Author Archives: Mwihaki Mundia

Africa Biosciences Challenge Fund fellow conducts inventive goat genetic diversity research in DR Congo

Goats are among the most common farm animals in developing countries. Africa is home to about 35% of the world’s goat population (FAO 2016). They play an important socio-economic, nutritional and cultural role in rural households. An important indicator of goats’ adaptation to environmental conditions is their reproductive efficiency.

DR Congo has three major agro-ecological zones: the alluvial basin in the northeast and the central part; savannah in the central, western and the southeast; and the high-altitude volcanic mountains in the east of the country. More than 4,082,624 indigenous goats are spread throughout these agro-ecological zones.

Herd of goats

In the Democratic Republic of Congo, goats are the second most domesticated species after chicken. Goats make up between 30% and 60% of the country’s total livestock numbers. The country hosts three major breeds: the small goat, dwarf goat and Kasai goat. Congolese goat farmers raise and breed goats for meat production and commercial transactions, contributing up to 72% of households’ income in rural areas in the country. The productivity of African’s indigenous goats is low, and little is documented on the genetic diversity, production system and distribution of goats in DR Congo.

Patrick Baenyi, an Africa Biosciences Challenge Fund (ABCF) fellow from the Evangelical University in Africa, DR Congo, undertook a survey on 202 goat farmers in the country to identify typology, production management and critical traits considered in goat selection by farmers in three agro-ecological zones — South Kivu, Tshopo and Kinshasa. In his pioneering research, he collected phenotypic data and used phenotypic and molecular markers, that are the basis for animal genetic diversity studies, to characterize goat genetic resources.

The survey revealed that goats in the three zones were clustered into breed clusters, grouped into small goat and dwarf goat, mostly characterized by a black coat colour and curved horn. The clusters were further distinguished by their reproductive traits (i.e. the number of kids per gestation period, such as twins or triplets) and the total number of kids per goat’s lifespan.

Baenyi and a member of his team collect a blood sample from a goat in Tshopo, DR Congo

Baenyi’s study was an important first step towards goat breeding in the country and aids decision-making on goat genetics improvement in the country. Its findings suggest that molecular characterization by sequencing and genotyping should be considered by animal breeders to clarify the physical differences in goat breeds that were observed and to identify whether these differences are genetic or adapted from environmental influence. A good understanding of this genetic characterization is useful in designing effective strategies for managing, improving and conserving domesticated animal resources.

‘Working with the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub reinforced my skills in conducting genetics research and showed me the value of collaborating with other researchers and sharing my findings with the public. I was also trained in bioinformatics and proposal writing and I have continued with the invaluable mentorship relationships that started during my time at the hub,’

says Baenyi.

He is currently working under the supervision of ILRI’s Roger Pelle and his and is studying for his PhD in animal genetics and breeding at the University of Nairobi.

Ko Awono promises to improve Brachiaria grass production and marketing to secure farmers’ livelihoods in Cameroon

Cameroon, like other African countries, relies on agriculture as a main economic activity with livestock employing at least 30% of the country’s rural population. The livestock sector in Cameroon is crucial to its economic growth, food and nutrition security, and job creation. Forages of African origin, such as Brachiaria have been instrumental in the transformation of the livestock sector in many parts of the world including tropical America, Australia and East Asia. But the potential of native forages to alleviate livestock feed shortage in Africa has been little explored.

In 2012, the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub started the ‘Climate-smart Brachiaria Program’ in partnership with the National Agricultural Research Systems (NARS) and development partners in sub-Saharan Africa. This program aims to increase livestock productivity in the region by providing high-quality and climate-resilient Brachiaria grass.

Paul Ko Awono, an Africa Biosciences Challenge Fund (ABCF) fellow at BecA-ILRI Hub from the Institute of Agricultural Research for Development (IRAD) in Cameroon, is researching how to improve Brachiaria seed production technology in Africa. His study, which is supervised by Sita Ghimire and Kingsley Etchu from BecA-ILRI Hub and IRAD, involves collecting information about Brachiaria seed production systems in the North and Adamawa regions of Cameroon, evaluating agronomic performances of Brachiaria landraces and improved cultivars, and examining the quality of Brachiaria seeds produced by farmers in the country. In Cameroon, Brachiaria seed is often traded as a cash crop and is a source of income for many farmers.

