New genetic tricks for boosting crop yield take clues from ancient farmers

When farmers in ancient times harvested their crops, some saved the seeds produced by the best performing plants and sowed them the following year. Gradually, this selection led to better and better results, such as increasing the size and number of kernels of maize—traits that helped pave the path to modern corn. Now, a team led by researchers in China has identified a single gene behind this crucial productivity boost in maize and linked it to early improvements in rice harvests as well.

“I’ve never seen anything really like this before,” says Matthew Paul, a plant geneticist at Rothamsted Research, who was not involved with the new study. And the discovery suggests it may be possible to improve other cereal crops, such as wheat, by just changing a single gene. “To find something like this that can move the needle is intriguing,” says Jeff Habben, a plant physiologist with Corteva, a company that breeds new varieties of maize and other crops.

Grain yield is typically controlled by a complex set of many genes, which makes it hard for traditional plant breeders to make more than incremental gains each year. In 2004, maize geneticist and breeder Li Jiangsheng of China Agricultural University (CAU) began to explore the genetics of teosinte, the puny wild ancestor of maize, which early farmers domesticated and bred to create edible corn. One big change: Whereas teosinte has just two rows of kernels, modern maize has more than a dozen. To understand what changed genetically, Li and colleagues spent years creating an experimental intermediate type of maize that has six rows.

By mapping genetic markers, Li and an even larger team identified a gene that influences the number of rows of kernels in this lab-grown corn. They called the gene KRN2, for kernel row number. Two kinds of experiments demonstrated KRN2’s effects. When researchers increased the gene’s activity, plants produced cobs with two fewer rows of kernels. In contrast, when they knocked out, ordisabled, the gene, plants produced cobs with two additional rows. In field tests, knocking out the gene increased the weight of the corn harvest by 10% with no obvious undesirable side effects, the team reports today in Science.

The researchers say their studies suggest ancient maize farmers had, in effect, selected for genetic changes in a region of DNA that puts a brake on KRN2’s activity; those changes eased the brake, thereby increasing kernel rows. And the team discovered ancient rice farmers might also have exploited a similar genetic mechanism. Yang Xiaohong, a molecular biologist at CAU, helped show that a very similar gene, which they call OsKRN2, has the same function in rice, influencing the number of panicles—the small seed-bearing branches. “When we got the results in the fall of 2020, we were excited,” she says. Field tests showed knocking out OsKRN2 boosted rice yields by 8%.

Researchers are still trying to understand exactly how the two genes influence the number of grains in rice or maize. Most of that work involves varieties of rice and maize mainly used for research, but the team has also modified KRN2 in one of the most common varieties of maize planted in China, named Zhengdan958. “That’s where the rubber hits the road, from an industry standpoint,” Habben says. Initial results suggest knocking out the gene adds one extra row of kernels.

Meanwhile, researchers at CAU are trying to modify a version of KRN2 in wheat on the hunch that KRN2 might also boost grain in other cereals. The CAU team is also planning to check whether KRN2 could help increase grain yield in wild relatives of grasses, a first step toward creating new crops that have improved resilience against tougher environmental conditions such as drought or heat.

There might turn out to be many more key crop genes that ancient farmers unknowingly favored—and could now be put to good use by modern plant breeders. In a first step toward identifying them, one author of the new study, molecular breeder Yan Jianbing of Huazhong Agricultural University, looked for signs of selection across the genomes of rice and maize. He and colleagues found 488 genes in addition to KRN2 and OsKRN2 that underwent selection in both grains. Kan Wang, a molecular biologist at Iowa State University, is impressed by the scope of the analysis. “They provide great evidence,” she says. “It’s hard work.”

Many of these genes are involved in starch metabolism, which makes sense because plants fill their seeds with starch. Long ago, farmers likely selected plants carrying those genes to help fill their stomachs with more bountiful harvests of rice and maize.

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