DOI: 10.5061/dryad.w3r22810n
title: Data from: Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

description: 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.
description: Illumina® BovineHD 777K BeadChip SNP data sets generated for 39
 African cattle: 8 Boran, 8 N’Dama, and 23 Somba.<br>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.<br>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:<br> - bora-ndam-somb.ped<br> -
 bora-ndam-somb.map The data are in PLINK ped and map
 format, see:<br> -
 [https://www.cog-genomics.org/plink/1.9/formats#ped](https://www.cog-genomics.org/plink/1.9/formats#ped)<br> - [https://www.cog-genomics.org/plink/1.9/formats#map](https://www.cog-genomics.org/plink/1.9/formats#map)<br> - [https://zzz.bwh.harvard.edu/plink/data.shtml#ped](https://zzz.bwh.harvard.edu/plink/data.shtml#ped)<br> - [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.<br>The files have not undergone filtering, and contain the complete set of 777,962 variants from 39 animals.<br>The individual sample codes include their previous IDs and the population codes are as follows:<br> - Boran (BORA)<br> - N’Dama (NDAM)<br> - Somba (SOMB) <br><br>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. <em>Molecular Ecology</em> <strong>13</strong>, 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. <em>BMC Genomics</em> <strong>10</strong>, 207.<br><br>
description: # Illumina® BovineHD 777K BeadChip SNP data sets generated for 39 African
 cattle: 8 Boran, 8 N’Dama, and 23 Somba.
 [https://doi.org/10.5061/dryad.w3r22810n](https://doi.org/10.5061/dryad.w3r22810n) 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. ## Description of the data and file structure 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) ## Sharing/Access information Samples were derived from the following sources: \- Freeman AR, Meghen CM, MacHugh DE, Loftus RT, Achukwi MD, Bado A, Sauveroche B, Bradley DG (2004). Admixture and diversity in West African cattle populations. *Mol Ecol* **13**(11): 3477-3487. doi:[10.1111/j.1365-294X.2004.02311.x](https://doi.org/10.1111/j.1365-294X.2004.02311.x). \- O'Gorman GM, Park SD, Hill EW, Meade KG, Coussens PM, Agaba M, Naessens J, Kemp SJ, MacHugh DE (2009). Transcriptional profiling of cattle infected with *Trypanosoma congolense* highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility. *BMC Genomics* **10**: 207. doi:[10.1186/1471-2164-10-207](https://doi.org/10.1186/1471-2164-10-207). ## Code/Software The samples were prepared using PLINK (v. 1.90 beta 6.25).