So far, Ko Awono’s research has revealed that the size of the farmlands dedicated to Brachiaria production are smaller (0.25 to 0.5 ha) in the North region compared to those in the Adamawa region (1 to 15 ha). His research also shows that Brachiaria seed yield is low in both regions (≤ 300 kg/ha). Major constraints on Brachiaria production in both regions include weed infestation, wandering animals and lack of market for Brachiaria seeds. Additionally, he has found that Brachiaria landraces mature earlier and are better adapted to harsh environmental conditions than improved cultivars. His research has also uncovered that Brachiaria seeds samples produced by farmers in the two regions are of variable qualities (poor to excellent) and some seeds samples are superior for germination than the improved cultivars.

Paul (middle) with his supervisors at Brachiaria experimental plots at Garoua, North Cameroon

Paul’s research revealed that the size of the farmlands dedicated to Brachiaria production by a farmer were smaller (0.25 to 0.5 ha) in the North region as compared to Adamawa region (1 to 15 ha). His research also indicated that Brachiaria seed yield was low in both regions (≤ 300 kg/ha) and the major constraints of Brachiaria production in both regions were weed infestation, wandering animals, and lack of market for Brachiaria seeds. Additionally, Brachiaria landraces were earlier in maturity and were better adapted to harsh environmental conditions than improved cultivars. His research also uncovered that Brachiaria seeds samples produced by farmers in North and Adamawa region were of variable qualities (poor to excellent) and some seeds samples were superior for germination than improved seeds.  

Ko Awono recognizes the role of the ABCF fellowship, which he received in 2019, has played in his work as a forage researcher. ‘It gave me several opportunities: I learnt how to write research proposals, set up agronomic trials, and collect, analyse, and interpret data.’ He also learned several techniques related to seed quality determination in the laboratory and greenhouse settings.  ‘The training and mentorship I received at BecA-ILRI Hub has played a key role in my work. It helped me to improve my scientific skills, which has made me a better researcher. ‘I am using the skills and knowledge I gained to help Cameroonian farmers increase the quality and quantity of Brachiaria seeds, which will improve their livestock production, incomes and livelihoods,’ he concludes.

Speed Breeding, a promising approach to crop breeding

Speed Breeding is a new and exciting approach to breeding originally inspired by the US National Aeronautics and Space Administration (NASA) that promises to develop new crop varieties faster, offering hope for food security in the continent. Through Speed Breeding, African researchers are working to develop new crop varieties faster.

The technique involves growing plants under continuous light (20–22hours). This allows plants to photosynthesize for longer, resulting in faster growth. With this technique, four to six generations of wheat plants can be grown per year instead of two generations under normal growth conditions. The result is researchers develop new crop varieties quicker.

Researchers at the Biosciences eastern and central Africa–International Livestock Research Institute Hub, known as the BecA-ILRI Hub and the John Innes Centre, UK, are bringing the benefits of Speed Breeding to Africa. Scientists Peter Emmrich and Oluwaseyi Shorinola are applying Speed Breeding to grass pea and wheat breeding in Africa, demonstrating that the technique can be used for major and orphan crop breeding.

Breeding for improved wheat lines under Speed Breeding conditions at the BecA-ILRI Hub

Shorinola is developing new wheat lines that have seen increased grain size and protein content and that are resistant to major wheat diseases in East Africa. His research has already resulted in faster growth of wheat plants under Speed Breeding conditions in Africa.

‘Speed breeding is such a simple way of growing plants faster. Unlike many advanced technologies that do not easily translate to Africa, Speed Breeding can easily be adopted by African breeders to accelerate their work. There is no “magic” or complicated science behind it; we are simply using LED lights to extend the length of day for plants, and this makes plants grow faster’, remarks Shorinola.

