ILRI Research Methods Group: Team-wide outputs

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Chromosome-scale assembly of the African yam bean genome
(Journal Article, 2024-12-18) Waweru, Bernice; Njaci, Isaac; Paliwal, R.; Maranga, M.; Muli, Collins; Murungi, E.; Kaimenyi, D.; Lyimo, B.; Nigussie, H.; Ahadi, B.B.; Assefa, E.; Ishag, H.; Olomitutu, O.; Abberton, M.; Darby, C.; Uauy, C.; Yao, Nasser; Adewale, D.; Emmrich, P.; Domelevo Entfellner, Jean-Baka; Shorinola, Oluwaseyi
Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining Nanopore-based assembly with Hi-C scaffolding, we produced a high-quality chromosome-scale assembly with an N50 of 69.5 Mbp. Using transcriptome evidence from Nanopore RNASeq and protein homology evidence from related crops, we predicted and annotated 31,614 putative protein coding genes. We also show how this genome substantially improves anchoring of genetic markers from African yam bean, confirming its significance as a resource for genetic research in African yam bean.
Protocol for a Tier 2 approach to generate context-specific enteric methane emission factors (EF) for cattle production systems using IPCC method
(Manual, 2024-12-15) Balcha, Endale; Wilkes, A.; Poole, Elizabeth J.; Marquardt, S.; Ndun’gu, P.; Onyango, A.A.; Merbold, L.; Korir, Daniel; del Prado, A.; Pardo, G.; Wisser, D.; Lanzoni, L.; Scholtz, M.; Katongole, C.; Lind, Vibeke; Assouma, M.H.; Dossa, L.H.; du Toit, L.; Rosenstock, T.; Steward, P.; Kagai, Jesse; Tadese, M.; Gibbons, J.; Odubote, I.K.; Bateki, C.A.; Kimoro, B.; Bronsvoort, B.M. de C. ; Arndt, Claudia
Protocol for a Tier 2 approach to generate context-specific enteric methane emission factors (EF) for small ruminants’ production systems based on IPCC method
(Manual, 2024-12-15) Korir, Daniel; Balcha, Endale; Wilkes, A.; Poole, Elizabeth J.; Marquardt, S.; Ndung’u, P.; Onyango, A.A.; Merbold, L.; del Prado, A.; Pardo, G.; Wisser, D.; Lanzoni, L.; Scholtz, M.; Katongole, C.; Lind, Vibeke; Assouma, M.H.; Dossa, L.H.; du Toit, L.; Rosenstock, T.; Steward, P.; Kagai, Jesse; Tadese, M.; Gibbons, J.; Odubote, I.K.; Bateki, C.A.; Kimoro, B.; Bronsvoort, B.M. de C. ; Arndt, Claudia
Pioneer Farmer Manual: Step-by-step guide on How to use citizen science data collection form
(Manual, 2024-10-15) Njamba, Harrison; Kiptoo, Emmaculate; Gichuki, Leah; Maiyo, Nathan
The citizen science data collection guide is designed to help pioneer farmers collect and submit farm records on dairy production to the scientist at ILRI. The manual focuses on information for data collectors[farmers] to keep monthly farm records and make observations on changes happening on the farm. The guide will assist pioneer farmers in filling out the Livestock and Climate Initiative data collection questionnaire. Pioneer households are expected to fill out the ODK form at the end of every month and send it to the research team by the 2nd day of the following month. The answers the farmer enters on this form are largely informed by the recording-keeping sheets that they fill regularly.
Complete genome sequencing and comparative phylogenomics of nine African swine fever virus (ASFV) isolates of the virulent East African p72 genotype IX without viral sequence enrichment
(Journal Article, 2024-09-14) Domelevo Entfellner, Jean-Baka; Okoth, Edward A.; Onzere, C.K.; Upton, C.; Njau, E.P.; Höper, D.; Henson, Sonal P.; Oyola, Samuel O.; Bochere, Edwina; Machuka, Eunice M.; Bishop, Richard P.
