A look into the science of genome editing in Africa to optimise agriculture

Genome editing is one of the latest tools that has been developed by scientists to effect changes in organisms of agricultural, medical, and economic importance. The advent of genome editing has increased the available tools and the effectiveness of developing new productive and better-adapted organisms of economic importance.

Genome Editing (GEd) involves the deliberate introduction of mutations to the genome of an organism through insertion, replacement, or deletion of DNA sequence.  GEd usually aims to improve desirable traits of a crop or livestock. It enables modifications at specific sites of DNA through a DNA repair system (Khalil, 2020). Meganucleases (MN), Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated proteins methods of GEd are becoming popular because they are precise and do not introduce foreign DNA into the cell (Mengstie and Zawdie, 2020).

African Case Studies of Successful and On-going Applications of GEd in Agriculture 

Genome editing technology in Africa finds wider applications in crop improvement.

Below are some examples of how researchers are using CRISPR/Cas-based genome editing to improve African staple crops for various purposes.

In Ethiopia, the Addis Ababa University, in collaboration with the Swedish University of Agricultural Sciences, is working on improving the oil quality and quantity of Ethiopian Mustard through CRISPR-Cas9. This research seeks to develop novel lines with edible or healthy seeds and oil quality.

The Kenyan Agricultural and Livestock Research Organization (KALRO) partnered with CIMMYT and Corteva Agriscience using genome editing to develop maize lines resistant to the maize lethal necrosis virus. These resistant lines will soon be undergoing field testing.

In Kenya (Kenyatta University) and Ethiopia (Addis Ababa University), there is a USAID-Striga Smart Sorghum for Africa (SSSfA) project, which intends to use CRISPR genome editing technology to develop new sorghum varieties resistant to Striga (a parasitic weed). The successful development and commercialization of this genome-edited sorghum is expected to have a spill-over effect across Africa.    

Researchers at the Ethiopian Institute of Agricultural Research (EIAR) have embarked on a genome-editing project to address the lodging problem in tef to improve grain productivity. The project is a collaboration between EIAR and the Donald Danforth Plant Science Center’s Institute for International Crop Improvement, USA, and seeks to target the same genes in the tef genome to develop semi-dwarf tef varieties using the CRISPR Cas9 gene editing technology.

In Burkina Faso, rice lines resistant to bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is being evaluated in confined field trails. These lines have been developed by the HealthyCrops consortium ( https://www.healthycrops.org ) through the editing of three genes of the SWEET family (SWEET11, SWEET13, and SWEET14) using the CRISPR-Cas9 technique (Eom et al., 2019; Olivia et al, 2019). The edits aim to prevent the expression of the three SWEET genes in the presence of the pathogen. The bacterium induces the plant to produce sugars, a source of nutrients that it exploits for its advantage to multiply. The edited lines do not express the SWEET genes, thus the bacterium is no longer capable of hijacking the sugar production pathway, and the plant becomes resistant.

In Uganda and Kenya, an efficient genome editing proof of concept was demonstrated by editing native phytoene desaturase (PDS) gene (Odipio et al., 2017) and knowledge used to identify anti-flowering genes in cassava (Odipio et al., 2018). Researchers are now using genome editing technology to make cassava plants more resistant to the cassava brown streak disease (CBSD), a viral plant disease spread by whiteflies. Some people have called CBSD the “Ebola” of plants because it is hard to detect and highly infectious from plant to plant.

Plant scientists are using CRISPR/Cas9 technology to edit multiple genes involved in the plant’s susceptibility to the virus, resulting in tolerance to the disease (Gomez et al., 2018). Cassava with reduced levels of toxic cyanide has been produced by successfully editing two genes CYP79D1 and CYP79D2 involved in the cyanide biosynthesis pathway (Gomez et al., 2023, Juma et al., 2022). These changes could be made to virtually any cassava variety without changing qualities that make it particularly useful or popular to a certain group of farmers or consumers

The CRISPR/Cas 9 technique has been used to edit banana genes making it resistant to the banana streak virus in Kenya and Nigeria (Tripathi et al., 2021). This has the potential to greatly improve the yield and productivity of bananas in these countries and Africa at large.

Genome Edited Animals

Africa has made significant progress in the improvement of various domestic animals using selective breeding. This approach is greatly constrained by limited genetic variations in the various species populations. Genome editing offers opportunities for the improvement of livestock since it facilitates the creation of novel mutations in various traits. Globally, farm animals have been improved using genome editing (See table below).

Table

In Africa, the International Livestock Research Institute (ILRI) in Nairobi, Kenya, is using genome editing to manipulate various traits in livestock and poultry. such desirable traits as heat tolerance and disease resistance in cattle and poultry. The following are some examples of the traits being worked on using genome editing:

• African trypanosomiasis-resistant goats
• Heat and disease tolerance in cattle and poultry
• Development of goat surrogate sires
• Development of attenuated vaccine against African swine fever in pigs