Emmrich is working on eradicating the toxin produced in grass pea, making it safe to eat in East Africa. Speed Breeding is helping the researchers to breed the low-toxin trait developed at the John Innes Centre, UK, into high-yielding varieties that are adapted to East Africa.

Grass pea is great at surviving extreme weather conditions such as drought and flooding, so the researchers hope non-toxic varieties will contribute to maintaining food and nutritional security as climate change progresses, especially in Ethiopia, where grass pea is already widely consumed.

According to Emmrich: ‘The amount of power needed for the lights and temperature control makes this too expensive for farmers to use. Breeders, however, often have to put their plants through many generation cycles, and in this context Speed Breeding can save both time and money. That means improved varieties can be made available quicker.’

Recognizing the potential of Speed Breeding for accelerating crop improvement in Africa, the BecA-ILRI Hub is planning to expand its Speed Breeding capacity and to integrate it with other modern technologies like gene editing and genomic selection and to make it accessible to African researchers.

Cathrine Ziyomo, BecA-ILRI Hub’s Program lead, says that most of the crops that make significant contributions to Africa’s food security have a lengthy generation time and complex biology. She adds that Speed Breeding presents researchers and plant breeders with unique opportunities to fast track genetic improvements for important traits. 

‘We hope that by establishing a Speed Breeding platform in Africa, the Hub can simultaneously increase access to modern and innovative methods of crop improvement while increasing the efficiency and cost-effectiveness of breeding for under-researched crops’, says Ziyomo.

Shorinola and Emmrich’s research is done in partnership with the John Innes Centre, with support from the Royal Society and Biotechnology and Biological Sciences Research Council (BBSRC), UK.

Africa sits at the frontline of a changing climate system and is very vulnerable to climate change. Agriculture in sub-Saharan Africa needs a boost to feed the 600 million people currently experiencing food insecurity, and the extra 1 billion people expected to live in the next 30 years on the continent. In this light, developing better yielding and more nutritious, climate-resilient crop varieties faster is a major priority for Africa’s researchers.

BecA-ILRI Hub partners with scientists in Ethiopia and Europe to help improve Tef production in Ethiopia

In a truly international collaboration, BecA-ILRI hub is partnering with a team of scientists from the John Innes Centre (JIC, UK), University of Bern (Unibe, Switzerland) and the Ethiopia Institute of Agricultural Research (EIAR, Ethiopia) to use modern genomics tools to address some of the constraints to tef production.

The team, whose other members include Dr Kebebew Assefa, Dr Solomon Chaleyew, Dr Brande Wulff, Dr Kumar Guarav, Dr Dejene Girma and Dr Zerihun Zadele (Universität Bern), will be sequencing the entire genome of a representative collection of the 200 tef lines from Ethiopia. This will be the first time genome sequencing will be done at this scale in this primarily neglected crops.

In addition to this valuable genomic data, the team will extensively measure different aspects of tef’s growth in the field, allowing them to identify genes controlling different characteristics in tef including grain size and plant height.

Knowing these genes will enable Ethiopian researchers to mix-and-match different essential genes through breeding to develop tef varieties with bigger grain and studier stem.

“We are delighted to work alongside our partners at BecA-ILRI Hub, EIAR and Bern on this important crop. We hope that the use of genomic approaches and training will provide new tools for breeders to develop improved tef cultivars for farmers.”

Prof Cristobal Uauy, Project lead

Tef is an ancient crop grown in Ethiopia for more than 2000 years. It constitutes a large part of the diet of the 112 million people in Ethiopia as it is used to make Ethiopia’s main staple dish – injera, a flat fermented bread eaten daily in virtually every household.

Tef’s ability to grow under harsh environmental conditions and marginal soils makes it a fail-safe crop of choice by many subsistence farmers in Ethiopia.

Tef is also attracting a lot of attention beyond the border of Ethiopia. Over the last decade, tef popularity as a global “superfood” is growing in the western world mainly due to its high nutrient profile with high Fe, Ca, fibre, resistant starch and lysine content. Tef flour is gluten-free.

Although a vital food security crop and an increasingly popular crop, tef is particularly challenging to produce compared to many cereal crops. One big problem with tef production is the very tiny size of its seed small seed.

