Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex mosaic of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White cattle populations. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and Italian cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle, we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

Illumina® BovineHD 777K BeadChip SNP data sets generated for 39 African cattle: 8 Boran, 8 N’Dama, and 23 Somba.
The Boran and N’Dama data were obtained using cattle DNA samples from a trypanosome challenge time-course experiment (O'Gorman et al., 2009) and were generated by Neogen Europe (Ayr, Scotland) using standard procedures for Illumina® SNP array genotyping.
The Somba data were obtained using DNA samples previously published as part of a microsatellite-based survey of cattle genetic diversity (Freeman et al., 2004) and were generated by Weatherbys Scientific (Naas, Ireland) also using standard procedures.

The samples were prepared using PLINK (v. 1.90 beta 6.25).

The data are provided in the following two files:
 - bora-ndam-somb.ped
 - bora-ndam-somb.map

The data are in PLINK ped and map format, see:
 - [https://www.cog-genomics.org/plink/1.9/formats#ped](https://www.cog-genomics.org/plink/1.9/formats#ped)
 - [https://www.cog-genomics.org/plink/1.9/formats#map](https://www.cog-genomics.org/plink/1.9/formats#map)
 - [https://zzz.bwh.harvard.edu/plink/data.shtml#ped](https://zzz.bwh.harvard.edu/plink/data.shtml#ped)
 - [https://zzz.bwh.harvard.edu/plink/data.shtml#map](https://zzz.bwh.harvard.edu/plink/data.shtml#map)

The SNP locations refer to the UMD 3.1 bovine genome assembly.
The files have not undergone filtering, and contain the complete set of 777,962 variants from 39 animals.
The individual sample codes include their previous IDs and the population codes are as follows:
 - Boran (BORA)
 - N’Dama (NDAM)
 - Somba (SOMB)

Freeman A.R., Meghen C.M., MacHugh D.E., Loftus R.T., Achukwi M.D., Bado A., Sauveroche B. & Bradley D.G. (2004) Admixture and diversity in West African cattle populations. Molecular Ecology 13, 3477-87.

O'Gorman G.M., Park S.D., Hill E.W., Meade K.G., Coussens P.M., Agaba M., Naessens J., Kemp S.J. & MacHugh D.E. (2009) Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility. BMC Genomics 10, 207.