Evidence map›Paper›PMID 42092788›Full record

ArticleBMC genomics2026

Accurate imputation of African cattle genomes using a diverse reference panel.

Said I Ng'ang'a, James A Ward, Stephen J Rossiter, Chris G Faulkes, Katia Bougiouri, Gillian P McHugo, Fenton P D Cotterill, Atunga Nyachieo, Olaf Thalmann, Ivica Medugorac and 7 more

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Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

17 authors.

Said I Ng'ang'aPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany. I.Nganga@lmu.de.
James A WardAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
Stephen J RossiterPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
Chris G FaulkesPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
Katia BougiouriSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
Gillian P McHugoAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
Fenton P D CotterillSilverStreet Capital, London, UK.
Atunga NyachieoBioinformatics and Health Informatics Group, Institute of Primate Research, Nairobi, Kenya.
Olaf ThalmannSchool of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
Ivica MedugoracPopulation Genomics Group, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Munich, Germany.
Stefan KrebsLaboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany.
Tad S SonstegardAcceligen, Eagan, MN, USA.
Olivier HanotteInternational Livestock Research Institute, Addis Ababa, Addis Ababa, Ethiopia.
Daniel G BradleySmurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
Gary Vaughan-SmithSilverStreet Capital, London, UK.
David E MacHughAnimal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland. david.machugh@ucd.ie.
Laurent A F FrantzPalaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany. laurent.frantz@lmu.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIn cattle, most commercial single-nucleotide polymorphism (SNP) genotyping arrays have been shown to be suboptimal for capturing genomic variation in non-European populations, particularly in African cattle. Low-coverage whole-genome sequencing (LCWGS) followed by imputation provides a cost-effective method for genotyping that is more adaptable and can outperform genotyping arrays.

resultsHere, we generate a high-quality reference imputation panel representative of the complex ancestries of cattle populations in Africa to enable the deployment of LCWGS. To do so, we generated 116 high-coverage (between 20‒24×) new African cattle genomes, representing most cattle breeds across the continent. We combined this data with publicly available genomes from other regions to build a reference panel that comprised over 3,300 cattle genomes from 133 cattle populations, thus capturing the genetic diversity of domestic cattle across the world. After applying a high filtering step to remove poor genome sequences with very low sequence coverage, we retained 1,882 with an average coverage of 7×. We show that the imputation pipeline implemented, based on this reference panel, provides highly accurate genotypes of common (> 99% accuracy) and rare (> 98% accuracy) variants in genome coverage as low as 0.5×.

conclusionThis panel provides an important new resource for genetic improvement and conservation of African cattle populations.

Indexed as

GenomeGenomicsAfricaAnimalsBreedingCattleGenotypeGenotyping TechniquesPolymorphism, Single NucleotideReference StandardsWhole Genome SequencingCattleGenome-enabled BreedingImputationLow-Coverage Whole Genome Sequencing

Identifiers

PMID42092788
PMCPMC13154541

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