The review’s scientific foundation rests on the mechanics of CRISPR/Cas systems. CRISPR, originally discovered as a bacterial immune mechanism, relies on an RNA-guided endonuclease such as Cas9 that cuts DNA at sequences matching a designed guide RNA. When plant cells repair these targeted breaks, typically through non-homologous end joining, they generate small insertions or deletions that can knock out a gene. Alternative repair through homology-directed repair, and newer tools such as base editing and prime editing, allow precise nucleotide substitutions and more complex sequence changes without introducing foreign DNA. Crucially, many resulting edits fall into the SDN-1 and SDN-2 categories, which produce genetic changes often indistinguishable from natural mutations or conventional mutagenesis, a point with major regulatory implications.

The technology’s track record in African-relevant crops is now substantial. Editing the MusaDMR6 gene in banana has produced enhanced resistance to Banana Xanthomonas Wilt, one of the most destructive bacterial diseases in East and Central Africa, while CRISPR has also been used to permanently inactivate endogenous Banana Streak Virus sequences and delay fruit ripening through targeting of the MaACO1 gene. In cassava, edited lines show reduced susceptibility to cassava brown streak disease, which causes annual losses estimated at 100 million dollars in East Africa, and mutagenesis of the MeCYP79D1 gene has lowered toxic cyanogenic compounds in the roots. In maize, editing of the ARGOS8 gene has been associated with improved drought tolerance and yield stability under water-limited field conditions.

The disease burden these tools address is staggering. Striga, a parasitic weed, can wipe out between 30 and 100 percent of sorghum yields in affected fields in Kenya and Ethiopia, while maize lethal necrosis, first detected in Kenya in 2011, can destroy up to 90 percent of a crop. In wheat, CRISPR-based modification of resistance loci has generated lines with strong resistance to powdery mildew. Ethiopian researchers are pursuing editing of semi-dwarfing gene orthologs such as SbSD1 and TefSD1 in teff, a staple grain whose tendency to lodge under wind and rain constrains yields across the highlands. Multiplex editing, in which several genes are modified simultaneously, is highlighted as especially promising for complex traits such as drought tolerance and durable disease resistance, though it demands careful evaluation of pleiotropic effects.

Nutritional improvement represents a third major application. The review describes how CRISPR approaches have been investigated for raising iron, zinc, carotenoid and amino acid content across crops including rice, wheat, potato, sweet potato and tomato, strategies directly relevant to African diets dominated by starchy staples. Reducing anti-nutritional compounds, as demonstrated with cyanogenic glycosides in cassava, simultaneously improves food safety. The authors argue that these edits can be stacked with disease resistance and drought tolerance through multiplex editing, producing varieties that address several constraints at once without requiring farmers to change what they plant or eat.

Yet the pipeline from laboratory to farm remains bottlenecked at nearly every stage. Plant transformation and regeneration, the step in which edited cells are grown into whole plants, is inefficient or genotype-dependent in many African staple crops, including sorghum, teff, pearl millet, cowpea and enset. Delivery methods such as Agrobacterium-mediated transformation, particle bombardment and DNA-free ribonucleoprotein delivery each carry trade-offs in cost, efficiency and scalability. Off-target effects, though now well characterized and controllable through careful guide RNA design, still require empirical validation in each crop. High-throughput phenotyping, essential for confirming that edited alleles perform under real field conditions across diverse African agro-ecologies, remains scarce, and multi-location, multi-season trials are urgently needed.

Regulation is perhaps the decisive variable. The review contrasts product-based regulatory approaches in Argentina, Brazil, Japan and the United Kingdom with a fragmented African landscape. Kenya has emerged as a research leader with active gene editing programs, Nigeria has produced leading biosafety guidelines, and Ethiopia published new genome editing guidelines in 2025 that distinguish SDN-1-type edits without foreign DNA from transgenic events, while also approving biotech maize and cotton for commercial cultivation. The authors welcome these moves, noting that regulatory clarity is helping to shorten the so-called valley of death between research and deployment, but they caution that implementation across variety release committees, biosafety authorities and seed regulators still lags behind publication of the guidelines themselves.

Economics and intellectual property add further friction. Overlapping patents on editing systems, delivery technologies and edited traits create licensing costs and freedom-to-operate constraints that fall hardest on orphan crops such as teff, enset, finger millet and Bambara groundnut, where small markets rarely justify expensive licensing. More than half of African smallholders obtain seed through informal networks, meaning even a perfect edited variety must navigate weak seed multiplication, quality control and extension systems to reach farmers. The review also engages with critics, including some civil society organizations who argue gene editing is a costly distraction from agroecological approaches, and counters that editing should be complementary, guided by participatory varietal selection and farmer-defined priorities such as reduced lodging in teff and Striga resistance in sorghum.

The authors close with a set of priorities: harmonizing SDN-1 and SDN-2 regulatory pathways across the continent, strengthening biosafety and transformation infrastructure, applying artificial intelligence to guide RNA design, adopting pangenomics and machine learning, and expanding research on orphan crops like finger millet, cowpea and enset that underpin food security but remain under-studied. They also point to de novo domestication and epigenome editing as emerging frontiers. With coordinated investment from national governments, donors and public-private partnerships, the review concludes, gene editing can meaningfully contribute to a sustainable and climate-resilient agricultural transformation in Africa, provided the benefits ultimately reach the smallholder farmers who produce most of the continent’s food.

Subject of Research: Applications, opportunities and challenges of CRISPR-based gene editing for improving major and orphan food crops in Africa

Article Title: Gene editing applications, opportunities and challenges for crop improvement in Africa a review

Article References: Gene editing applications, opportunities and challenges for crop improvement in Africa a review. (n.d.). https://doi.org/10.1007/s44279-026-00780-4

Image Credits: AI Generated

DOI: 10.1007/s44279-026-00780-4

Keywords: CRISPR, gene editing, African agriculture, crop improvement, food security, cassava, banana, teff, maize, disease resistance, drought tolerance, regulation