ILRI Livestock Genetics, Nutrition and Feed Resources theme outputs (2025-)

Permanent URI for this collectionhttps://hdl.handle.net/10568/169328

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The genetic structure and diversity of smallholder dairy cattle in Rwanda
(Journal Article, 2025-05-27) Opoola, O.; Shumbusho, F.; Rwamuhizi, I.; Houaga, I.; Harvey, D.; Hambrook, D.; Watson, K.; Chagunda, M.G.G.; Mrode, Raphael A.; Djikeng, Appolinaire
Previous genomic characterisation of Rwanda dairy cattle predominantly focused on the One Cow per Poor Family (locally called “Girinka”) programme. However, smallholder farmers in Rwanda have benefited from other livestock initiatives and development programmes. Capturing and documenting the genetic diversity, is critical in part as a key contribution to genomic resource required to support dairy development in Rwanda. A total of 2,229 crossbred animals located in all dairy-producing regions of Rwanda were sampled. For each animal, a hair sample was collected and genotyped by using the Geneseek Genomic Profiler (GGP, Neogen Geneseek®) Bovine 50 K (n = 1,917) and GGP Bovine 100 K arrays (n = 312). The combined dataset was subject to quality control, data curation for use in population genetics and genomic analyses. To assess the genetic structure and diversity of the current population, key analyses for population structure were applied: Principal Component Analysis (PCA), population structure and diversity, admixture analysis, measures of heterozygosity, runs of homozygosity (ROH) and minor allelic frequency (MAF). A dataset of global dairy population of European taurine, African indicus and African taurus (n = 250) was used as reference. Results showed that Rwanda cattle population is highly admixed of diverse pure and crossbred animals with average MAF of 33% (standard error; se = 0.001) with proportion of foreign high yielding (taurine) dairy breeds of Jersey Island (18%); 12% non-Island Jersey and 42% Holstein-Friesian ancestries. Two African Bos taurus and five Bos indicus breeds contributed 28% of their genetics. Genetic distances were highest in Gir and N’dama (0.29); and Nelore and N’dama (0.29). There were 1,331 ROH regions and average heterozygosity were high for Rwanda cattle (0.41 se = 0.001). Asides well-established genes in cattle, we found evidence for a variety of novel and less-known genes under selection to be associated with fertility, milk production, innate immunity and environmental adaptation. This observed diversity offers opportunity to decipher the presence and/or lack of genetic variations to initiate short- and long-term breed improvement programmes for adaptation traits, disease resistance, heat tolerance, productivity and profitability of smallholder dairy systems in Rwanda.
Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)
(Journal Article, 2025-05-26) Jones, M.R.W.; Kebede, W.; Teshome, Abel; Girija, A.; Teshome, A.; Girma, D.; Brown, J.K.M.; Quiroz-Chavez, J.; Jones, Christopher S.; Wulff, B.B.H.; Assefa, K.; Tadele, Z.; Mur, L.A.J.; Chanyalew, S.; Uauy, C.; Shorinola, Oluwaseyi
Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free “superfood” with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited “omics” resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1—a transcription factor regulating inflorescence morphology in cereals. We also observe a previously unknown relationship between grain size, colour, and fatty acids. These traits are highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.
Whole genome resequencing of a global collection of Napier grass (Cenchrus purpureus) to explore global population structure and QTL governing yield and feed quality traits
(Journal Article, 2025) Teshome, Abel; Lire, H.; Higgins, J.; Olango, T.; Habte, Ermias H.; Negawo, Alemayehu T.; Muktar, Meki S.; Assefa, Yilikal; Pereira, J.F.; Azevedo, A.L.S.; Machado, J.C.; Nyamongo, D.; Zhang, J.; Qi, Y.; Anderson, W.; De Vega, J.; Jones, Christopher S.
