From corn to bananas, farmers stand to gain from cultivating edited crops that are resilient and sustainable, paired with precision insecticides and microbe engineering. But reaching those with the greatest need remains a challenge.
The world’s growing population needs feeding, but climate change is already bearing down on agricultural production. Crop varieties will in the future need to be more resilient to physical and biological threats. They will also need to be more efficient in converting the energy and nutrients they receive into food, and in this space, there is plenty of scope for innovation. Genetic engineering has improved a handful of traits in a narrow range of crops — even if they are grown at a massive scale. But more must be done. Now, with the precision and flexibility of gene editing, plant biotechnology is addressing a much greater variety of important food crops and a much wider range of genetic traits.
Genome-edited crops can help address some food security and environmental challenges.
Credit: Zbynek Pospisil / Alamy Stock Photo
Precision breeding with biotech tools to improve crops has lagged developments in precision medicine. Today, only a handful of gene-edited plants is commercially available. A high-quality wheat genome sequence only became available in 2018, says Catherine Feuillet, CSO at Inari Agriculture, who, during her academic career, was a co-founder of the International Wheat Genome Sequencing Consortium. For breeders, knowing what to edit and how to edit it has only become possible thanks to the knowledge generated recently by genomic data and computational tools. “We can’t have plant breeding as an art — it has to be a science,” she says. Inari has raised over $575 million in equity financing since its formation in 2016 to develop high-yielding wheat, corn and soybean varieties and is now close to launching its first commercial product. “We are looking at traits that modify the plant architecture to increase yield,” Feuillet says. Its technologies include a CRISPR-based epigenetic programming tool that can activate expression of target genes, which company co-founder Steve Jacobsen of the University of California, Los Angeles, developed.
Pairwise has used base editing in corn to modify the number of rows of kernels present in the ears of the mature plant. Sixteen rows is standard, says CEO and co-founder Tom Adams, but plants with 18 to 20 appear to have 10% higher yield, although this is not fully confirmed as yet. “It’s in early field testing.” The company is also investigating whether it is possible to tweak the same pathway in blackberries to increase the number of drupelets — the individual bead-like components of each berry. The company gained a license to the base-editing technology through its co-founder David Liu, of the Broad Institute of MIT and Harvard. The company has also used the Cas12 nuclease enzyme, again licensed through Liu, to avoid “the patent mess around Cas9,” says Adams. Much of its initial focus was on an alliance with Bayer, of Leverkusen, Germany, to work on corn, soybean, canola, wheat and cotton. “We edited hundreds of different genes in those crops.” That effort resulted in 27 novel traits, which Bayer is now exploring further. A second alliance between the two firms is tackling short corn: they aim to develop plants that are 30–40% shorter but that produce the same number of ears. As well as being more able to withstand strong winds, they would also allow better access for machinery, allow more flexibility to apply fertilizer or other inputs, and eliminate the need for spraying crops from aircraft, an energy-intensive and polluting practice.
Bananas are another crop in which gene editing is about to make a splash. In the first quarter of 2025, Tropic Biosciences plans to launch the first commercially grown gene-edited banana, which is designed to resist browning. The Norwich, UK-based biotech developed the variety by silencing expression of two genes, each of which encodes a polyphenol oxidase enzyme. These are upregulated in the edible, fleshy part of the fruit in response to physical bruising. Apart from that particular feature, the gene-edited banana is identical in every other respect to the mass-market variety consumed across the world, says company co-founder and CSO Eyal Maori. Taste, for instance, is not affected in the gene-edited banana, in contrast to that in hybrids developed by conventional breeding. The new variety is intended to cut post-harvest losses, extend bananas’ shelf-life, and open up new commercial opportunities in the freshly prepared fruit salad market.
The imminent arrival of a gene-edited banana variety is noteworthy because genetic diversity in bananas is extremely low. Commercially grown varieties are descended from sterile, mutant relatives of inedible wild bananas. The banana industry has, famously, relied heavily on a single variety, the Cavendish, for about 70 years, because a fungal infection, Fusarium wilt, wiped out its predecessor in the 1950s. Large monocultures are vulnerable to disease.
