Cassava is an important food security crop and income earner for millions of smallholder farmers in Africa. It is the second most important food crop after plantain in Uganda. However, according to Uganda Bureau of Statistics, cassava production has been on the decline. Poor flowering is a key factor that has constrained improvement of cassava. Poor flowering results into low seed set making it difficult for breeders to cross and produce new cassava varieties faster.

It is for this reason that Dr. John Odipio, a biotechnologist and genome editing expert, has set out on a mission to address this flowering challenge using genome editing. Dr. Odipio works with Uganda’s National Agricultural Research Organization at National Crops Resources Research Institute (NaCRRI), Namulonge. In an exclusive interview with the DrumBeat, the scientist shares insights into his intervention.

  1. Briefly take us through your personal journey into the science of genome editing. What motivated you into this field?

I was born in a family whose main livelihood practice is agriculture. My parents grew cassava, and so was I as I grew up. Cassava served us as staple source of food and income, and it still does even now. It was from money generated through cassava that I was able to access education. Upon completion of my undergraduate studies, I looked forward to working with NARO, and I was glad to join the organization to work in a cassava program at NaCRRI, Namulone in 2007. My role then was to oversee confined field trials (CFTs) and collect data on genetically modified (GMO) cassava resistant to cassava mosaic and cassava brown streak diseases. Over time, the data from the trials, and even elsewhere where cassava is grown, showed that the crop produces flowers at different times. No one could explain this irregular flowering behavior. These interesting results inspired my interest into finding out why this is so. It was against this interest that in 2014 I secured a PhD scholarship at the Donald Danforth Plant Science Center, United States. The scholarship presented me with an opportunity to study and understand the molecular flowering behavior in cassava. During this time, the novel CRISPR/Cas9-mediated genome editing technology had been discovered two years earlier, and no one had used the technology on cassava. When I looked at the attributes of genome editing I found it was the right one to use for my study because it employs a natural system that has been in use in bacteria and other organisms, and what happens in bacteria can be re-purposed and used in plants. Thus the end product of genome editing is similar to conventional products. I decided to use this technology since it cheaper, precise, and faster and gene edited products would not undergo unwarranted costly biosafety regulation.

  1. Explain what your genome editing project is about?

My project seeks to address the challenge of asynchronous flowering in cassava using genome editing. Cassava produces both male and female flowers on the same plant. When the male and female germ cells meet and fertilize, they produce a seed. The seeds are used by plant breeders in development of new varieties, and it is for this reason that flowers are essential. Under field environment, cassava does not flower at the same time as breeders would prefer especially in carrying out crosses. Partly because of this flowering challenge, breeders take up to ten years to develop new varieties. My project’s intervention is to generate information on why there is delayed flowering, and develop techniques by which non- or late flowering cassava can be made to flower at the same time for efficient development of new varieties. Through my PhD studies, I have been able to identify reasons for cassava’s ‘refusal’ to flower at uniform time, and therefore this project’s goal is to develop cassava that can flower at the same time saving breeders time for development of new cassava varieties from ten to six years.

  1. In the long run, what does it mean if this cassava flowering challenge is not addressed?

If the challenge is not addressed, development of new cassava varieties will continue to take over ten years, making it difficult for farmers to access superior varieties. Secondly, as climate change becomes real, we will not be able to have new cassava varieties with climate resilience, improved nutrition and disease resistance developed and released in time. Thirdly, cassava as a crop will not fully exploit the benefits of genomic selection for which synchronous flowering is essential. Ultimately, this means we shall be late in achieving international obligations such as the United Nation’s Sustainable Development Goals (SDGs 1-3) on time.

  1. Explain how your project will ultimately develop superior cassava varieties using genome editing. Why is it necessary to use genome editing?