Napier grass (Cenchrus purpureus) is a C4 perennial grass species native to Sub-Saharan Africa (SSA) and widely used for feed cattle in the region. In this study, we sequenced the genomes of 450 Napier grass individuals from 18 countries, identifying over 170 million DNA variants (SNPs and Indels). Approximately 1% of these SNPs were informative and used to assess genetic diversity within the collection. Our resequencing study provided valuable insights into the global genetic diversity of Napier grass. Additionally, a genome-wide association study on two independent populations identified multiple quantitative trait loci (QTL) significantly associated with key agronomic traits, including biomass yield, nitrogen and cellulose content. These findings serve as a crucial resource for preserving and understanding Napier grass genetic diversity in the context of climate change. Moreover, they will support genomics-based breeding programs aimed at developing high-yielding and drought-tolerant varieties for forage and biofuel production.
Digital data platform to close the data gap in smallholder dairy systems
(Presentation, 2025-03-18) Mrode, Raphael A.; Ojango, Julie M.K.; Ekine-Dzivenu, Chinyere C.; Gebreyohanes, Gebregziabher
Comparative genomics reveals common diversity and adaptation to harsh environments in the Arabian Peninsula indigenous chickens
(Journal Article, 2025-06) Assiri, A.; Vallejo-Trujillo, A.; Al-Abri, M.; Bahbahani, H.; Almathen, F.; Ahbara, A.; Al Marzooqi, W.; Tijjani, A.; Lawal, R.; Hanotte, Olivier H.
Identifying genomic regions under selection is crucial for comprehending the evolutionary history of the domestic chicken. Arabian Peninsula (AP) indigenous chickens are mostly found outdoors, being reared alongside other livestock for production purposes. These birds show high resilience to extreme temperatures (hot and cold), typical of the desert environment. The selection pressures responsible for unique local adaptations in these birds remain largely unidentified. Here, we aimed to investigate the genome diversity and structure of 15 indigenous chicken populations including 13 populations from the AP (n = 5), Ethiopia (n = 6), and the People's Republic of China (n = 2). We also included two commercial chicken populations, Fayoumi (selected for heat tolerance) and Chantecler (known for its cold tolerance). Principal component (PC) analysis separated all the populations based on their geographic areas of origin. PC1 separates the Ethiopian populations from the Chinese and AP populations, while PC2 separates the AP populations from the Chantecler, and the Ethiopian populations from the Dulong and Chantecler. The genome-wide signatures of analyses identified many candidate regions under positive selection. They include genes that may be associated with thermotolerance. These are involved in energy balance and metabolism (SUGCT, HECW1, MMADHC), cells apoptosis (APP, SRBD1, NTN1, PUF60, SLC26A8, DAP, SUGCT), angiogenesis (RYR2, LDB2, SOX5), skin protection to solar radiation (FZD10, BCO2, WNT5B, COL6A2, SIRT1) as well as growth (NELL1). Our findings suggest that Arabian chicken populations have a distinct gene pool polymorphism in relation to their adaptation to the harsh climatic environments of the AP.
Small-scale poultry: Science-innovation-business
(Presentation, 2025-05-08) Dessie, Tadelle
This keynote presentation explores the transformation of small-scale poultry production in sub-Saharan Africa and Southeast Asia through science, innovation, and business-oriented approaches. Drawing on the experience of the Tropical Poultry Genetic Solutions (TPGS) initiative, the session highlights how high-producing, farmer-preferred chicken breeds, combined with robust public-private partnerships and inclusive innovation platforms, are addressing longstanding challenges in the poultry sector. Emphasis is placed on leveraging genetic improvement, empowering women, and integrating poultry production with broader nutrition and livelihood outcomes. The presentation also reflects on lessons learned, the shift to participatory approaches, and the importance of sustainable commercialization for long-term impact. TPGS's work across more than 20 African countries underscores the potential of context-specific, science-based interventions to drive inclusive growth in smallholder poultry value chains.
Stakeholders meeting on scaling the homegrown school feeding program through chicken eggs in Yirgalem, Sidama Region
(Report, 2025-05-01) Yemane, Tsion; Argaw, Amare
Various agriculture sector stakeholders explored collaborative efforts, shared insights and developed actionable plans to enhance the Homegrown School Feeding Program’s impact on Sidama Region schools and communities. They discussed strategies for expanding the program in the Sidama Region, emphasizing incorporating chicken eggs as a key component of the feeding initiative. During the meeting, an overview of the existing Home Grown School Feeding Program in Murancho Qutela Primary School, Sidama Region, Hawela Woreda, was provided, highlighting its achievements and areas for improvement; the benefits of adding chicken eggs to the feeding initiative, challenges, and potential solutions for scaling up, roles of different stakeholders in implementation, and further strategies for monitoring and evaluation were discussed. The meeting successfully deliberated on expanding the Home Grown School Feeding program in Yirgalem. By incorporating chicken eggs, the program will be able to enhance nutrition for more primary school students while fostering community involvement. The collaborative efforts of all stakeholders will be crucial in overcoming challenges related to resource, production, management and implementing effective strategies for monitoring and evaluation. Further action plans will be developed in subsequent meetings to ensure the program’s successful expansion.
Adopting technologies to enhance productivity, resilience and equity in ruminant livestock resources under pastoral systems of Africa
(Report, 2025-04-30) Ojango, Julie M.K.; Kirui, Peter; Tumanka, F.O.; Rowan, T.N.; Pedreira, B.C.; Mason, K.M.; Martinez, C.C.
Lamb survival and ewe longevity in a crossbreeding program between indigenous and exotic sheep in semi-arid lands
(Journal Article, 2025-08) Oyieng, Edwin P.; Ojango, Julie M.K.; Gauly, M.; Mrode, Raphael A.; Okeyo Mwai, Ally; König, S.
The survival of lambs and longevity of ewes within flocks are important for the sustainability of sheep populations especially in arid and semi-arid lands (ASAL). In this study we conducted pre- and post-weaning survival analysis of lambs and the longevity of ewes of indigenous pure Red Maasai (RRRR), pure Dorper (DDDD), and their crosses comprising F1 (DDRR) and 75%Dorper-25%Red Maasai (DDDR) using Cox and Weibull proportional hazard models. The objective was to determine the genetic and non-genetic factors affecting lamb survival to yearling as well as ewe longevity. Data comprised records on 6,313 lambs and 2,003 ewes. Overall pre-weaning mortality was lower (5%) compared to post-weaning mortality rate (17%). Lambs born during the long dry season had a higher risk of dying than those born during the wet seasons. For both lambs and ewes, the Dorper had the highest risk of dying or being culled. Among the crossbreds, the DDDR lambs and ewes had higher risks of dying or being culled relative to F1 lambs and ewes. The risk of ewes being culled reduced with increasing age at first lambing and parity. Heritability estimates for pre-weaning mortality were higher (0.10 - 0.14) than post-weaning mortality (0.01 - 0.05). The higher heritability for pre-weaning lamb survival in indicates greater genetic variation, presenting an opportunity for selection for lamb survival. Interventions to improve the production environment in the ASAL areas would also improve the survival of lambs and longevity of ewes.
Growth curve fitting and analysis of intestinal flora changes of the Magang Goose (Anser domesticus) during 1 to 70 days post hatch
(Journal Article, 2025-08) Li, X.; Song, G.; Cao, Q.; Mo, Q.; Fu, Y.; Chen, J.; Lukuyu, Ben A.; Wang, S.; Ye, H.; Zhu, Y.; Muhammad, K.S.; Yang, L.; Pan, J.; Wang, W.
