The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. We report here the genome sequences of 573 samples (198 new genomes) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.4 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetic and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource. We hope this resource will be utilised by the global scientific community and breeders for sustainable global livestock improvement.

This project was funded by the Bill and Melinda Gates Foundation (BMGF) and with UK aid from the UK Government's Department for International Development (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland's Rural College), and the International Livestock Research Institute. The findings and conclusions are those of the authors and do not necessarily reflect the positions or policies of the BMGF or the UK Government. We thank the CGIAR livestock program (CRP) for supporting the sampling component of the research. We also thank the AU-IBAR for linking us to the various African partners, and we acknowledge the valuable support of the various African National Institutes for granting the Nagoya permits for sampling and utilization of the genomic resources from their countries. We are grateful to the Chinese Government's contribution to the CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources in Beijing (2023-YWF-ZX-02). We thank Professor Apollinaire Djikeng for his continuous support to the CTLGH - GRRFAC project.