A Tool Kit to Help Scientists Find the Ultimate Chickpea

When you open a can of chickpeas and fish out the nutty, savory little beans, you’re partaking in a history that began around 10,000 years ago. The modern chickpea’s ancestor, a wild Middle Eastern plant that likely had tiny, hard seeds, was cultivated by humans around the same time as wheat and barley, and began to evolve as early farmers selected plants whose seeds were larger and more succulent. Archaeologists have even found what appear to be domesticated chickpeas buried beneath Jericho in the West Bank, so deep that they would have been grown even before the inhabitants of one of history’s longest occupied cities began to make pottery.

The humble chickpea has had a somewhat rocky road to its present popularity, however, suggests a new study published last week in Nature that sequences the genomes of more than 3,000 examples, making it one of the largest plant genome sequencing efforts ever completed.

“I’m truly excited to see what else will be uncovered from this massive resource,” said Patrick Edger, a professor of horticulture at Michigan State University who was not involved in the study.

The researchers now believe that after chickpeas were first domesticated in Turkey’s southeastern Anatolia region, their cultivation may have stagnated for millenniums. The result was a genetic bottleneck that makes all chickpeas today descendants of a relatively small group from a thousand years ago. What’s more, the modern varieties grown by most farmers are low in genetic diversity, which means that they are at risk of failing under the stress of climate change. By mapping the legume’s genetic makeup in such rich detail, the scientists hope to make it easier for plant breeders — who develop new kinds of crops — to bring diversity back into the chickpea’s genes, giving it a flexible tool kit to survive drought, flooding and diseases.

While hummus may have become ubiquitous in American grocery stores only in the past 15 years, chickpeas have long been a staple crop in the developing world, said Rajeev Varshney, a research program director at the International Crops Research Institute for the Semi-Arid Tropics in Hyderabad, India, as well as a professor at Murdoch University in Australia and an author of the new paper.

India is the world’s largest producer of chickpeas, growing more than 10 million metric tons in 2019, as well as one of the largest importers.

But chickpeas’ status as a developing world crop has meant that they have not received as much attention from breeders as commodities like corn, Dr. Varshney said. Chickpea farmers grow a handful of varieties that have been improved over the years without, for the most part, the benefit of genetic information that might give breeders more control over what traits the beans will have.

In the present study, the researchers sequenced the DNA of 3,366 samples of chickpeas, ranging from wild relatives of the crop to modern stock. They identified a set of genes the plants had in common, as well as a wide variety of others, including some that scientists had not discovered before. These common genes are likely to handle the basic traits that all the plants share, while the unique genes, on the other hand, may encode special abilities like resistance to drought and protection from diseases. Going further, the researchers flagged sets of genes, some found in older varieties, that may prove helpful to modern chickpeas.

The way plant breeding usually works, Dr. Varshney said, is that once a genetic trait, like resistance to a fungal disease, is brought into a given variety, all the individuals will have the exact same tool to block infection. That means that if a form of the disease evolves that can get past that defense, the results could be disastrous.

“The whole crop — the whole field — will be wiped out,” Dr. Varshney said.

Using the gene sets identified in this study, and making sure that many different sets are represented in chickpea populations, could be a protection against crop failures, he hopes. And he said that breeding more resilient chickpeas is a process that should start now, using genetic information to speed the process: If farmers wake up one day and find they need a chickpea that can thrive at 104 degrees Fahrenheit, “this would be very challenging,” said Dr. Varshney. “It needs to be incremental.”

The study also peers into what the chickpea’s genes can tell us about its travels. The bean left the Middle East along independent routes to the Indian subcontinent and the land that borders the Mediterranean. And although patterns in its genes suggest a gradual decline in popularity for thousands of years, the scientists are not sure why that might have been.

“Maybe farmers thought, this is not useful,” Dr. Varshney said.

That changed about 400 years ago, when, according to the data, humans seem to have rediscovered the wonders of the chickpea, for reasons unclear to the researchers. Next time you dunk pita in hummus, you can be glad they did.