ILRI papers in published proceedings
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Item Testing phenotypes for degree of resilience using fluctuations in milk yield of dairy cows in sub-Saharan Africa(Conference Paper, 2022-02-09) Oloo, Richard Dooso; Ekine-Dzivenu, Chinyere C.; Ojango, Julie M.K.; Mrode, Raphael A.; Okeyo Mwai, Ally; Chagunda, Mizeck G.G.Despite the relevance of dairy production in the fight against food insecurity and unemployment in sub-Saharan Africa (SSA), negative effects of climate change and general changes in the production environment pose huge challenges to its profitability. Thus, there is a need to improve resilience capacity of dairy animals to adapt to this changing environment. In the current study, we tested two indicators of resilience, logtransformed variance (LnVar) and Skewness (Skew) of deviation, based on fluctuations in animals’ milk yield. Further, we assessed the effects of genotype, agroecological zone, and genotype by agroecological zone (G×E) interaction for these phenotypes. Cows with less than 50% of exotic genetics had higher degree of resilience (P<0.05). Cows performing in semi-arid zones had higher resilience capacity compared to those in semi-humid environment (P<0.05). G×E did not significantly influence both indicators. The results provide valuable information that would inform dairy cattle improvement initiatives in SSA.Item Determining optimal seasonal integration times of NDVI series for index-based livestock insurance in East Africa(Conference Paper, 2015-07) Vrieling, Anton; Meroni, Michele; Mude, Andrew G.Item Supporting the development of biobanks in low and medium income countries(Conference Paper, 2016-05) Klingström, Tomas; Mendy, Maimuna; Meunier, Dominique; Berger, Anouk; Reichel, Jane; Christoffels, Alan; Bendou, Hocine; Swanepoel, Carmen; Smit, Lemoene; Mckellar-Basset, Campbell; Bongcam-Rudloff, Erik; Soderberg, Jonas; Merino-Martinez, Roxana; Amatya, Suyesh; Kihara, Absolomon; Kemp, Stephen J.; Reihs, Robert; Muller, HeimoItem Nutritional management of dual purpose youngstock in Costa Rica 1. A dynamic characterisation of management intensity and productive orientation(Conference Paper, 1998) Solano, C.; Pérez, E.; Vargas, B.; Herrero, MarioItem The prediction of genetic structure of East African smallholder dairy cattle(Conference Paper, 2013) Weerasinghe, W.M.S.P.; Gondro, C.; Jeyaruban, M.G.; Okeyo Mwai, Ally; Mujibi, Denis; Gibson, John P.Item SNP-panel design for dairy proportion estimation and parentage testing(Conference Paper, 2017-07-05) Strucken, E.M.; Esquivelzeta-Rabell, C.; Al-Mamun, H.A.; Gondro, C.; Okeyo Mwai, Ally; Gibson, John P.Item Signatures of selection in admixed dairy cattle of Kenya(Conference Paper, 2019-11-01) Aliloo, H.; Mrode, Raphael A.; Okeyo Mwai, Ally; Gibson, John P.Item Genetic structure and differentiation among African Bos Taurus cattle breeds(Conference Paper, 2019-11-01) Gebrehiwot, N.Z.; Strucken, E.M.; Aliloo, H.; Marshall, Karen; Gibson, John P.Item Perceptions of women and men smallholder pig keepers in Uganda on pig keeping objectives, and breed and trait preferences(Conference Paper, 2019-11-01) Babigumira, B.M.; Ouma, Emily A.; Sölkner, Johann; Marshall, KarenItem Integrating gender considerations into livestock genetic improvement programs in low to middle income countries(Conference Paper, 2019-11-01) Marshall, Karen; Haan, Nicoline C. de; Galiè, AlessandraItem Animal welfare in Africa: Strength of cultural traditions, challenges and perspectives(Conference Paper, 2019-06-15) Qekwana, D.N.; McCrindle, C.M.E.; Cenci-Goga, B.T.; Grace, DeliaItem Genetic conservation through effective utilization of the improved indigenous chicken breeds by rural households in Nigeria(Conference Paper, 2018) Adebambo, Ayotunde Olufunmilayo; Adeleke, M.; Adeleye, A.; Adeyinka, Isaac A.; Ajayi, F.; Akinola, W.; Alabi, O.; Bamidele, O.; Dessie, Tadelle; Ikeobi, C.; Ogundu, U.; Ojoawo, H.; Osinbowale, D.; Ozoje, M.; Peters, S.; Sonaiya, B.; Wheto, M.; Yakubu, A.SUMMARY. Our collection and genetic characterization of various indigenous chicken genotypes in Nigeria started in 1984 at the National Animal Production Research Institute, Shika, Zaria, (Shika Brown) in 1994 at the Federal University of Agriculture, Abeokuta, Nigeria (FUNAAB) and in 2014 in Obafemi Awolowo University, Ile-Ife (FULANI). Collections were screened and characterized for genetic improvement and effective utilization by rural households in Nigeria With the financial and technical support of the Bill and Melinda Gates Foundation and the International Livestock Research Institute, Ethiopia, respectively, improved chicken genotypes were developed and evaluated alongside some other tropically adapted chicken breeds. A total of six improved tropically adapted chicken breeds (three Nigerian – Shika Brown, FUNAAB alpha and Fulani; three imported – Kuroiler, Sasso and Noiler) were tested for 52 weeks on-farm, across five agro-ecological zones of Nigeria and on-station in a public University farm and a private farm in Ogun and Oyo States, respectively. Results showed the Nigeria’s improved Indigenous chicken breed, the FUNAAB-Alpha, to be of comparable performance with the three imported breeds. It