African swine fever virus (ASFV) is endemic to African wild pigs (Phacochoerus and Potamochoerus), in which viral infection is asymptomatic, and Ornithodoros soft ticks. However, ASFV causes a lethal disease in Eurasian domestic pigs (Sus scrofa). While Sub-Saharan Africa is believed to be the original home of ASFV, publicly available whole-genome ASFV sequences show a strong bias towards p72 Genotypes I and II, which are responsible for domestic pig pandemics outside Africa. To reduce this bias, we hereby describe nine novel East African complete genomes in p72 Genotype IX and present the phylogenetic analysis of all 16 available Genotype IX genomes compared with other ASFV p72 clades. We also document genome-level differences between one specific novel Genotype IX genome sequence (KE/2013/Busia.3) and a wild boar cell-passaged derivative. The Genotype IX genomes clustered with the five available Genotype X genomes. By contrast, Genotype IX and X genomes were strongly phylogenetically differentiated from all other ASFV genomes. The p72 gene region, on which the p72-based virus detection primers are derived, contains consistent SNPs in Genotype IX, potentially resulting in reduced sensitivity of detection. In addition to the abovementioned cell-adapted variant, eight novel ASFV Genotype IX genomes were determined: five from viruses passaged once in primary porcine peripheral blood monocytes and three generated from DNA isolated directly from field-sampled kidney tissues. Based on this methodological simplification, genome sequencing of ASFV field isolates should become increasingly routine and result in a rapid expansion of knowledge pertaining to the diversity of African ASFV at the whole-genome level.
Establishing African genomics and bioinformatics programs through annual regional workshops
(Journal Article, 2024-08) Sharaf, Abdoallah; Nesengani, Lucky Tendani; Hayah, Ichrak; Kuja, Josiah Ochieng; Mdyogolo, Sinebongo; Omotoriogun, Taiwo Crossby; Odogwu, Blessing Adanta; Beedessee, Girish; Smith, Rae Marvin; Barakat, Abdelhamid; Moila, Acclaim M; El Hamouchi, Adil; Benkahla, Alia; Boukteb, Amal; Elmouhtadi, Amine; Mafwila, Antoine Lusala; Abushady, Asmaa Mohammed; Elsherif, Assem Kadry; Ahmed, Bulbul; Wairuri, Charles; Ndiribe, Charlotte C; Ebuzome, Chukwuike; Kinnear, Craig J; Ndlovu, Deborah-Fay; Iraqi, Driss; El Fahime, Elmostafa; Assefa, Ermias; Ouardi, Faissal; Belharfi, Fatima Zohra; Tmimi, Fatim Zohra; Markey, Fatu Badiane; Radouani, Fouzia; Zeukeng, Francis; Mvumbi, Georges Lelo; Ganesan, Hamilton; Hanachi, Mariem; Nigussie, Helen; Charoute, Hicham; Benamri, Ichrak; Mkedder, Ikram; Haddadi, Imane; Meftah-Kadmiri, Issam; Mubiru, Jackson Franco; Domelevo Entfellner, Jean-Baka Kodjo; Rokani, Joan Bayowa; Ogwang, Joel; Daiga, Jude Bigoga; Omumbo, Judy; Ideozu, Justin Eze; Errafii, Khaoula; Labuschagne, Kim; Komi, Komi Koukoura; Tonfack, Libert Brice; Hadjeras, Lydia; Ramantswana, Madeleine; Chaisi, Mamohale; Botes, Marietjie W; Kilian, Mariëtte; Kvas, Marija; Melloul, Marouane; Chaouch, Melek; Khyatti, Meriem; Abdo, Michael; Phasha-Muchemenye, Mmatshepho; Hijri, Mohamed; Mediouni, Mohammed Rida; Hassan, Mohammed Ahmed; Piro, Mohammed; Mwale, Monica; Maaloum, Mossaab; Mavhunga, Mudzuli; Olivier, Nicholas Abraham; Aminou, Oumaima; Arbani, Oumayma; Souiai, Oussema; Djocgoue, Pierre François; Mentag, Rachid; Zipfel, Renate Dorothea; Tata, Rolland Bantar; Megnekou, Rosette; Muzemil, Sadik; Paez, Sadye; Salifu, Samson Pandam; Kagame, Samuel Paul; Selka, Sarra; Edwards, Sean; Gaouar, Semir Bechir Suheil; Reda, Shaimaa Roshdy Abdullah; Fellahi, Siham; Khayi, Slimane; Ayed, Soumia; Madisha, Thabang; Sahil, Tulsi; Udensi, Ogbuagu Ugorji; Ras, Verena; Ezebuiro, Victor; Duru, Vincent C; David, Xavier; Geberemichael, Yonas; Tchiechoua, Yves H; Mungloo-Dilmohamud, Zahra; Chen, Zhiliang; Happi, Christian; Kariuki, Thomas; Ziyomo, Cathrine; Djikeng, Appolinaire; Badaoui, Bouabid; Mapholi, Ntanganedzeni; Muigai, Anne; Osuji, Julian O; Ebenezer, ThankGod Echezona
The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.
