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.

Analysis of the Genetic Diversity and Population Structure of Four Senegalese Sheep Breeds Using Medium-Density Single-Nucleotide Polymorphisms.

In Senegal, sheep breeds have adapted to their environment and play a key socio-economic role. This study aimed to explore the genetic diversity and structure of four Senegalese sheep breeds (Peul-peul, Djallonke, Touabire, and Ladoum) and their relationships with global sheep breeds. To that end, forty-seven sheep were genotyped using the OvineSNP50 BeadChip, and these genotypic data were analysed with those of 73 sheep breeds representative of worldwide ovine diversity (2729 animals). The average observed heterozygosity (Ho) ranged from 0.293 in Djallonke sheep to 0.339 in Touabire sheep. The estimated Fis values were low, ranging from 0.019 for Ladoum to 0.034 for Peul-peul sheep. The estimated Fst values were low (0.003-0.044) among the trypanosusceptible breeds (Peul-peul, Touabire, and Ladoum) but high between the previous breeds and the trypanotolerant Djallonke breed (0.075-0.116), indicating better genetic conservation of the Djallonke sheep. A principal component analysis revealed clustering of the Senegalese sheep breeds according to their geographic distribution. However, owing to genetic improvement practices, the introgression of Touabire sheep blood seems to have reshaped the genetic landscape of the trypanosusceptible sheep breeds in Senegal. The Senegalese sheep breeds showed lower genetic diversity than their presumed ancestral sheep breeds of the Middle East. They also presented some relatedness with Caribbean sheep breeds, which reveals their contribution to the global genetic diversity and to the development of Caribbean sheep breeds.

Analysis of microbiological and chemical quality of poultry meat in the vicinity of the Mbeubeuss landfill in Malika (Senegal).

A total of 100 samples of poultry meat were collected in poultry farms in the vicinity of the Mbeubeuss landfill in the Niayes (Senegal) for microbiological and chemical analysis. Fifty-four (54) samples were collected in farms located less than 1 km from the landfill and 46 samples were collected in farms located a bit further (more than 1 km from the landfill). Microbiological quality was determined using techniques recommended by Association Française de Normalisation (AFNOR). Lead and cadmium concentration in poultry meat was measured by flame spectrometry while total mercury was determined by atomic absorption spectrometry. Three percent (3%) of the samples' quality were unsatisfactory for E. coli, 1% for Staphylococci and 7% for Salmonella spp. Poor meat quality was found either in farms located less than 1 km of the landfill or in farms located at more than 1 km of the landfill. Except for Salmonella, only meat samples from poultry receiving drinking water from well showed unsatisfactory microbiological quality. The samples were free of cadmium and lead but were contaminated by mercury. Sixty-eight percent (68%) of the samples contained mercury with a high contamination level (>0.011 mg/kg) in 20% of the samples. No significant difference was found between the farms that were nearest to and further away from the landfill while the source of drinking water seemed to be the main cause of contamination of poultry meat by mercury.

Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations.

Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.

Comparative Study of Intake, Apparent Digestibility and Energy and Nitrogen Uses in Sahelian and Majorera Dairy Goats Fed Hay of Vigna unguiculata.

This study aimed to compare digestive and metabolic characteristics in Sahelian (S) and Majorera (M) goat breeds. Six lactating females from each breed, with an average weight 27.0 ± 1.93 and 23.7 ± 1.27 kg, respectively, were used. Cowpea hay, variety 58/74, was offered as sole feed ingredient, at a rate of 2 kg of fresh matter per animal per day. The animals were placed in metabolic cages and a digestibility test was conducted according to an adaptation period of 15 days and a collection period of 7 days. The daily chemical components offered and refused and recovered faeces, urine and milk were measured in order to assess energy and nitrogen utilization. The M and S goats had similar levels of dry matter (DM) intake as well as nutrient digestibility. On a metabolic weight basis, dry matter intake, gross energy intake, metabolizable and energy intake, digestible energy and energy lost as methane production were significantly higher (p < 0.01) in M than in S goats. Urinary energy excretion was similar (p = 0.9) between breeds, while faecal energy output was higher in M than in S goats. The milk energy output from the M goats was higher than that the S goats (p < 0.05). However, metabolizable to net energy conversion efficiency (klm) was not affected by breed (p = 0.37), while N intake, milk N yield and faecal N losses, relative to metabolic weight, were significantly higher (p < 0.05) in M than in S goats. Similarly, the percentage of dietary N intake excreted in urine (UNIN) was higher in S than in M breeds. The breed factor had no effect on N retained, N digestibility, urinary N and N use efficiency. In conclusion, the M and S goats were similar in terms of energy and nitrogen use efficiency, despite higher daily milk production and DM consumption in the M goat. This suggests that the M breed is possibly more dependent on a dense nutrition diet than the S breed but requires less maintenance nitrogen.