Tropic has developed its GEiGS platform, which combines CRISPR–Cas9 gene editing with RNA interference (RNAi) gene silencing to improve the crop’s resistance to pathogens or other useful traits. It does so by targeting DNA sequences encoding small interfering RNA (siRNA) molecules and redirecting their RNAi activities toward new genetic targets. “We have, in a way, unlocked the banana,” says Maori. To identify appropriate target genes, the company has developed a proprietary RNA expression atlas, which profiles gene expression patterns in different plant tissues. Bananas are triploid and encode nine browning polyphenol oxidases in all. Targeting all of them, says Maori, would have entailed developing a transgenic variety, which would carry a much higher regulatory burden and a much lower level of consumer acceptance than the edited variety. It is the first in a pipeline that also includes rice and coffee varieties.
Although at an earlier stage, Paris-based Meiogenix is also exploiting CRISPR-mediated recognition of DNA sequences to improve genetic diversity in plants. It aims to introduce CRISPR-programmed chromosome edits to crops to boost homologous recombination in regions of the genome where it normally does not occur, and to do so in a targeted fashion. A random process that occurs during meiosis, homologous recombination is intrinsic to sexual reproduction in all eukaryotes — it is the means by which a species maintains genetic diversity. In plants, however, it is generally limited to the ends of chromosomes, says Meiogenix’s chief technology officer Gaganpreet Sidhu. To direct the process and to enable it to target other genomic regions, the company has fused a catalytically dead Cas9 enzyme to Spo11, the protein responsible for initiating homologous recombination during meiosis. “We’re just doing what nature does but at another location,” she says. The approach does not introduce any mutations or external DNA — the fusion construct that starts the process, which is introduced on a plasmid by Agrobacterium-mediated transformation, can be selected out (with the help of a reporter gene) from those plants that have undergone homologous recombination.
The technology promises to open up new breeding possibilities by enabling the targeted transfer of large genomic regions that are associated with complex traits. What’s more, because of the precision of CRISPR-based recognition, the approach avoids linkage drag, a common problem in conventional breeding, which involves the introduction of deleterious genes along with desired traits. This typically requires laborious, time-consuming backcrosses to eliminate the unwanted genes.
Meiogenix’s scientific founder Alain Nicolas and colleagues established the chromosome editing system in yeast seven years ago. The company has since been working on proof of principle in plants and on improving its efficiency. It recently concluded a collaboration with Bayer that established that the system works in corn, Sidhu says, and it has also established that it works in tomato and rice. The company now plans to test the system in other commercially important crops. A collaboration to develop a disease-resistant tomato variety is already underway with a partner. “It’s a linkage drag problem we’re planning to resolve,” Sidhu says.
Resistance to drought and heat stress will both be needed to avoid the devastating effects that crops are likely to experience during the coming decades. Even though they typically happen together in the field, funding agencies historically favored studying each in isolation, says Ron Mittler of the University of Missouri’s Christopher S. Bond Life Sciences Center. Climate change has reset the agenda, however, and Mittler’s studies on combined stressors are starting to bear fruit. Several years ago, his group identified an adaptation strategy in heat- and drought-exposed soybeans. To conserve water and still allow reproduction to proceed, the stomata — the plant pores that control evaporation —open only in the flowers, remaining closed in the vegetative parts of the plant. This lowers the flowers’ internal temperature by 2–3 °C and protects the reproductive process, which is essential for growers aiming to harvest seeds (or beans). “Biomass is not that critical in soyabean,” Mittler says. “What’s critical is the yield — how many seeds are you going to get?” Mittler’s group also established that the plant hormone abscisic acid triggers the stomata to close. Abscisic acid pathways are naturally upregulated in reproductive tissue and could be tweaked further to provide additional protection from drought and heat stress. Mittler and his collaborators are planning field trials of such modified soybeans to ascertain whether they are more able to maintain yield in stressful conditions.
