Develop, Demonstrate and Deploy’: Building capacity in DNA sequencing for agricultural biosciences in Africa

Africa is incredibly rich in plant, animal, and human diversity. Uncovering the genetic basis of this diversity could hold the key to improving the productivity of crops and livestock and enhancing human health on the continent. 

A unique and comprehensive bioinformatics training programme has been launched which aims to help African researchers take advantage of long-read DNA sequencing to unlock the genetic potential of crops and livestock in Africa. 

The training titled ‘3rd Generation Genomics and Bioinformatics in Africa' is jointly organized by the International Livestock Research Institute (ILRI, Kenya), the John Innes Centre (JIC, UK) and the Earlham Institute (EI, UK) with support from UK Research and Innovation (UKRI) Biotechnological and Biological Science Research Council (BBSRC) and Oxford Nanopore Technologies. It is delivered in three phases: ‘Develop’, ‘Demonstrate’ and ‘Deploy’.

The 'develop' phase is a two-month long hybrid (residential and online) training programme that introduces all the major steps in long-read sequencing from DNA extraction, library preparation, sequencing, and bioinformatics analyses. The 'demonstrate' phase allows for project-based learning where trainees get hands-on experience from three short projects.  The 'deploy' phase will extend the impact of the training to the home institutions of the trainees across the continent. In this phase, the trainees will implement a long-read sequencing project they design themselves and will also train others in their home institutions. 

Trainees, Daniel Ouso (Kenya) and Sumaya Kambal (Sudan), loading a sample on an Oxford Nanopore Technology flow cell.

Using technology from Oxford Nanopore, it’s possible to sequence DNA of any length, making it easier to analyse the genomes of crops, livestock and pathogens. This is particularly useful for uncovering large variations that conventional short read sequencing platforms are blind to. Oxford Nanopore Technology also offers unprecedented access to sequencing in Africa due to its low acquisition costs and easy portability - the MinION sequencer is a palm-sized device that can be setup in any laboratory.

Associate Director Market Development at Oxford Nanopore Technologies, Iain MacLaren-Lee, said, ‘We are delighted to support this programme, which gives the training fellows an opportunity to advance their own research using nanopore sequencing. We hope they will go on to become leaders that will enable many more African scientists to benefit from such genomics insights.

Fifteen early-career researchers - seven women and eight men - from Kenya, Zimbabwe, Sudan, Senegal, Zimbabwe, Ethiopia, Madagascar,Cameroon and Rwanda, have benefited from the residential training at ILRI, Nairobi, with over 200 other African researchers participating online. 

‘Participating in the training has been a valuable experience in my pursuit of becoming a skilled researcher in bioinformatics and agricultural bioscience,’ says Sumaya Kambal, one of the training fellows. ‘I have gotten good experiences in designing genomics experiments, thinking critically and dealing with challenges related to both laboratory and bioinformatics work. With the skills acquired and the networks built, I look forward to developing a bioinformatics training capacity at my home institution.’

The training also builds on the first Bioinformatics Community of Practice (BixCoP) training that started in 2018. More detail on the 2018 programme can be found here.

Rob Davey from EI, said ‘it was fantastic to be able to return to deliver training and to see previous BiXCoP fellows become trainers. This is a vital component of our strategy - building capacity in-country through in-depth and focused technical training in key areas of real-world informatics”.

‘We firmly believe that the African continent must develop its research capacity in genomics and bioinformatics. ILRI is very proud to empower African scientists with cutting-edge tools they need in long reads sequencing and in bioinformatics analysis. They will leave a mark in their respective fields of study and pass on their knowledge to dozens of their colleagues all across the continent,’ said ILRI’s Jean-Baka Domelevo Entfellner.

Meet the training fellows: