Abstract
Domestic cattle (Bos taurus and Bos indicus) underpin food security and livelihoods worldwide but face intensifying pressures from climate change, infectious disease, and inconsistent feed supplies. African and European indigenous cattle provide a natural comparative framework spanning gradients of climate, pathogen burden, and husbandry, and possess genomic mosaics comprising African taurine, European taurine, and indicine ancestry. We analyzed whole-genome sequences from 519 cattle across 24 African and European indigenous populations and 117 publicly available genomes from Africa, Asia, Europe, and the Americas. This dataset reveals admixture mosaics among major lineages and identifies 36 candidate genes exhibiting adaptive retention of ancestral alleles associated with response to heat stress (e.g., HSPA12B, DDIT3), immunity (IRAK3), productivity (ACSF3), and reproductivity (SSMEM1, SPEF1). Our study suggests that historical admixture introduced variation shaped by local ecological selection, clarifying how environmental heterogeneity drives the retention of advantageous alleles and informing sustainable breeding and diversity conservation.
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Data availability
Population-level variant calls (VCF files) for the 636 indigenous and reference cattle analyzed in this study have been deposited in the European Variation Archive under accession PRJEB102975 (ERP184337)141. Whole-genome sequence data for the 519 African and European indigenous cattle analyzed in this study are available from the European Nucleotide Archive under accessions PRJEB90914142 and PRJEB90816143. Publicly available reference variant datasets were obtained from the 1000 Bull Genomes Project (PRJNA391427; ERZ14211345)144 and the African Genomic Reference Resource (PRJEB74565; Muturu)145. Sample IDs for the ancestry reference panels (AFT, n = 34; EUT, n = 29; AFI, n = 25; AAI, n = 29) are provided in Supplementary Data 1. Supplementary Data 2 contains genome-wide haplotype-mosaic files for locus-level inspection, provided for two AFT reference configurations (N’Dama + Muturu and Muturu only). Supplementary Data 3 lists putative ancestry-retention genes together with retention rates. Supplementary Data 4 provides window-based nucleotide diversity (π) and genetic differentiation (weighted Fst) for Mertolenga and EUT populations. All supplementary datasets are available via the project repository on GitHub: https://github.com/junxingao888/ancestral_retention_signals_cattle/. Source data underlying the figures are provided as follows: Supplementary Table 3 (Fig. 2a,b), Supplementary Table 4 (Fig. 2c,d), Supplementary Table 5 (Fig. 4c), Supplementary Table 6 (Fig. 4e), and Supplementary Data 4 (Fig. 5d,e).
Code availability
All custom code and workflows (Linux shell, R, and Python) for read processing, variant calling, local-ancestry inference, selection scans, and figure generation are available at GitHub (https://github.com/junxingao888/ancestral_retention_signals_cattle/tree/main/Code_availability) and Zenodo140.
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Acknowledgements
This study was supported by the Long-term EU-Africa Research and Innovation Partnership on Food and Nutrition Security and Sustainable Agriculture (LEAP-Agri) as part of the OPTIBOV project (LEAP-Agri-326), and by the European Union’s Horizon 2020 Research and Innovation Program (grant agreement No. 727715). Additional funding was provided by Fundação Nacional para a Ciência e a Tecnologia (FCT), Portugal (Leap Agri-326/LEAPAgri/0003/2017 and 2020.02754.CEECIND, C.G.); the Research Council of Finland (319987); the Netherlands Organization for Scientific Research (NWO-WOTRO, 2018/WOTRO/00488849); the Science, Technology & Innovation Funding Authority of Egypt (STDF, LEAP-Agri 326); the Ministry of Science, Technology and Innovations of Uganda (MoSTI/LEAP-11); the National Research Foundation of South Africa (NRF, 115577); and the China Scholarship Council (CSC, 202208610017). The funding bodies had no role in study design, data collection, analysis, interpretation, or manuscript writing.
We thank all collaborators for their assistance with sample collection, laboratory work, and technical support, including Bert Dibbits, Kimberley Laport, Rania Agamy, Mohamed Hamada Elsawy, Filipe Ribeiro, Ricardo Loureiro, Daniel Gaspar, Ludmilla Blaschikoff, Ana Elisabete Pires, Carolina Bruno-de-Sousa, Heli Lindberg, Tiina Reilas, Dr. Avhashoni Zwane, Khanyisani Nxumalo, Maano Malima, and all breeders and breed associations involved. We also acknowledge the 1000 Bull Genomes consortium and the African Genomic Reference Resource for providing sequence data.
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J.G. and R.C. conceived the study. J.G. drafted the manuscript and interpreted the results. C.G. defined reference data sets. J.G. and Y.L. participated in data analysis. C.G., J.K., N.G., D.K., M.M., R.O., and R.C. collected the samples. H.B., M.G., and R.C. supervised the study. All the authors read and approved the manuscript.
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Communications Biology thanks Alana Alexander and the other anonymous reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: George Inglis. A peer review file is available.
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Gao, J., Ginja, C., Liu, Y. et al. Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09856-9
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DOI: https://doi.org/10.1038/s42003-026-09856-9
