Making high-yielding rice affordable and sustainable

Rice is a staple food crop for more than half the world’s population, but most farmers don’t grow high-yielding varieties because the seeds are too expensive. Researchers from the University of California’s Davis and Berkeley campuses have identified a potential solution: activating two genes in rice egg cells that trigger their development into embryos without the need for fertilization, which would efficiently create high-yielding clonal strains of rice and other crops.

A team led by Venkatesan Sundaresan, a Distinguished Professor in the departments of Plant Biology and Plant Sciences at UC Davis, previously showed that a gene called BBM1 in rice egg cells could switch on the ability of a fertilized egg to form an embryo. However, the method only worked about 30% of the time. Now, in collaboration with researchers from UC Berkeley’s Innovative Genomics Institute, the team has shown that simultaneously activating a second gene, WOX9A, increases the success rate to around 90%.The finding was published Nov. 12 in Nature Plants.

 “It’s remarkable that after 20 years of unsuccessful efforts in clonal hybrids, there has been so much recent progress -- from showing that it is actually possible back in 2019, to showing now that it can work efficiently in 2024,” said Sundaresan. “I’m very optimistic now that hybrids will no longer be the barrier to achieving sustainable agriculture with high yields all over the world.”

A cost-effective way to feed the world

Hybrid strains of rice, which are produced by crossing two pure strains, can yield almost double the harvest, but producing them is expensive and requires farmers to purchase new seed each year. If the hybrid plants could reproduce asexually, farmers could save seed from one year to the next. How to engineer asexually reproducing rice has been a puzzle that scientists have been trying to solve for more than 30 years.

Sundaresan’s team previously showed that BBM1 is an essential trigger for plant embryo development, and that activating this gene in eggs can override the need for fertilization.

“Switching on BBM1 artificially in the egg cell is enough to start embryogenesis and make a new plant, but this process only worked about a third of the time,” said Sundaresan. “One of the things we wondered was, maybe BBM1 is not enough; maybe it needs help.”

By examining which genes are turned on in fertilized plant eggs, the researchers identified a gene, WOX9A, for which only the sperm-carried copy of the gene is expressed. When they simultaneously activated both BBM1 and WOX9A in rice egg cells, it resulted in embryo formation 90% of the time, though activating WOX9A alone did not result in embryo initiation.

“We think BBM1 is flipping a switch that primes the egg cell to transition into an embryo, but the switch is not fixed,” said Sundaresan. “So, then WOX9A comes in and clamps down on the switch so that it doesn’t flip back.”

Hybrid vigor without need for hybrids

Because they arose from unfertilized eggs, the plants produced via this method are haploid, meaning they contain half the usual number of chromosomes. Though haploid rice plants do germinate and grow, they tend to be stunted compared to diploid plants that carry two copies of each gene.

“Haploids are valuable tools in plant breeding for producing pure lines, which enable uniform crop production,” said corresponding author Imtiyaz Khanday, assistant professor in the Department of Plant Sciences in the UC Davis College of Agricultural and Environmental Sciences. “These findings also have significant implications for producing clonal seeds at high frequencies that retain the benefits of hybrid vigor.”

The next step, the researchers say, is to combine this method of activating both BBM1 and WOX9A with “synthetic apomixis,” a technique that they previously developed for asexually producing clonal seeds. This will mean that farmers can reap the benefits of hybrid vigor year after year by simply saving some of the harvest to plant the following year. 

“If we combine this trick of making an egg cell turn into an embryo without fertilization along with another technique that knocks out meiosis, we can efficiently produce high-yielding hybrid seeds,” said Sundaresan. “In a world where resources are increasingly limited, it provides a path forward for sustainable agriculture for rice farmers, and in the future, for other crops as well.” 

Additional authors on the study are: Hui Ren and Kyle Shankle, UC Davis and Myeong-Je Cho and Michelle Tjahjadi, UC Berkeley. The work was supported by the National Science Foundation and the United States Department of Agriculture (USDA) Agricultural Experiment Station.