Nonlinear models are frequently utilized to study the growth and development of livestock and poultry, and to investigate the dynamic relationship with the intestinal microbiota changes. In this study, a total of 180 Magang geese (1-day-old) were selected and randomly divided into 6 replicates with 30 geese in each replicate. The growth performance, organ development, and intestinal flora composition of geese aged 7, 14, 21, 28, 42, 50, 60, and 70 d were observed. A total of 3 nonlinear growth models were applied to fit the development curves, aiming to explore the ontogenic development of Magang geese and the dynamic changes in the intestinal flora. Our results demonstrated that the Gompertz model serves as the most suitable model for simulating the growth pattern of Magang geese (R²=0.996). Using this model, the weight of the inflection point in Magang geese was 3.470 kg, the age of the inflection point was 25.460d, and the maximum daily gain was 0.061 kg. The development curves of the liver, kidney, and pancreas conform to the Logistic model (R²=0.901, 0.978, 0.971), while the intestinal development also followed this model. The bacteria involved in energy metabolism (Subdoligranulum, Bacteroides, Romboutsia) and the bacteria inhibiting the colonization of harmful bacteria (Blautia) in cecum changed rapidly from 7 to 14 d, and microbial community composition stabilized after 21 d. In conclusion, our findings indicated that the ontogenic pattern of the Magang goose conformed to the Gompertz growth curve. The period from 7 to 42 d represents the rapid growth phase for Magang geese, during which organ development occurs, and cecal microbiota composition becomes increasingly stable.
How did chicken conquer the world? A brief history of our most successful agriculture species
(Video, 2025-04-07) Hanotte, Olivier H.
The history of our most common livestock species, the chicken, from its birth as domesticated animal in the Asian jungles to its world conquest. Olivier Hanotte, International Livestock Research Institute (ILRI) principal scientist and deputy director at the Centre for Tropical Livestock Genetics and Health (CTLGH), explains how chickens are saving the lives of millions daily and will increasingly do so as survivors and saviours.
Estimation of heterosis, combining ability and reciprocal effects for body weight in four genetic groups of chicken from a full diallel cross
(Journal Article, 2025-08) Teshome, Philimon; Goshu, G.; Esatu, Wondmeneh; Dessie, Tadelle
This study aims to estimate the heterotic effects (H^e), general combining abilities (GCA), specific combining abilities (SCA), and reciprocal effects (RE) for body weight (BW) in a 4 × 4 full diallel cross involving Improved Horro (H), commercial Sasso (S), Potchefstroom Koekoek (K), and Dz-white feathered (D) chickens. A total of 960 purebred and F1 hybrid chickens were used in this study, comprising sixteen genetic groups. The birds were reared from hatch to 14 weeks (wk) of age in a deep litter floor house partitioned with wire mesh. Chickens of different genotypes were randomly assigned to three pens per genetic group in a completely randomized design. BW measurements were recorded at hatch, 2, 4, 6, 8, 10, 12, and 14 wk of age. Heterosis estimates indicated that crosses between S males with K and D females (including their reciprocal crosses) exhibited the strongest H^e for BW from early to late ages. In contrast, crosses between H males and K females (and their reciprocals) showed positive but low H^e, which increased slightly at later ages. Meanwhile, the cross between K males and D females displayed negative H^e across all ages, whereas its reciprocal cross had low but positive H^e. GCA effects were high (p < 0.0001) among purebreds, which shows the importance of additive gene effects on BW. SCA highly (p < 0.0001) influenced BW at hatch, wk 2, 4, and 10, highlighting the role of non-additive genetic variance at the early age of BW inheritance. RE was generally non-significant except at hatch (p = 0.002), wk 2 (p < 0.0001), and wk 10 (p = 0.036), indicating potential maternal or paternal contributions during these early developmental stages. In conclusion, the results indicated that breeding strategies should prioritize selecting parents with superior GCA to ensure consistent and predictable gains in BW. Furthermore, developing a broiler line from S sires crossed with the K and D dams and H sires with S dam lines should also be considered.
Prevalence and risk factors for lameness in dairy cattle on selected farms located in Dessie and Kombolcha, Northeast Ethiopia
(Journal Article, 2025-04-28) Mekonin, H.A.; Reda, A.A.; Assen, Alula A.; Assen, A.M.