Tef seeds are (< 1 mm wide and 75 tef seeds weigh as much a single rice grain. The tiny seed size is, however, not the only problem tef farmers are grappling with. Tef plants also have very tiny, slender and weak stems which falls over (lodge) when the plants are ready for harvest causing massive seed losses.

The name tef is actually derived from the Amharic word for lost (“teffa”) bearing reference to the fact that the tiny seeds are lost during harvest.

The project is funded through a FLAIR collaboration grant award from the Royal Society UK to Prof Cristobal Uauy (JIC) and Dr Oluwaseyi Shorinola (BecA-ILRI Hub).

“This is a genuinely equitable north-south collaboration to improve a very important but largely neglected crop in Africa. Our collaboration will produce lasting and valuable genomics resource that Ethiopian researchers can use and re-use for a long time to improve any characteristic of interest in tef.”

Dr Oluwaseyi Shorinola, a co-lead on the project

New partnership with U.K research network creates training opportunities for early career researchers

CONNECTED conducts Virus and vector diagnostics workshop for selected researchers at BecA-ILRI Hub

The Community Network for African Vector-Borne Plant Viruses (CONNECTED) formed a partnership with BecA-ILRI Hub in 2018 that led to a five-day full-funded training course for early career plant molecular biologists from across Africa. The course titled: An introduction to virus and vector diagnostics took place on 11-15 March and was hosted by BecA-ILRI Hub in Nairobi, Kenya.

The group pose for a photo

The course trained 17 participants from 10 countries, carefully selected after a call for early career researchers interested in virus and vector diagnostics was put out by CONNECTED and shared on various digital platforms. The trainers were Professor Neil Boonham from Newcastle University and Professor Gonçalo Silva from The Natural Resources Institute, University of Greenwich, UK. Their key objective was to empower the participants with the ability to diagnose cassava and yam diseases by empowering them with practical skills that can easily be used in their fieldwork.

The training began with opening remarks from Jacob Mignouna, BecA-ILRI Hub’s Director: “This training highlights the functions and goals of our diagnostic platform, that is set up to provide knowledge and technologies to help researchers advance their career goals.” This was followed by an introduction of BecA’s technology platforms in a presentation made by BecA’s Technology Manager, Josephine Birungi and a round table introduction of the participants conducted by Julius Osaso, BecA’s diagnostic platform manager.

Professor Boonham then took the trainees through an introduction to DNA Bar-coding and instructed them on how to achieve high quality results to start off the training, which was followed by a lab induction by ILRI’s health and safety department (EOHS). After lunch, the trainees began their lab training that involved DNA extraction and PCR amplification.

Over the next couple of days, the trainees were taken through gel electrophoresis, product purification, DNA prep for sequencing, LAMP and RPA amplification, Database searching and DNA clustering. The training sessions included a morning outline of activities and questions from the trainees, and a recap of the day’s activities and general questions at the end of the training days.

“I am glad that this workshop has brought in participants from our partner institutions such as NACRRI with whom we already have on-going projects, but also the renewed opportunities for other partnerships.” Julius Osaso, Diagnostics Manager, BecA-ILRI Hub.

 “I have learnt techniques such as bar-coding that will help me distinguish the species of insects like the whitefly, which is very important for the work that I do. I have to thank CONNECTED network and BecA for this opportunity.” Helen Apio, NACRRI, Uganda

“I am a trained entomologist with no prior experience on some of these techniques such as PCR and DNA extraction, which are very important to me and my project work, which is on aphids. I am grateful to CONNECTED because I can now integrate entomology and microbiology to reach greater heights in my career.” Honest Machekano, Botswana International University of Science and Technology (BIUST), Botswana.

“The training has strengthened my skills, which is great for my career, I now know how to diagnose viruses and identify insect pests for plans, I will now be to identify what lies in resistant virus lines.” Fred Masika, ABCF alumni, Uganda.

The course funding included travel, accommodation, course fees and subsistence. The participants came from 10 countries: Benin, Burundi, Democratic Republic of Congo, Ghana, Kenya, Nigeria, South Africa, Tanzania, Uganda and Zambia.

