancestry with domestic varieties. So far he has found two areas where domesticated beans can be traced – an Andean region between south Peru and northwestern Argentina and the state of Jalisco in Mexico.

By tracing the spread of beans through the Americas, Gepts has also been able to show that although beans were domesticated later than maize, they reached the United States about the same time.

“Which makes sense, when you consider how beans and corn make such a nice, nutritious combination,” Gepts says.

The Gepts lab also develops genetic markers that correspond to resistance against pathogens and other adverse conditions. Plant breeders use DNA markers to help select parents that will pass the desired traits to their offspring. Breeding plants using DNA-assisted selection dramatically reduces the time required to develop new varieties.

It’s easy to see why the adventurer in Gepts loves his wild-bean hunting expeditions, driving over hill and dale in search of species that could make the difference between scarcity and abundance in our fast growing world. Lab work, he says, can be just as exciting.

DNA in the Court

Take, for example, DNA fingerprinting – a process of analyzing DNA fragments to identify the unique genetic makeup of an individual plant or animal. Gepts made headlines last year when the Board of Patent Appeals and Interferences cited his DNA research as the definitive evidence in a controversial intellectual property dispute over a common yellow bean.

The story begins in the 1990s when a Colorado man purchased some beans, similar to kidney beans, in a market in Mexico. He grew the beans for several seasons and then claimed to have developed a new field bean variety with a distinctive pale yellow seed color. He called it “Enola” and filed a patent application.

1n 1999, the United States Patent and Trademark Office granted him a 20-year patent protecting the Enola variety. The legality of the patent was challenged in court amid international allegations that the case was a prime example of biopiracy and abuse of intellectual property rights. Gepts and colleagues applied DNA technology to genetically determine whether the bean was truly a new variety or just a new generation of an existing variety.

“The analysis showed the Enola bean was produced through direct selection of pre-existing yellow-bean varieties from Mexico, most likely a bean known as Azufrado Peruano 87,” Gepts says. “The judge cited the DNA fingerprinting as indisputable evidence in the case.”

How’s that for practical application? But there’s much more. Genetics is also helping alleviate hunger in East Africa. Gepts is the lead scientist for a project called the African Bean Consortium-Kirkhouse Trust which helps breeders in East Africa analyze plant DNA linked to disease-resistance genes, the better to increase bean production and the sustenance and revenue that can provide. Financed by a British charity, the project provides local breeders the training and resources they need to improve the production of beans, which provide up to 40 percent of the protein intake in Africa.

Besides beans, Gepts’ lab also studies peppers, wild maize, amaranth and agaves. Sure, the last two crops are not household names in America (amaranth is an herb genus and agave is a succulent plant), but the four crops provide a comparative dimension to studies of crop evolution because they encompass a wide range of reproductive systems, life histories, and human uses, Gepts says.

Beans are still Gepts’ baby, with more than 30 years devoted to their research.

“They are such an important part of the human diet, especially in developing countries, and provide a wide range of health benefits to us all,” Gepts says.

And on top of all that, they are pretty.