Weed genes help boost crop resilience

Plant geneticist Susan McCouch sees weeds as part of the solution for adapting crops to thrive in hotter climates.

Susan McCouch
Susan McCouch

Photo Credit: Robert Baker, Cornell University

Rice is one of the top three grains consumed worldwide, but global warming is threatening the crop’s ability to continue thriving in its current growing areas. Among the potential solutions? Weeds.

Weeds are unlikely heroes of biodiversity that could benefit modern, cultivated plant varieties in the face of climate change, says Susan McCouch, professor of plant breeding and genetics at Cornell University and head of the Susan R. McCouch Rice Genetics Lab. She’s counting on these diverse ancestors to possess natural traits that can help rice and other food crops in the quest for resilience to climate variations.

Under climate change, we are breeding [crops] in a sense with a completely new concept in mind.”
—Susan McCouch

Seeds of wild crops and landraces (ancient plant species that adapted to their local environments) are readily accessible in 1,700 gene banks throughout the world, yet “they are not used to their full potential in plant breeding,” says McCouch. That’s mostly because not much is known about the traits the seeds possess—such as drought and pest resistance—and how the seeds respond to certain weather conditions.

“There are still vast reserves of valuable genes and traits hidden in low-performing wild ancestors and long-forgotten early farmer varieties of rice that can be coaxed out of these ancient plants by crossing them with higher-yielding modern relatives,” she adds. “These crosses give rise to families of offspring that carry a myriad of new possibilities for the future.”

Smart rice

To survive in the coming highly variable environment, crops will need to sense and respond to their individual environments. “That’s a lot different than breeding a plant for conditions we know it will encounter, when conditions are fixed,” says McCouch.

Researchers have already made significant progress breeding wheat—another one of the top three grains—with its wild varieties; wheat has a large genome that allows breeders to incorporate more wild traits that better withstand heat and drought. Now, innovations in biology and breeding have made it possible to direct more focus on rice too.

Researchers found a trait in an ancient variety of wild rice, for example, that senses when the plant is underwater and tolerates being submerged while still growing, says McCouch. They identified the gene and then bred that trait into a line of rice now being used in Bangladesh. While most rice varieties can withstand only three or four days of being submerged, this rice can virtually hold its breath for two weeks and survive oxygen starvation, an important quality for handling the unpredictable rainfall and more frequent flooding expected with climate change.

“The gene confers the ability in the rice plant to basically stop growing under flooding so it doesn’t use up what little oxygen it has. When the flood subsides, it will continue growing,” says McCouch.

The Submergence 1 gene, as it is called, has already saved thousands of acres of rice in South Asia from catastrophe since it was introduced in 2009, according to the International Rice Research Institute (IRRI).

Jumping into the gene pool

In the future, researchers will continue to add traits to core varieties of rice, “much like you put ornaments on a tree,” says McCouch, but the breeding time could accelerate with better information. When more becomes known about the characteristics of all the wild and ancient varieties of seeds in gene banks, future breeding programs will have the ability to move hundreds of genes at once from wild plants to modern cultivars, a groundbreaking concept, she says.

To access the needed information about the 7 million samples of crop varieties and wild relatives in the world’s gene banks, researchers are now translating and organizing each gene bank and putting the data in a master directory. McCouch is currently at work on an international effort that includes 69 organizations seeking to identify what traits or genes or genomic composition is contained by the plant material in each gene bank. The project, called DivSeek, is aiming to assess and identify new sources of genetic variation to enhance productivity, sustainability and resilience of crop varieties to adapt to climate change.

Ultimately dozens of crops will likely be improved by genetic variation from wild ancestors, particularly in countries hardest hit by climate change, says McCouch. In East and West Africa, as well as Latin America, breeders are looking for new sources of genes to boost drought tolerance in traditional varieties of corn (maize), and they are turning to ancient varieties of millet and sorghum to replace corn in regions where drought is too prolonged and soils are too poor to grow corn. In Africa and Latin America, where cassava is a staple food among the poor, McCouch says breeders are seeking all kinds of exotic species that could have genes to help cassava become more disease and pest resistant and increase its physiological resistance to post-harvest deterioration.

For beans, wild ancestors and ancient landraces likely possess traits that will help modern crops grow in shorter time frames, such as maturing earlier in the season, and be more tolerant of extremes in temperature, pests and disease. For peanuts, breeders in Latin America and Africa are looking to wild varieties and ancient landraces not only for new sources of heat tolerance but also for resistance to the human carcinogen aflatoxin, which is more likely to contaminate crops under hot and dry conditions.

Technology transfers

Traits originally identified in wild relatives or early landraces will find their way into food production in a few different ways, says McCouch. Submergence tolerance in rice, for example, can be introduced through cross-breeding and marker-assisted selection (using a marker linked to the trait). Traits with more complexity may be introduced from wild relatives and landraces using traditional crossing and a more complicated form of marker-assisted selection known as genome-wide prediction, or genomic selection. This approach is fairly new and is just beginning to be used in public breeding programs, although it is more common in the private sector, particularly for corn.

When wild ancestors are used as parents in crossing and selection, the process is essentially that of traditional breeding, assisted by the use of molecular markers, and requires no special biosafety testing or labeling. “This will continue to be a common use of the materials that DivSeek is helping to document and make more accessible,” says McCouch.

In a process still under development, a breeder may choose genome editing technology to change the sequence of a particular gene in a modern variety to match the gene from a wild species in order to confer a trait from the wild plant, such as disease resistance. Another option is cloning a gene from a wild species and introducing it in a modern crop using transgenic technology (biotechnology), says McCouch, but that approach would require years of biosafety testing.

Ultimately, global warming may prove to be an unexpected stimulus for a huge wave of advancements in plant breeding that haven’t been needed until now, says McCouch.

“Climate change is introducing completely new, unpredictable weather patterns in which we have rain during the dry season and drought during the rainy season and flood season,” she says. “So, under climate change, we are breeding in a sense with a completely new concept in mind.”

Lisa Palmer

Lisa Palmer is a freelance journalist and writer based in Maryland. She reports on food, the environment and sustainable business for publications such as Slate, Scientific American, Nature, Yale e360, and The Guardian. She is a fellow for socio-environmental understanding at the National Socio-Environmental Synthesis Center (www.sesync.org) in Annapolis, Md.

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