has met with high acceptance and demand after exhibition of the six breeds during the 2017 Science and Technology Expo in Abuja, Nigeria.Item Deriving genomic breeding values for feed intake and body weight in dairy goats(Conference Paper, 2018) Desire, S.; Mucha, S.; Coffey, M.; Mrode, Raphael A.; Broadbent, J.; Conington, J.Item Genetic parameters for longevity traits in UK dairy goats(Conference Paper, 2018) Geddes, L.; Desire, S.; Mucha, S.; Coffey, M.; Mrode, Raphael A.; Conington, J.Genomic selection on UK dairy goats began in 2015. New traits for selection have evolved since that time with the addition of new genotypes for the reference population. The objectives of this study were to define longevity in terms of lifespan and production, to estimate their heritabilities, and calculate phenotypic and genetic correlations. The dataset comprised records on 12,233 female dairy goats based on two genetically linked farm sites. The pedigree contained information on 40,422 individuals. Heritabilities of the longevity traits were found to range from 0.08 to 0.46, with moderate to high phenotypic and genetic correlations between the lifetime longevity and production longevity traits. The results will allow genetic improvement in dairy goats by incorporating longevity into a breeding index with production, health and maintenance traits. The next step following this work is to produce genomic breeding values for longevity traits that will allow genomic selection for use in UK dairy goat breeding programmes.Item Optimal design of low density marker panels for genotype imputation(Conference Paper, 2018) Aliloo, Hassan; Mrode, Raphael A.; Okeyo Mwai, Ally; Ojango, Julie M.K.; Dessie, Tadelle; Rege, J.E.O.; Goddard, M.; Gibson, John P.Cost-effective genotyping of livestock species can be done through a process which involves genotyping part of the population using a high density (HD) panel and the remainder with a lower density panel and then use imputation to infer the missing genotypes that are not included on the low density panel. Therefore, it is desirable to have a method of selecting markers for an assay that maximises imputation accuracy. Here we present a marker selection method that relies on the pairwise (co)variances between single nucleotide polymorphisms (SNPs) and the minor allele frequency (MAF) of SNPs. The performance of the developed method was tested in a 5 fold cross-validation process using genotypes of crossbred dairy cattle in East Africa, a population in which it is unclear whether existing low density SNP assays designed for purebred populations will maintain high imputation accuracies. Various densities of SNPs were selected using the (co)variance method and alternative SNP selection methods and then imputed up to the HD panel. The (co)variance method provided the highest imputation accuracies at all marker densities, with accuracies being up to 19% higher than the random selection of SNPs. The presented method is straightforward in its application and can ensure high accuracies in genotype imputation of crossbred dairy population in East Africa.Item Genetic diversity of the indigenous cattle of Kenya, Uganda, Ethiopia and Tanzania using high-density SNP data(Conference Paper, 2018) Weerasinghe, Shalanee; Gibson, John P.; Gondro, Cedric; Okeyo Mwai, Ally; Ojango, Julie M.K.; Rao, E.J.O.; Dessie, Tadelle; Mujibi, Denis; Rege, J.E.O.Genetic diversity of the indigenous cattle of Kenya, Uganda, Ethiopia and Tanzania using high-density SNP data. The indigenous cattle make a significant contribution to the livelihood of many communities in Ethiopia, Tanzania and other countries in eastern Africa. Here, we identify the genetic structure and the admixture levels of several East African indigenous cattle breeds in Ethiopia and Tanzania. Two ‘groups’ were studied: Indigenous cattle consisting of a number of breeds; and Mpwapwa cattle – a composite breed. A total of 386 individual animals from the two groups were genotyped using the Illumina high-density Bovine SNP chip (778k Panel). Principal component analysis was used to study the genetic structure and admixture levels of the indigenous cattle, and Mpwapwa were estimated using the ADMIXTURE program. All East African indigenous breeds other than the Ankole appear genetically closely related to each other and consist of a mixture of African taurine and indicine signals. Ethiopian indigenous breeds, Fogera, Danakil Harar and Ethiopian Boran show high purity, whereas Ethiopian Central Highland Breed and the Begait samples show significant amounts of European Bos taurus admixture. Tanzanian indigenous cattle, Singida White and Iringa Red, have a high degree of purity while the TALIRI Boran shows some European Bos taurus genetic background. The synthetic Mpwapwa breed had estimated breed proportions of Bos indicus, African Bos taurus and European Bos taurus of 0.82, 0.05 and 0.13 respectively. These results are useful for genetic conservation and genetic improvement programs.Item Alternative learning technologies for developing capacity in animal breeding and genetics in middle and low income countries(Conference Paper, 2018-10) Ojango, Julie M.K.; Rege, J.E.O.; Dror, Iddo; Kugonza, Donald R.; Chagunda, Mizeck