Plants are not the only targets for intervention to improve crop yields sustainably. Bacteria offer possibilities for boosting soil fertility and reducing synthetic fertilizer use. Nitrogen fertilizers and nitrogen-containing manure account for an estimated 5% of all greenhouse gas emissions through the release of carbon dioxide, nitrous oxide and methane, throughout their production and use in agriculture. The process is inherently wasteful — less than half of the applied nitrogen is taken up by crops. The rest is lost, either to the atmosphere or as polluting agricultural run-off that harms freshwater and marine ecosystems. Harnessing bacterial nitrogen fixation, which entails the conversion of atmospheric nitrogen to ammonia, has long been considered a possible solution. Back in the 1970s, some scientists advocated transferring the bacterial nif genes involved in nitrogen fixation into major cereal crops, such as wheat, rice and corn. Modern gene editing approaches instead focus on soil-dwelling nitrogen-fixing bacteria, which are abundant. Some, such as Rhizobium and Frankia species, form nodules on the roots of leguminous plants and live in symbiosis with their hosts. But many free-living bacteria, including Klebsiella, Azotobacter and Bacillus species, are also capable of nitrogen fixation.
In agricultural settings, the presence of exogenously applied nitrate fertilizer inhibits nif gene expression, but Pivot Bio has developed a Klebsiella variicola strain that can fix nitrogen regardless of the external nitrate concentration. It replaced the nifL gene, which encodes the inhibitory protein NifL, with an endogenous promoter that drives constitutive expression of nifA. Its gene product, NifA, activates expression of the other nif genes. The bacterial strain, Kv137-2253, is shipping commercially for use with wheat, sorghum, barley, oats and sunflower. For corn, Pivot has combined Kv137-2253 with a second organism, Kosakonia sacchari strain Ks6-5687, whose nif genes have also been edited for constitutive expression. At present, these products — which are either sprayed during sowing or applied to the seeds in a coating — can supply about one quarter of the plants’ nitrogen needs. “That’s a reflection of the efficiency we’ve been able to capture in the system,” says Karsten Temme, co-founder and chief innovation officer at Pivot. The company aims to improve this by further boosting nitrogen fixation in the presence of nitrate and by increasing the amount of ammonia the bacteria export into the rhizosphere. Pivot’s bacteria are currently used in conjunction with about 5% of US corn production. “It’s had a massive impact already,” says Temme. The company is now gearing up to export the technology to Brazil and is also starting testing in Kenya.
Biotech innovation is also taking aim at the harmful environmental impact of insecticides. Solasta Bio is among a clutch of companies developing precision insecticides with pharmaceutical-like selectivity for their target organisms — unlike the broad-spectrum agents that have historically dominated the crop protection sector. The Glasgow, UK-based company is developing insect-derived peptides that alter the behavior of the organism. “These are very small peptides, based on what were historically called insect neuropeptides,” says CEO and founder Shireen Davies. Some 55 such peptide families have been identified so far. They exhibit high levels of diversity both within and between families. “We rationally identify and design the peptides for the targets of interest,” she says. That allows precise targeting of the peptide’s cognate receptor to elicit the desired effect, without affecting beneficial insects, such as pollinators. “We predispose the insect to be less able to withstand environmental stress,” she says. Its lead agent is in development for aphids, which are a particular problem for farmers growing leafy green vegetables. “We are seeking EPA approval,” she says. That could happen by 2027. Further back in the pipeline are agents in development for spotted wing Drosophila, Lepidoptera, and plant and leaf hoppers. Other firms in this space include IBI-Ag, of Ness Ziona, Israel, which is developing single-domain antibodies; and Biotalys, of Ghent, Belgium, which is developing peptide-based fungicides.
Gene editing and other forms of biological innovation are, of course, not the only factors that will determine whether farming can become more resilient and environmentally sustainable. Input from agronomists is important for translating innovation into practice, says Charles Spillane, professor of plant science at the University of Galway in Ireland. That kind of expertise “can be thinly spread” in parts of sub-Saharan Africa and other regions where food production is already under severe pressure. “The challenges are most pronounced for the two billion people who rely on rainfed cropping systems, particularly in the expanding drylands,” he says.