Leveraging AI and digital technologies to transform ILRI’s research and operations
(Presentation, 2024-05-12) Dhulipala, Ram; Paliwal, Ambica; Bett, Bernard K.; Domelevo Entfellner, Jean-Baka; Ojango, Julie M.K.; Gerba, Michael; Victor, Michael
Designing and delivering bioinformatics project-based learning in East Africa
(Journal Article, 2024) Kibet, C.K.; Domelevo Entfellner, Jean-Baka; Jjingo, D.; de Villiers, E.P.; de Villiers, S.; Wambui, K.; Kinyanjui, S.; Masiga, D.
Background The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings. Results In response to the pandemic, we developed a program to maintain “residential” training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects. Conclusion We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment.
Molecular and serological diagnosis of multiple bacterial zoonoses in febrile outpatients in Garissa County, north-eastern Kenya
(Journal Article, 2024-05-28) Wainaina, Martin; Lindahl, Johanna F.; Mayer-Scholl, A.; Ufermann, C.-M.; Domelevo Entfellner, Jean-Baka; Roesler, U.; Roesel, Kristina; Grace, Delia; Bett, Bernard K.; Al Dahouk, S.
Bacterial zoonoses are diseases caused by bacterial pathogens that can be naturally transmitted between humans and vertebrate animals. They are important causes of non-malarial fevers in Kenya, yet their epidemiology remains unclear. We investigated brucellosis, Q-fever and leptospirosis in the venous blood of 216 malaria-negative febrile patients recruited in two health centres (98 from Ijara and 118 from Sangailu health centres) in Garissa County in north-eastern Kenya. We determined exposure to the three zoonoses using serological (Rose Bengal test for Brucella spp., ELISA for C. burnetti and microscopic agglutination test for Leptospira spp.) and real-time PCR testing and identified risk factors for exposure. We also used non-targeted metagenomic sequencing on nine selected patients to assess the presence of other possible bacterial causes of non-malarial fevers. Considerable PCR positivity was found for Brucella (19.4%, 95% confidence intervals [CI] 14.2–25.5) and Leptospira spp. (1.7%, 95% CI 0.4–4.9), and high endpoint titres were observed against leptospiral serovar Grippotyphosa from the serological testing. Patients aged 5–17 years old had 4.02 (95% CI 1.18–13.70, p-value = 0.03) and 2.42 (95% CI 1.09–5.34, p-value = 0.03) times higher odds of infection with Brucella spp. and Coxiella burnetii than those of ages 35–80. Additionally, patients who sourced water from dams/springs, and other sources (protected wells, boreholes, bottled water, and water pans) had 2.39 (95% CI 1.22–4.68, p-value = 0.01) and 2.24 (1.15–4.35, p-value = 0.02) times higher odds of exposure to C. burnetii than those who used unprotected wells. Streptococcus and Moraxella spp. were determined using metagenomic sequencing. Brucellosis, leptospirosis, Streptococcus and Moraxella infections are potentially important causes of non-malarial fevers in Garissa. This knowledge can guide routine diagnosis, thus helping lower the disease burden and ensure better health outcomes, especially in younger populations.
