Genome Editing for Sustainable Agriculture in Africa

Abstract

Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.

Keywords: African crops; CRISPR/Cas; agriculture; genome editing; regulatory policies.

FIGURE 1

Map of Africa showing the major staple food crops addressed in this article. Also indicated are the countries where genome-edited projects are being implemented in Africa (based on the information from Karembu, 2021).

FIGURE 2

Application of genome editing in banana for developing improved varieties with biotic and abiotic resistance and enhanced nutrition. BSV, Banana Streak Virus; BBTV, Banana Bunchy Top Virus.

FIGURE 3

Plants resistant or susceptible to maize lethal necrosis (MLN) in Naivasha. Susceptible (in front) and resistant (in the back) plants 2 weeks after inoculation with a combination of MCMV and SCMV (A). A closeup of the leaves from plants susceptible (B) or resistant (C) to MLN.

FIGURE 4

Mapping of QTL for resistance against maize lethal necrosis in CIMMYT germplasm. Figure reproduced from Murithi et al., 2021. Manhattan plot of GWAS using MLM in the selective genotyping populations. Combined genome-wide association scan for MLN disease severity (MLN_DS) (A) and the area under the disease progressive curve (AUDPC) values (B) based on the first three F2 populations (selective genotyping - SG) with KS23 background. Manhattan plots for MLN_DS (C) and AUDPC values (D) based on two F2 populations (CML494 X CZL068 and DTP-F46 X CML442) with no KS23 background. The horizontal dotted line indicates genome-wide significance and the plots above the line represent SNP markers that showed significance above threshold of p = 5 × 10⁻⁷.

FIGURE 5

A schematic diagram summarizing potential genome editing approaches for Striga resistance in sorghum. Resistance can be imparted at the pre-attachment stage (gray arrows) by CRISPR/Cas9 mediated knock out of the LOW GERMINATION LOCI I (LGS1) to obtain lgs1 edits that do not effectively stimulate parasite seed germination. And post-attachment resistance (peach arrows) can also be imparted by CRISPR/Cas9 mediated knock out of susceptibility genes such as DOWNY MILDEW RESISTANT 6 (DMR6) to create host-parasite incompatibility that inhibits unsuccessful parasite attachments (red spots). Both approaches can be used to develop multi-level resistance using breeding or CRISPR/Cas9 double knockouts of LGS1 and DMR6.

FIGURE 6

Schematic illustration of plant traits and genes that could be targeted by genome engineering for yam improvement. (A) Yam nutritional enhancement, e.g., increasing the beta carotene content by mutating the Lycopene epsilon-cyclase (LCYE) gene, or reducing post-harvest browning by targeting polyphenol oxidase genes (PPOs). (B) Engineering yams with improved resistance to abiotic stress, e.g., mutating ethylene response factors (ERFs) to improve the crop’s performance under stress conditions, upregulating the expression of anti-oxidative enzymes (SOD, CAT, APX, and GPX) or targeting genes that contribute to ROS redox balance such as Respiratory Burst Oxidase Homologue (RBOH) and WRKY53 to increase ROS quenching capacity. (C) Improving the crop yield, e.g., mutating specific genes to modulate sink strength partitioning and promote sucrose translocation to the tubers, or enhancing photosynthetic rate by knocking out negative regulators of photosynthesis (NRPs) in the chloroplast and mitochondrion. (D) Engineering herbicide tolerance in yam plants for effective weed management and improved yields. (E) Accelerated yam breeding through allele replacement by homologous recombination-based knock in. (F) Enhancing biotic stress tolerance by mutating host susceptibility genes or upregulating the expression of disease resistance genes.