Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.

BACKGROUND: In cattle, genome-wide association studies (GWAS) have largely focused on European or Asian breeds, using genotyping arrays that were primarily designed for European cattle. Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. RESULTS: We found that commercially available arrays were not effective in capturing variants that segregate among African indicine animals. Only 6% of these variants in high linkage disequilibrium (LD) (r2 > 0.8) were on the best performing arrays, which contrasts with the 17% and 25% in African and European taurine cattle, respectively. However, imputation from available HD arrays can successfully capture most variants (accuracies up to 0.93), mainly when using a global, not continent-specific, reference panel, which partially reflects the unusually high levels of admixture on the continent. When considering functional variants, the GGPF250 array performed best for tagging WGS variants and imputation. Finally, we show that imputation from low-density arrays can perform almost as well as HD arrays, if a two-stage imputation approach is adopted, i.e. first imputing to HD and then to WGS, which can potentially reduce the costs of GWAS. CONCLUSIONS: Our results show that the choice of an array should be based on a balance between the objective of the study and the breed/population considered, with the HD and BOS1 arrays being the best choice for both taurine and indicine breeds when performing GWAS, and the GGPF250 being preferable for fine-mapping studies. Moreover, our results suggest that there is no advantage to using the indicus-specific arrays for indicus breeds, regardless of the objective. Finally, we show that using a reference panel that better represents global bovine diversity improves imputation accuracy, particularly for non-European taurine populations.

Economic analysis of smallholder dairy cattle enterprises in Senegal.

Smallholder dairy production in Senegal is important to both livelihoods and food and nutrition security. Here, we examine the economic performance of smallholder dairy cattle enterprises in Senegal, using data from longitudinal monitoring of 113 households. The mean (and standard deviation) of the net returns (NR) per cow per annum (pcpa) was 21.7 (202.9) USD, whilst the NR per household herd per annum (phpa) was 106.1 (1740.3) USD. Only about half (52.2%) of the dairy cattle enterprise had a positive NR. The most significant income components were milk sale followed by animal sale, whilst the most significant cost components were animal feed followed by animal purchase. When households were grouped by ranking on NRpcpa, an interesting trend was observed: whilst the mean NRpcpa showed a fairly linear increase from the lowest to highest NR groups, income and cost did not. Income and costs were both higher for the lowest and highest NR groups, in comparison to the intermediate NR groups. The mean NRs of households grouped by the main breed type they kept were not significantly different from each other, due to large variances within the breed groups. However, the mean total income and costs were significantly higher for households mainly keeping improved dairy breeds (Bos taurus or Zebu × Bos taurus crosses) in comparison to those keeping indigenous Zebu or Zebu by Guzerat crosses. This study highlights the highly variable (and often low) profitability of smallholder dairy cattle enterprise in Senegal. Further actions to address this are strongly recommended.