Evaluation of genetic variability in four Nigerian locally-adapted chicken populations using major histocompatibility complex-linked LEI0258 microsatellite marker
(Journal Article, 2023-09-15) Oladejo, O.A.; Oseni, S.O.; Kyallo, Martina M.; Domelevo Entfellner, Jean-Baka; Tor, N.E.; Tiambo, Christian K.; Pelle, Roger
Major Histocompatibility Complex (MHC) is a group of genes that generally influence immune response in vertebrates, and it has been explored among different animal species in various countries. However, there is a paucity of information on its application in Nigerian locally-adapted chickens (NLAC). This research investigated genetic polymorphism, allele variability, and genetic relationships using LEI0258 major histocompatibility complex-linked microsatellite marker among four NLAC populations: Fulani × Yoruba ecotypes, FUNNAB Alpha × Noiler breeds. Blood samples were randomly collected from 50 mature birds in each population and DNA was extracted and subsequently subjected to PCR, Sanger sequencing, and bioinformatic analysis. There were two variable numbers of tandem repeats (VNTRs), with 90% of the alleles containing only one R13 and varying numbers of the R12 motifs that ranged from 1 to 19. Additional polymorphism was revealed by the presence of five SNPs and three indels in the upstream and downstream regions of LEI0258. A total of 48 alleles were observed with sizes ranging from 188 to 530 base pairs while the allele frequencies within the populations ranged from 1.9 to 29.2%. However, only 17 out of the 48 alleles had corresponding MHC-B haplotypes. Haplotypes B2, B12, and B21 found in this study had been reported to confer resistance to infectious poultry diseases especially avian influenza in locally adapted chickens. There were high allelic variability and genetic polymorphisms observed via the atypical LEI0258 microsatellite in describing the MHC-B region.
Research Computing at ILRI: brief overview of HPC resources for genomics
(Presentation, 2023-06-22) Orth, Alan S.
A farmer-friendly tool for estimation of weights of pigs kept by smallholder farmers in Uganda
(Journal Article, 2023-06) Marshall, Karen; Poole, Elizabeth J.; Oyieng, Edwin; Ouma, Emily A.; Kugonza, Donald R.
Pig keeping is important to the livelihoods of many rural Ugandans. Pigs are typically sold based on live weight or a carcass weight derived from this; however this weight is commonly estimated due to the lack of access to scales. Here, we explore the development of a weigh band for more accurate weight determination and potentially increased farmer bargaining power on sale price. Pig weights and varied body measurements (heart girth, height, and length) were collected on 764 pigs of different ages, sex, and breed types, from 157 smallholder pig keeping households in Central and Western Uganda. Mixed-effects linear regression analyses, with household as a random effect and the varied body measurements as a fixed effect, were performed to determine the best single predictor for cube root of weight (transformation of weight for normality), for 749 pigs ranging between 0 and 125 kg. The most predictive single body measurement was heart girth, where weight in kg = (0.4011 + heart girth in cm × 0.0381)3. This model was found to be most suitable for pigs between 5 and 110 kg, notably more accurate than farmers’ estimates, but still with somewhat broad confidence intervals (for example, ±11.5 kg for pigs with a predicted weight of 51.3 kg). We intend to pilot test a weigh band based on this model before deciding on whether it is suitable for wider scaling.
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
(Journal Article, 2023-04-17) Njaci, Isaac; Waweru, Bernice; Kamal, N.; Muktar, Meki S.; Fisher, D.; Gundlach, H.; Muli, Collins; Muthui, Lucy; Maranga, M.; Kiambi, D.; Maass, Brigitte L.; Emmrich, P.M.F.; Domelevo Entfellner, Jean-Baka; Spannag, M.; Chapman, M.A.; Shorinola, Oluwaseyi; Jones, Christopher S.
Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).
DSpacing the CGSpace Way: Lessons in content tagging, vocabularies, and curation
(Presentation, 2023-04-04) Orth, Alan S.
Development of a weigh-band for pigs in Uganda (Data on weights and body measurements of Ugandan pigs)
(Dataset, 2022-12-07) Marshall, Karen; Poole, Elizabeth J.; Ouma, Emily A.; Kugonza, Donald R.
