The genetic structure and diversity of smallholder dairy cattle in Rwanda

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cg.authorship.typesCGIAR and developing country institute
cg.authorship.typesCGIAR and advanced research institute
cg.contributor.affiliationUniversity of Edinburgh
cg.contributor.affiliationRwanda Agriculture and Animal Resources Development Board
cg.contributor.affiliationLand O’Lakes Venture37
cg.contributor.affiliationRoyal Jersey Agricultural & Horticultural Society
cg.contributor.affiliationUniversity of Hohenheim
cg.contributor.affiliationScotland's Rural College
cg.contributor.affiliationInternational Livestock Research Institute
cg.contributor.donorJersey Overseas Aid
cg.contributor.donorGates Foundation
cg.contributor.donorForeign, Commonwealth and Development Office, United Kingdom
cg.coverage.countryRwanda
cg.coverage.iso3166-alpha2RWen_US
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierRaphael Mrode: 0000-0003-1964-5653
cg.creator.identifierAppolinaire Djikeng: 0000-0001-9271-3419
cg.howPublishedFormally Published
cg.identifier.doihttps://doi.org/10.1186/s12863-025-01323-4
cg.isijournalISI Journal
cg.issn2730-6844
cg.journalBMC Genomic Data
cg.reviewStatusPeer Review
cg.subject.ilriCATTLE
cg.subject.ilriDAIRYING
cg.subject.ilriGENETICS
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 2 - Zero hunger
cg.volume26
dc.contributor.authorOpoola, O.
dc.contributor.authorShumbusho, F.
dc.contributor.authorRwamuhizi, I.
dc.contributor.authorHouaga, I.
dc.contributor.authorHarvey, D.
dc.contributor.authorHambrook, D.
dc.contributor.authorWatson, K.
dc.contributor.authorChagunda, M.G.G.
dc.contributor.authorMrode, Raphael A.
dc.contributor.authorDjikeng, Appolinaire
dc.date.accessioned2025-05-28T09:02:28Z
dc.date.available2025-05-28T09:02:28Z
dc.identifier.urihttps://hdl.handle.net/10568/174855
dc.titleThe genetic structure and diversity of smallholder dairy cattle in Rwandaen
dcterms.abstractPrevious 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 <i>Bos taurus</i> and five <i>Bos indicus</i> 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.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademics
dcterms.audienceScientists
dcterms.available2025-05-27
dcterms.bibliographicCitationOpoola, O., Shumbusho, F., Rwamuhizi, I., Houaga, I., Harvey, D., Hambrook, D., Watson, K., Chagunda, M.G.G., Mrode, R. and Djikeng, A. 2025. The genetic structure and diversity of smallholder dairy cattle in Rwanda. BMC Genomic Data 26: 38.
dcterms.extent38
dcterms.issued2025-05-27
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherBioMed Central
dcterms.subjectcattle
dcterms.subjectdairying
dcterms.subjectgenetics
dcterms.typeJournal Article

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