High-Density SNP Genotyping and Quality Control for West African Cattle

Individuals were genotyped on the Illumina BovineSNP50 chip assay [9 (link)] at the Centre National de Génotypage (CNG) platform (Evry, France) using standard procedures http://www.illumina.com. Among the 54,001 SNPs included in the chip, only the 51,581 mapping to a bovine autosome on the latest bovine genome assembly Btau_4.0 [68 (link)] were retained for further analysis. To limit ascertainment bias favouring SNPs from European origin, we subsequently discarded 13,786 SNPs (~25%) which were not polymorphic (MAF > 0.01) in at least one West African taurine (ND1, ND2, LAG, SOM or BAO) and one West African zebu (ZCH or ZFU). Among the remaining ones, 1,422 SNPs which were genotyped on less than 85% of the individuals from at least one of the nine West African breeds, were also eliminated. An exact test for Hardy-Weinberg Equilibrium (HWE) [69 (link)] was subsequently carried out within each breed separately. Based on the obtained p-values, q-values [70 (link)] were estimated for each SNP using the R package qvalue http://cran.r-project.org/web/packages/qvalue/index.html. Fifty three SNPs with a q-value < 0.01 in at least one breed were then discarded from further analysis. In total, 36,320 SNPs were finally considered for the study leading to an average marker density of 1 SNP every 70 kb over the genome (Table S8 in additional file 2). Moreover, as shown in Figure S6 (additional file 1) and detailed in Table S8 (additional file 2), the genome coverage was homogeneous with a median distance between consecutive SNPs equal to 47.54 kb. Few large gaps between SNPs were present since the 95^th (99^th) percentile of this distance was 189 kb (385 kb), the largest gap localized on BTA10 being 2 Mb long. Conversely, less than 0.5% of the distances between successive SNPs were shorter than 20 kb. Genotyping data are given in additional file 3.