Knowledge of the body weight in pigs is important in informing management decisions and, often, negotiating a sale price. In the smallholder pig system in Uganda the smallholder pig keepers usually do not know the body weights of their animals nor have access to scales. To overcome this, we propose to collect body measurement of pigs with the following objectives: 1. Determine the best predictive equation for weight from body measurement for (a) all animals, and (b) subsets of animals (e.g., grouped by weight, age, sex) 2. Estimate the loss in predictive accuracy in only using one variable for all animals and subsets of animals (testing this as one predictive variable makes a weigh-band a viable option) 3. Should one variable not be viable explore the options for making a farming friendly tool for predicting weight (weigh band, table, app etc.) 4. Synthesis and reporting of results including sharing with local partners 5. Production and dissemination of weight bands (or alternative tool) to participating farmers. Exploration of options for a distributor of these (e.g.private sector partner) The dataset is provided along with the ODK tool used to collect the data (the dictionary for coded variables can be found on the Choices sheet)
Co-creation of theories of changes at value-chain level for the One-CGIAR initiative Sustainable Animal Productivity for Livelihoods, Nutrition and Gender Inclusion
(Presentation, 2022-06-15) Marshall, Karen; Teufel, Nils; Poole, Elizabeth J.; Altshul, Helen J.
A locus conferring tolerance to Theileria infection in African cattle
(Journal Article, 2022-04-21) Wragg, D.; Cook, Elizabeth A.J.; Latré de Laté, Perle; Sitt, Tatjana; Hemmink, Johanneke D.; Chepkwony, Maurine C.; Njeru, Regina; Poole, Elizabeth J.; Powell, J.; Paxton, E.A.; Callaby, R.; Talenti, A.; Miyunga, Antoinette; Ndambuki, Gideon M.; Mwaura, Stephen; Auty, H.; Matika, O.; Hassan, M.; Marshall, Karen; Connelley, T.; Morrison, L.J.; Bronsvoort, B.M. de C.; Morrison, W.I.; Toye, Philip G.; Prendergast, J.G.D.
East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva.
ODK Viewer: A tool to visualise ODK (version 1) data on Android devices
(Source Code, 2014-02-24) Quirós, Carlos F.
ODK Viewer is a tool that complements ODK by displaying on-device data in tabular form and allows easier reviewing and editing of data before submission to the server.
Maziwa Zaidi: Selection of agripreneurs and linked households for testing delivery of bundled technology packages in Tanzania
(Brief, 2022-06-15) Rao, E.J.O.; Omondi, Immaculate A.; Poole, Elizabeth J.; Omore, Amos O.
Inherited tolerance in cattle to the apicomplexan protozoan Theileria parva is associated with decreased proliferation of parasite-infected lymphocytes
(Journal Article, 2021-11-05) Latré de Laté, Perle; Cook, Elizabeth A.J.; Wragg, David; Poole, Elizabeth J.; Ndambuki, Gideon M.; Miyunga, Antoinette; Chepkwony, Maurine C.; Mwaura, Stephen; Ndiwa, Nicholas N.; Prettejohn, Giles; Sitt, Tatjana; Aardt, Richard van; Morrison, W. Ivan; Prendergast, James G.D.; Toye, Philip G.
Theileria parva is the causative agent of East Coast fever and Corridor disease, which are fatal, economically important diseases of cattle in eastern, central and southern Africa. Improved methods of control of the diseases are urgently required. The parasite transforms host lymphocytes, resulting in a rapid, clonal expansion of infected cells. Resistance to the disease has long been reported in cattle from T. parva-endemic areas. We reveal here that first- and second-generation descendants of a single Bos indicus bull survived severe challenge with T. parva, (overall survival rate 57.3% compared to 8.7% for unrelated animals) in a series of five field studies. Tolerant cattle displayed a delayed and less severe parasitosis and febrile response than unrelated animals. The in vitro proliferation of cells from surviving cattle was much reduced compared to those from animals that succumbed to infection. Additionally, some pro-inflammatory cytokines such as IL1β, IL6, TNFα or TGFβ which are usually strongly expressed in susceptible animals and are known to regulate cell growth or motility, remain low in tolerant animals. This correlates with the reduced proliferation and less severe clinical reactions observed in tolerant cattle. The results show for the first time that the inherited tolerance to T. parva is associated with decreased proliferation of infected lymphocytes. The results are discussed in terms of whether the reduced proliferation is the result of a perturbation of the transformation mechanism induced in infected cells or is due to an innate immune response present in the tolerant cattle.

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