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Feature Story: Your Breakfast Could Be Going Extinct

a cacao pod

Your Breakfast Could Be Going Extinct

Livestock and crops are increasingly vulnerable due to "genetic homogeneity." Here's how scientists are trying to save what's on your plate.


What did you eat for breakfast this morning? Was anything in it genetically modified? The answer may surprise you: No matter how organic or “GMO-free” your meal was, unless it was hunted or gathered directly from nature, you almost certainly ate food that had been in some sense “genetically modified.” The term is often used to refer to organisms that have had genes transplanted from other species – corn plants engineered to carry bacterial genes that make a chemical toxic to pests, for instance. But in a broader sense, it can simply mean organisms whose genomes have been influenced by human activities – and that includes all food that comes from farms. Almost by definition, agriculture entails the manipulation of animal and plant genomes, sometimes with unexpected results.

if an entire group is both homogeneous and lacking in protective genes, it’s goodbye, group.

One such inadvertent outcome currently has a lot of farmers worried. Generations of culling and interbreeding have resulted in herds and crops with little genetic diversity. Those animals and plants are now vulnerable to threats such as pathogens and climate change. In the wild, genetic diversity – the material on which natural selection acts – usually ensures that some individuals are equipped to survive such threats; those individuals then thrive and reproduce. But if an entire group is both homogeneous and lacking in protective genes, it’s goodbye, group.

Agricultural scientists are now using genomics – and sometimes “genetic modification” in the bioengineering sense – to try to fix this problem. Here are some snapshots of their strategies for saving what’s on your plate:

Tropical fruits
In the wild, bananas are extraordinarily diverse – there are more than 1,000 varieties. But in American, European, and Chinese markets, there’s only one kind: the Cavendish. The banana industry has focused on this variety largely to keep costs down. (Exporting only a single kind is simpler than exporting several, because all the bananas ripen at roughly the same rate.) The trouble is that the Cavendish has no genetic resistance to a nasty soil fungus known as Tropical Race Four, which could decimate it, just as a different disease destroyed a previous banana variety that used to be a favorite of Western markets. Tropical Race Four has cut a swath through Asia in recent years, and producers fear it will eventually do similar damage on Central American plantations – much in the way that an invading Asian insect has lately been threatening the American citrus industry.  So scientists are trying to build a better Cavendish. Their work has yielded some promising, if early, results: In 2012, a group sequenced the genome of Musa acuminata, a relative of the Cavendish, and found several genes likely involved in pest resistance. They’re now expanding that research and making the data freely available.

Cow in a fieldMilk (and steak)
Last year, the agricultural division of the United Nations reported that an astonishing 22 percent of the world’s livestock breeds are at risk of extinction. Cattle farmers have long worried about diminishing genetic diversity, especially in the Holstein breed, the most popular type of dairy cattle. Individual cows have grown larger, but profits, in some cases, have grown smaller, because a bigger cow needs more food and other resources to stay healthy. (Put another way, “as you make progress to improve one trait, you often lose ground in another.”) Farmers worldwide are now implementing programs to keep their livestock more diverse. Genomics can help by allowing farmers to monitor diversity in their herds and by determining which animals have the most “net merit” based on many traits – such as disease resistance, meat quality, and milk production – that are influenced by variants found across the genome. But it is not a panacea in agriculture any more than it is in medicine. Environmental factors are still critical for raising healthy animals. Or, as Alison Van Eenennaam of the University of California, Davis puts it : “Good genetics will never overcome poor management.”

The United Nations reported that an astonishing 22 percent of the world’s livestock breeds are at risk of extinction.

Diagram of a Coffea arabicaCoffee
If your breakfast was accompanied by a cup of coffee, here’s hoping you savored it – because some scientists believe in the future a good cuppa joe will be harder to come by. Only two species of coffee (delicious Coffea arabica and less-delicious Coffea canephora) are widely farmed, and neither has a tremendous amount of diversity. It's difficult and time-consuming for coffee breeders to stir up the plant's gene pool with traditional cross-breeding techniques, because Coffea is a perennial; developing a new strain can take something like 25 years. And although scientists have made significant progress in bioengineering the coffee plant, that type of genetic modification still has such negative connotations that there's not much of a market for GM coffee at present. (Starbucks and other major coffee companies have explicitly said they it won't be exploring GMO as an option.)

But coffee scientists need to figure out another strategy, and fast. A fungal outbreak has been ravaging Central American coffee farms over the last year, and climate change could eventually kill off what's left by raising temperatures in the countries where coffee is grown. (Even an average temperature increase of one degree has a negative effect on taste; more, and plants may not grow at all.) It's possible in theory that Coffea could adapt to the higher temperatures – but none of the common farmed strains carries a heat-tolerance gene.

there are more than 100 other species of coffee in the wild. Some of them are bizarre

The good news is, there are more than 100 other species of coffee in the wild. Some of them are bizarre – plants with coffee beans the size of a thumbnail, plants that are naturally caffeine-free, plants that make a drink that smells like coffee but tastes like battery acid. Because one of these species may have a heat-tolerance gene, they have suddenly become valuable. So the coffee industry is funding a major effort to track down and genetically characterize the wild forms of the plant, and to reboot C. arabica with genetically assisted forms of cross-breeding. (It is looking to the chocolate industry, which faces a similar problem, as a model.) In a few years – the time it takes for an infant coffee plant to reach fruit-bearing maturity – the industry should know whether its new plan has successfully caused genetic diversity to perk up.

Mary Carmichael is a science writer based in Boston, Massachusetts.


(1) Genetic Diversity in Farm Animals - A Review. PubMed.

(2) An Introduction to Coffee Genetics. The Specialty Coffee Chronicle.

(3) Bananas and Genetic Engineering: Past, Present and Future. Los Angeles Times.