We investigated the prediction of live weight (LW) of dairy cattle in low- to medium-input systems in Senegal, based on measurements of heart girth (HG) and height at the withers (HW). A total of 459 ...female dairy cattle, mainly comprising indigenous Zebu and their crosses with Guzerat or Bos Taurus, were weighed (kg), and their HG (cm) and HW (cm) determined. Farmers were asked to provide their own weight estimates for each animal. The single explanatory variable that explained the most variation in LW was HG. The best model to predict LW from HG for the overall data was
with an adjusted R
2
of 0.85 and a root mean square error of 34.25 kg corresponding to 11.10% of the mean LW. This model predicted the LW of 91-100% of cows and 64-100% of heifers within 20% of their true-live weight, in the weight range of about 100-500 kg. In comparison, farmers could only estimate the LW of about a quarter of their animals within 20% of their true LW. This weight prediction equation, when translated into a weigh band, could provide a simple and reliable method for cattle keepers to estimate the weight of studied cattle breed types.
This work aims to assess the effects of the application of feed and health technological packages on the zootechnical-economic performance of local breeds pigs in Casamance. It involved 253 young ...pigs, provided by 44 traditional farms. The feed and health technological package group (FHT) pigs were kept in permanent confinement and fed ad-libitum with a diet containing 15% of dried cashew apple pulp, while the controls and health technological package (HT) pigs were raised in a free-range area and fed in the usual way by the farmers. The zootechnical and economic parameters were collected and processed by ANOVA test and linear regression. The results showed a significant improvement in health status, live body weight, carcass weight of pigs, daily weight gain mean of the pigs in the FHT group compared to the HT and controls (p < 0.05). The production costs of the FHT pigs were lower than those of the HT and control pigs' groups. They generated on average a gain for the selling in live body weight and a loss for those in carcass weight. The use of feed and health technological packages is advised in pig farming and price incentives are necessary to make the fattening activity sustainable.
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. 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) (r.sup.2 > 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. 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.
Senegal, like the other Sahelian countries, remains an important livestock area, particularly for ruminants, with almost 36% of its livestock population was goat in 2016. The national herd increased ...from 2010 to 2016, from 3.32 to 3.54 million head of cattle, 5.6 to 6.68 million sheep and 4.8 to 5.7 million goats, i.e. annual growth rates of 1.1%, 3.2% and 3.13% respectively. Thus, due to diversification of local agricultural resources and the strengthening of goat breeding techniques in the Fatick area, a programme aiming to develop the local goat sector was set up in 2010. The programme focused on improving animal husbandry, providing new added values to goat products and structuring the goat sector. This study’s aim is to better understand goat rearing systems in the area, in order to propose, together with the herders, ways of improving these systems, taking into account family and socio-cultural considerations. To better evaluate the diversity in different production systems, a survey of animal rearing practices was carried out. The survey involved 45 farmers in four localities. It revealed that the farmers were all agro-pastoralists practising a mixed farming system. The majority (93%) supplemented their animals with agricultural by-products, agro-forestry and kitchen leftovers. A multiple correspondence analysis identified three groups: cluster 1 (milk producers and processors into traditional curdled milk, selling animals for household needs), cluster 2 (milk processors into yoghurt and cheese) and cluster 3 (goat vendors in pastoral and the agro-pastoral system).
The study of the objectives and contexts of goat farming in the Fatick will enable policy-makers to design strategies for the sustainable development of family goat farming in the area.
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
from European
and African
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 (
≥ 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.
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.
Abstract The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our ...understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.
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 (
< 0.01) in M than in S goats. Urinary energy excretion was similar (
= 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 (
< 0.05). However, metabolizable to net energy conversion efficiency (klm) was not affected by breed (
= 0.37), while N intake, milk N yield and faecal N losses, relative to metabolic weight, were significantly higher (
< 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.
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
NR
pcpa
, an interesting trend was observed: whilst the mean
NR
pcpa
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
NR
s 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.
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