G.G.; Mrode, Raphael A.; Philipsson, J.; Okeyo Mwai, AllyIn today’s world where scientific progress and development of new knowledge is increasing rapidly, middle and low income countries must be able to train and retain versatile researchers in the field of animal breeding and genetics able to analyze, adapt and use technologies, and possess strong social skills. A modernized blended learning approach with flexible organizational structures that allow the integration of face to face with virtual learning environments using various e-learning technologies needs to be adopted. However, electronic learning tools addressing situations and needs for animal genetic resource management in middle and low income countries are few, and several challenges hinder wide adoption of e-learning. This paper presents some experiences with e-learning tools in middle and low income countries, outlines opportunities for enhanced adoption of e-learning and identifies some gaps and questions that still need to be addressed to facilitate e-learning.Item The impact of modelling and pooled data on the accuracy of genomic prediction in small holder dairy data(Conference Paper, 2018-10) Mrode, Raphael A.; Aliloo, Hassan; Strucken, E.M.; Coffey, M.; Ojango, Julie M.K.; Mujibi, Denis; Gibson, John P.; Okeyo Mwai, AllyThe lack of data recording in smallholder dairy cattle system implies that the availability of molecular data could offer some quick wins in terms of using the genomic information in genomic evaluation and therefore genomic selection (GS). Initial studies have reported low to medium accuracy of genomic prediction when the size of data is limited. The African dairy genetic gains (ADGG) project is generating more data across two countries in East Africa and would offer more opportunity to further examine the application of GS. In anticipation of having more data in future, this paper examined the impact of fitting GBLUP models with dominance effects, a multi-trait GBLUP that fits exotic breed and non-exotic breed proportion as different traits and the analysis of pooled data from Kenya and Tanzania on the accuracy of genomic predictions. In addition, it examines if chromosome regions with highest contributions to top GEBV cows with high exotic and high indigenous genes are different. The estimates of dominance variance were essentially zero, possibly due to the limited data set, and therefore the model with dominance effect resulted in no increase of genomic accuracy compared to a model with only additive effects. The fitting of the proportion of exotic and non-exotic genes as different traits resulted in slightly lower accuracies of cows with more than 35% exotic genes but almost doubled the accuracy of those with < 36% exotic genes. However, the model resulted in an increase in the predictive ability of the models with regressions tending toward unity and a reduction in prediction bias. The pooled data resulted in increased accuracy for the Tanzania data set but not for Kenya, mostly due to different breeds being involved in the crossbreeding and the genetic kinships between both populations was very weak. The chromosome regions with largest contributions to the top GEBV cows with high exotic genes were different from those with high levels of indigenous breed, indicating the need for a proper and well planned GWAS study.Item Innovative use of sheep and goats by women in climate smart villages in Kenya(Conference Paper, 2018-10) Ojango, Julie M.K.; Audho, James O.; Oyieng, Edwin P.; Recha, John W.M.; Muigai, Anne W.T.The Nyando Basin in Kenya, a rich agricultural flood plain around Lake Victoria with a population density exceeding 400 persons per square kilometre, has been adversely affected by extreme weather events that include droughts and floods. Literacy levels are low. Land sizes are small, generally less than one hectare, and poverty rates are high. Through a partnership around collective action, seven villages have been selected to pilot climate smart integrated crop and livestock production. The approach focusses on improving local knowledge of climate risks, variability in seasonal rainfall, and targeted introduction of technologies to increase productivity of crops and livestock in order to enhance livelihoods. Given the household composition and differential access and control over resources by men and women in the communities a gendered approach was adapted for sheep and goat improvement. Men generally control practices around goats, while women have a greater say on sheep. Past uncontrolled breeding of sheep and goats, closed to introduction of animals from elsewhere has resulted in smaller sized animals that take long to mature, and do not fetch good market prices. The CGIAR led project thus introduced improved strains of resilient but more productive indigenous breeds of Gala goats and Red Maasai sheep for crossbreeding with the local breeds and has resulted in women taking a lead in community led breeding programmes resulting in crosses with better performance and desirable traits.Item The role of contracts in improving access to credit in the smallholder livestock sector of Swaziland(Conference Paper, 2018-06) Mamba, T.X.; Machethe, C.; Mtimet, Nadhem