The CONNECTED network is a project that is working to build a sustainable network of international scientists and researchers to tackle vector-borne plant diseases that devastate lives in Sub-Saharan Africa.

Early career researchers who might be interested in similar opportunities are invited to join the CONNECTED network, which is free of charge by following this link.

Oluwaseyi Shorinola is awarded FLAIR Fellowship

The African Academy of Sciences and Royal Society announce the recipients of the FLAIR scheme that is awarding £25M, (£300,000 each) to 30 early career African research scientists.

We are proud to announce that Dr Oluwaseyi Shorinola is one of the scientists that have been awarded £300,000 (Approx. US$400,000) over 2 years. Oluwaseyi’s FLAIR research fellowship will be carried out at the BecA-ILRI Hub.

FLAIR (Future Leaders – African Independent Research) is a programme of The African Academy of Science and Royal Society, with support from the UK’s Global Challenges Research Fund (GCRF). The fellowship is designed to help talented early-career researchers, whose science is focused on the needs of the continent, establish independent careers in African institutions and ultimately, their own research groups. Up to 30 FLAIR fellowships will be awarded in 2019 to researchers from Cameroon, Nigeria, Rwanda, South Africa and Zimbabwe.

Dr Shorinola has a pre-existing relationship with the BecA-ILRI Hub, where he was on secondment as a post-doctoral scientist from the John Innes Centre (JIC), UK. His post-doctoral work focused on understanding the genetic control of important economic traits in wheat including grain quality and root development. He is using a combination of mutational genomics approaches, high-throughput phenotyping, next-generation sequencing and classical genetics to identify genes involved in grain quality traits and root development and will deploy these to develop improved wheat varieties.

He is additionally involved in the ACACIA (acaciaafrica.org) partnership – a strategic partnership between JIC and the BecA-ILRIHub. Under this partnership, Oluwaseyi is coordinating an extensive 2-year bioinformatics training programme to building a support network for agricultural research in Africa.

His research as a FLAIR fellow at BecA-ILRI Hub will focus on using genetics to improve the yield and quality of wheat production in East Africa.  Olywayesi will particularly focus on using “speed” breeding to introduce five beneficial genes for grain size, protein content and disease resistance into East Africa wheat.

Statement of condolence on the loss of Kodjo Glato, a fine young agricultural scientist from Togo

Kodjo Glato was one of 157 passengers and crew who tragically perished in the crash of flight ET302 on 10 March 2019

The International Livestock Research Institute (ILRI) and Biosciences eastern and central Africa (BecA)-ILRI Hub express their profound sympathy to all those who were bereaved when their family members, friends or colleagues tragically lost their lives in the Ethiopian Airlines crash on Sunday, 10 March 2019.

A Togolese national, Dr Glato was an assistant professor and researcher at the University of Lomé, Togo, a partner institution of ILRI’s. He was on his way to Nairobi to attend a BecA-ILRI Hub training course that is part of the Community Network for African Vector-Borne Plant Viruses (CONNECTED).

Dr Glato was a biotechnologist and plant physiologist working on agricultural genetic diversity and smallholder farming practices associated with sweetpotato cultivation. He received his PhD in 2015 from the University of Lomé.

Staff and partners at the BecA-ILRI Hub knew him as a hardworking, affable and dedicated young professional. He was part of a new generation of scientists contributing to Togo’s agricultural development.

Kodjo Glato inspired many with his drive and tenacity. He was known to take on challenges with monumental zeal. His passion for the smallholder farmer will be badly missed. May he rest in peace.
—Jacob Mignouna, director of the BecA-ILRI Hub
It is always sad to lose a colleague suddenly. But to lose a colleague at the very start of his career, with so much left to contribute, is a tragedy.
—Jimmy Smith, director general of ILRI

‘On behalf of ILRI’, Jimmy Smith said, ‘we extend our deepest condolences to Kodjo Glato’s family, friends and colleagues as well as to all those who lost colleagues, friends and loved ones on flight ET302.’

