Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants.

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.

Assessing farm biosecurity and farmers' knowledge and practices concerning antibiotics and antibiotic resistance in poultry and pig farms in Southern Togo.

Background and Aim: Several factors contribute to the unusual incidence of antibiotic resistance, which is now a primary public health concern. However, failure in managing preventive and therapeutic antibiotic use on farms is one of the most crucial factors. Therefore, this study aimed to evaluate the biosecurity of farms, farmers' competence, and practices related to antibiotics and their resistance in poultry and pig rearing in Togo. Materials and Methods: Through a cross-sectional survey, 121 commercial poultry farmers and 97 commercial pig farmers were questioned to evaluate the biosecurity of farms and farmers' competence and practices related to antibiotics and antibiotic resistance. Descriptive analyses, including the evaluation of proportions, were carried out. In addition, results from qualitative factors were evaluated in a defined grid and totaled up to assess cleanliness measures, awareness, and behavior regarding antibiotics and their resistance. Results: The results demonstrated that most farmers working on poultry farms had a university education, while most working on pig farms had secondary education. Most poultry (69%) and pig (44%) farms were of small sizes (<1000 animals in poultry and <10 animals in pig farming). The footbaths were used in just 51% of poultry farms and 4% of pig farms, respectively, with 37% and 82% of poultry and pig farms having inadequate levels of hygiene. In poultry farms, respiratory issues and periodic decline in egg-laying were the main problems. Simultaneously, skin disorders (scabies) and plagues (African swine fever) were the primary health constraints in pig farming. Tetracycline is the most commonly used antibiotic by farmers. However, in poultry and pig farms, 21% and 67% of farmers were unaware of antibiotics. In addition, 39% and 57% were unaware of antibiotic resistance. Poultry and pig farmers' competence were substantially linked to their education level. Poultry farmers demonstrated better practices, including procuring antibiotics based on veterinary prescriptions (63%) and they knew where antibiotics should be bought (90%). Nevertheless, 43% of farmers asserted unpleasant activities - no application for laboratory testing (93%) and use of antibiotics for prevention (82%). In pig farming, most farmers (69%) reported inadequate incidents of the use of antibiotics. Conclusion: This study identified a crucial non-compliance with biosecurity measures and good practices toward antibiotic use on many farms. Therefore, training of farmers is mandatory for safe livestock products.

Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo.

Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.

Characteristics of indigenous guinea fowl (Numida meleagris) family poultry production in northern Togo.

A survey was conducted in Dry Savannah and Atakora agroecological zones in northern Togo, between March and July 2018, to characterise indigenous guinea fowl management practices. A semi-structured questionnaire was administered to 82 farmers in 28 villages. The data were analysed using the chi-square test or Fisher's exact test, independent-sample t test and the multiple correspondence analysis with SPSS and XLSTAT. The results showed that guinea fowl production was mainly practised by men (91.5%) who did not have training in guinea fowl production (68.4%). In traditional poultry farming, the most popular management method was the semi-intensive system (86.2%). Guinea fowl, which was raised primarily for sale (100%), was the main bird species with 68.2 ± 92.5 birds per farmer. All respondents provided a dietary supplement to guinea fowl with a feeding management that varied according to the birds' developmental stage. Wing drooping (89.3%), diarrhoea (67.4%) and drowsiness (64.7%) were the main clinical symptoms of diseases observed. The majority of respondents (68.2%) used both conventional veterinary products and ethno-veterinary plant products as drugs in order to control guinea fowl diseases. Guinea fowl started laying at 8.4 ± 1.6 months and had 128.5 ± 51.2 eggs per year. The indigenous hen that hatched eggs naturally had 43.6 ± 17.1 hatching eggs per year with a hatchability of 85.0%. For 85.4% of the respondents, survivability was the main problem in guinea fowl production. Improving the survivability of the birds could improve their productivity, as they play an important socio-economic role for most rural households.