Genome editing is a technology that allows precise and targeted modification of genes responsible for desirable traits. Using this technology, I am able to target genes that inhibit flowering within cassava. I can turn off the function that suppresses flowering hence ensuring the crop develops the ability to produce flowers. Once this has been achieved, it becomes possible to make crosses with other varieties that have traits of interest to generate new seeds for breeding using genome editing; something that is not possible with traditional breeding. When this precise crossing happens, there is a high chance of obtaining new progenies for selection and development of superior varieties for the future. My interest is to take advantage of available cassava varieties that breeders have never used because they do not flower even if you use other methods like chemical spraying which is environmental unfriendly. The acquired knowledge can be extended to address other critical challenges affecting farmers such as developing novel and durable resistance to maize lethal necrosis and rice yellow mottle virus. The gene edited crops would contain small sequence modifications equivalent to those naturally present in traditionally bred or generated through mutation breeding and thus does not need to be regulated.

  1. At what stage is your project, and what are the achievements so far?

The project is at the proof of concept stage. The first thing I did after completing my PhD was to ensure what I learned and did in the developed world can be translated into success in Africa. I had successfully identified ant-flowering genes that cause late flowering as I conducted research at the Danforth Center laboratories. In 2021, in our Tissue Culture and Transformation Lab in Uganda, I was able to successfully produce embryogenic cassava tissues visually lacking green colour in which the gene for greenness has been turned off using genome editing. Therefore, I have demonstrated capacity to do genome editing back at home and this is enough proof that I can successfully conduct this research in Uganda. This makes me excited.

  1. Highlight any major challenges, if any, that the project has faced. How have you addressed them?

One big challenge is the lack of funds to carry out this research. Funds have been hard to come by. I have applied for several grants but with no success. In 2021, our joint application for a grant by a UK-based funding agent was approved. Unfortunately, with the surge of COVID-19 cases, all science attention and resources were channelled towards COVID-related medical research. One other challenge is the lack of biotechnology law in many African countries including my country Uganda which hinders donors from extending grants to scientists in particular countries due to lack of commercialization pathway.  Many individuals and institutions in Africa have not seen the potential of genome editing, partly due to the newness of the genome editing technology thus making it difficult to prioritize genome editing research and product developments.

  1. What is your take on regulation of genome editing technology and products thereof?

Regulations of products developed through biotechnology can be conducted on either process-basis or product-basis. Most African countries have adopted and are using a process-based approach from Europe thus the slow process in genome editing approvals. Products of genome editing are safe and equivalent to conventional products that are already in the market. It is for this reason that countries like the United States, Argentina and China have made tremendous progress in this area. Since the process of developing gene-edited products is precise and efficient, I would advise African countries and Ugandan regulators in particular to adopt the product-based regulation approach and exempt gene edited crops or products from being regulated.

  1. What is your message to other scientists working on genome editing projects across Africa?

I encourage my fellow colleagues that we, as scientists in genome editing, need to broaden our collaboration base and increase our synergies. By working together, we will ensure we do not duplicate our efforts and thus we will put the little resources that we have to a better use. We need to continue improving our skills and knowledge so that we are up-to-date with advances in this field of science.

  1. If you had three minutes with African leaders, what would you want them to know about genome editing?

I would tell our leaders that genome editing is the new gold mine that they have in their possession, so they should seize the opportunity and take the advantage to use the technology in accelerating the first green revolution in Africa. For this to happen, our leaders need to invest in science. They need to have deliberate and sufficient budget for scientists for them to have enough capability to develop climate-resilient crops and animals and forestall any unforeseen food-related disasters. With enough investment in science, farmers will benefit from superior crop varieties and better animal breeds. Our leaders also need to consider what is already working in other countries, and one of the options is going for deregulation of gene edited products just like the case in the United States, Argentina and China. They should also make deliberate efforts to fund biosafety regulatory bodies for them to have enhanced motivation and capacity to undertake objective and science-based biosafety regulation.

Story of the Month - AUTHOR_Photo

Dr. John Odipio is a crop biotechnologist and genome editing expert based at NARO in Namulonge Uganda. For more information contact us at