Background: Lameness in dairy cattle has continued to be a significant burden for farmers in modern dairy production due to its impact on animal welfare and productivity. A cross-sectional study was conducted from May 2022 to February 2023 to estimate the prevalence and identify associated risk factors of lameness in 433 dairy cows across 37 selected farms located in Dessie and Kombolcha, Northeast Ethiopia. Methods: The selected animals were examined for lameness using a five-point visual locomotion scoring technique during daily outdoor access on a solid walking surface in the designated refreshment areas. Cows with a lameness score of > 2 were considered clinically lame. The overall prevalence of lameness was defined as the total number of clinically lame animals divided by the total number of animals examined. The herd-level prevalence was calculated as the total number of positive herds divided by the total number of herds sampled. After variable screening using univariable analysis, separate multivariable mixed-effects logistic regression models that included farm as a random effect were fitted to identify risk factors for lameness at both the animal and herd levels. Results: The overall prevalence of lameness was 5.77% (95%CI = 3.57–7.98%). The herd-level lameness prevalence was 32.4% (95%CI = 18.0–49.8%), while the average within-herd lameness prevalence was 5.20% (95%CI = 2.46–7.95%, range = 0.00–25.0%). The animal- and herd-level risk factors included in the final multivariable mixed-effects model were age, body condition score, milking status, and farm history of lameness. Among these, only milking status and lameness history were significant in the final model. The odds of being lame were higher in the cows in the middle (OR = 10.8, 95%CI = 1.37–84.8, p = 0.024) and late (OR = 11.1, 95%CI = 1.38–88.8, p = 0.024) stages of lactation. Furthermore, the animals on farms with a history of lameness (OR = 10.0, 95%CI = 2.87–37.4, p = 0.001) were more likely to be clinically lame. Conclusion: Lameness was strongly associated with the middle and late stages of lactation, particularly on farms with a previous history of lameness. Therefore, farmers should regularly monitor and maintain cows’ lactation status and increase their awareness about lameness on farms to help reduce its occurrence.
Genetic estimates and genome-wide association studies of antibody response in Tanzanian dairy cattle
(Journal Article, 2025-04-24) Hernandez-Castro, L.E.; Cook, Elizabeth A.J.; Matika, O.; Mengele, I.J.; Motto, S.K.; Bwatota, S.F.; Zirra-Shallangwa, B.; Pong-Wong, R.; Prendergast, J.; Mrode, Raphael A.; Toye, Philip G.; Komwihangilo, D.M.; Lyatuu, E.; Karani, Benedict E.; Nangekhe, Gertrude; Okeyo Mwai, Ally; Shirima, G.M.; Bronsvoort, B.M. de C.
Identifying the genetic determinants of host defence against infectious pathogens is central to enhancing disease resilience and therapeutic efficacy in livestock. Here, we investigated immune response heritability to important infectious diseases affecting smallholder dairy cattle using variance component analysis. We also conducted genome-wide association studies (GWAS) to identify genetic variants that may help understand the underlying biology of these health traits. By assessing 668,911 single-nucleotide polymorphisms (SNPs) genotyped in 2,045 crossbred cattle sampled from six regions of Tanzania, we identified high levels of interregional admixture and European introgression, which may increase infectious disease susceptibility relative to indigenous breeds. Heritability estimates were low to moderate, ranging from 0.03 (SE ± 0.06) to 0.44 (SE ± 0.07), depending on the health trait. GWAS results revealed several loci associated with seropositivity to the viral diseases Rift Valley fever and bovine viral diarrhoea, the protozoan parasites Neospora caninum and Toxoplasma gondii, and the bacterial pathogens Brucella sp., Leptospira hardjo, and Coxiella burnetii. The identified quantitative trait loci mapped to genes involved in immune defence, tumour suppression, neurological processes, and cell exocytosis. We propose that our results provide a basis for future understanding of the cellular pathways contributing to general and taxon-specific infection responses, and for advancing selective breeding and therapeutic target design.