Demystifying Passion Fruit Woodiness Disease

Florence’s study aims to save smallholder farmers’ from losing passion fruit production

Florence Munguti was an ABCF fellow at BecA-ILRI Hub in 2014 when she began her study to identify viruses associated with passion fruit woodiness disease.

In Kenya, the passion fruit is one of the top three export fruits, coming close behind the mango and avocado in terms of foreign exchange earnings.  It is grown mainly by smallholder farmers for subsistence and commercialization and has great potential to alleviate poverty due to its high market value and the crop’s short maturity period. However, many farmers are making great losses due to the devastating effects of the woodiness viral disease that stifles passion fruit production. This makes it one of the most dangerous diseases of the purple passion fruit.

In November 2014, she began her study with the collection of passion fruit leaf samples already showing symptoms of the disease in Njoro, Nakuru county, Kenya. At our laboratories, she used next generation sequencing to identify viruses associated with passion fruit woodiness disease in Kenya. The sequence analysis revealed the presence of complete genome sequences for Cow pea aphid-borne mosaic virus (CABMV) previously associated with woodiness viral disease in Kenya.

Woodiness disease is caused by the CABMV, transmitted by sap sacking insects such as aphids and mites as well as using infected tools in the management of the crop for example during pruning. The disease is characterized by light yellow discoloration on the leaves and a woody hard fruit, hence the “woodiness” name.

The sequences and information obtained in this study will be useful in development of more sensitive diagnostic assays that can be used to detect the disease. Florence’s paper titled: Transcriptome Sequencing Reveals a Complete Genome Sequence of Cowpea Aphid-Borne Mosaic Virus from Passion Fruit in Kenya is available here



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How the ABCF program helped Bunmi develop new varieties to boost cassava production

Bunmi Olasanmi, a lecturer and a researcher at the University of Ibadan, Nigeria, swears that the most exciting thing about science is developing improved varieties of crops for greater yields.

Olasanmi’s work focuses on cassava, he chose to work on cassava because it is vital to the economy of Nigeria, which is also the world’s largest producer of the crop in the world mainly through subsistence farming.

A new variant of the root crop is the yellow cassava, that is fortified with Vitamin A, a critical nutrient that meets nutrition requirements and improves human health. But biofortified varieties of cassava are susceptible to cassava mosaic disease (CMD). They also have poor plant architecture making them unsuitable for intercropping, which is important to small-scale farmers.

Selecting outstanding genotypes to develop CMD resistant varieties of cassava using conventional screening methods alone may take about 10 years. As an ABCF fellow, Olasanmi used molecular markers to accelerate the process of developing new varieties. Out of over 600 genotypes screened at BecA-ILRI Hub, he was able to identify 68 cassava genotypes with resistance to CMD and high beta carotene content. The clonal evaluation of cassava genotypes for desirable traits are ongoing and the field evaluations will be conducted at different locations in Nigeria for two seasons starting in 2019.

The University of Ibadan has a laboratory where Olasanmi could have done this work. However, it does not have adequate infrastructure to support all his research activities. Olasanmi received his PhD in plant breeding from University of Ibadan. He was awarded a fellowship from the Institute for Genomic Diversity at Cornell University and was a finalist in the third Africa-wide young professionals in science competition that was run by the Young Professionals in Agricultural Research and Development.

Providing opportunities for women in science

Despite the growing demand for cross-nationally-comparable statistics on women in science, national data and their use in policymaking remains limited. A study conducted by UNESCO, published in June 2018 indicates that women account for 28.8% of the world’s researchers

BecA-ILRI Hub is constantly seeking to close the gender gap by encouraging women researchers to participate in the different opportunities the platform provides.

Obaiya Utoblo is a PhD student at the University of Ghana, West Africa Center for Crop (WACCI), who had the opportunity to participate in one of BecA-ILRI Hub’s trainee workshops that equipped students with skills in science communication. The trainees were equipped with data management and communication skills, which provided them with the essentials of effective communication especially while speaking to a non-scientific audience.

While at BecA, Obaiya had the chance to interact with other women in science which gave her the valiance necessary to work towards her career goals.

Read more about her experience as a woman in science on the ISAAA website here