Training of dairy farmers and extension workers on performance recording in Ethiopia
(Report, 2025-04-15) Meseret, Selam; Jufar, B.; Dagnew, M.; Damtie, M.; Hassen, Messay
User guide for poultry feed formulation application: A comprehensive user manual for the Feed Formulation App Version 1.0
(Manual, 2025-04-15) Esatu, Wondmeneh; Hoang Hai Hoa; Ninh Thi Huyen; Ngo Thi Kim Cuc; Phem, M.; Tum, S.; Chhay, T.; Osei-Amponsah, R.; Belete, S.; Ouko, O.; Goromela, E.; Yemane, Tsion; Dessie, Tadelle
Growth resilience to weather variation in commercial free-ranging chickens in Ethiopia
(Journal Article, 2025-04-14) Banos, G.; Girma, Mekonnen; Solomon, Bersabhe; Davoudi, P.; Esatu, Wondmeneh; Dessie, Tadelle; Psifidi, A.; Watson, K.; Hanotte, Olivier H.; Sánchez-Molano, E.
Background: The poultry industry in sub-Saharan Africa is a rapidly developing sector mostly based on smallholder farming. Increased demand for poultry-derived products, driven by the growing economy and population, has intensified importations of highly productive exotic breeds and crossbreeding with local ecotypes. However, commercial chickens with exotic genes often struggle to adapt to the local climate under smallholder farmers management. Understanding the chicken response to weather changes is crucial for developing selection schemes that ensure proper adaptation. In the present study, we derived individual phenotypes for growth resilience of commercial free-ranging chickens to changing weather conditions in Ethiopia. In addition, we performed genomic association analyses to assess the genetic background of these phenotypes and identify potential candidate genes of interest. Results: Novel resilience phenotypes describing changes in chicken growth profiles in response to weather fluctuation were developed. Variations in daily air temperature, relative humidity and amount of precipitation had the strongest impact on growth. Significant genomic variance was detected for growth resilience to changes in air temperature measurements and a temperature-humidity index. Genomic markers correlated with these resilience traits were mostly located within or near candidate genes associated with lipid metabolism and adipocyte homeostasis. Some of these genes have been previously linked to animal responses to environmental stressors in other species. Conclusions: The phenotypes of growth resilience of chickens to changing weather conditions exhibited significant genomic variation. The outcomes of this study may facilitate the genomic selection of commercial chickens that are not only highly productive, but also capable of maintaining their production levels under varying weather conditions.
Cassava as a feedstuff for ruminant feeding system in Belt and Road countries: innovations, benefits and challenges
(Journal Article, 2025-06-01) Hossain, M.D.; Yan, Q.; Zhou, Z.; Zhang, X.; Wittayakun, S.; Napasirth, V.; Napasirth, P.; Lukuyu, Ben A.
Cassava (Manihot esculenta), a versatile root crop, has garnered attention as a feedstuff for ruminant animals in Belt and Road Initiative (BRI) countries due to its widespread availability, adaptability, and high carbohydrate content. In numerous BRI countries, cassava was significant in supporting livestock industries from 2018 to 2022, especially in China, Senegal, Paraguay, Nigeria, and some African countries. This review delves into the diverse applications of cassava as an animal feed resource, with a focus on its nutrients, including carbohydrates, proteins, and minor components. It also discusses innovations, potential benefits, challenges, and possible mechanisms associated with utilizing cassava as an alternative feed source, particularly in ruminant diets. Effective techniques related to subduction of anti-nutrients and toxins, fiber degradation and protein enhancement, starch modification, and diet integration are described. Cassava products such as roots, leaves, and hay (whole crop), produced by these advanced techniques, have been demonstrated to improve growth performance, milk and meat quality, and body health when integrated into ruminant diets. Additionally, cassava by-products such as peels and foliage significantly contribution to animal feed, serving as an economical and efficient resource for farmers in BRI regions. Furthermore, multifaceted challenges related to variability in cassava quality, environmental concerns in production, and socioeconomic conflicts between feed, food and industrial uses are also pointed out. The information will provide practical ways for farmers to use cassava as ruminant feed, promote the application of more advanced technologies in cassava feeding, formulate national agricultural policies along the BRI regions, and ensure the global feed security.
Lessons from engaging with dairy cooperatives to foster irrigated forages development
(Presentation, 2025-03-27) Adie, Aberra; Bezabih, Melkamu
Livestock technological innovation adoption: Challenges and opportunities—Africa lens
(Presentation, 2025-03-27) Marshall, Karen

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