Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens.

BACKGROUND: Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated. RESULTS: In total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines. CONCLUSIONS: Identification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.

Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress.

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.

Antibiotic Resistance of Bacterial Isolates from Smallholder Poultry Droppings in the Guinea Savanna Zone of Nigeria.

There is a growing risk of antibiotic resistance (AR) in smallholder poultry (SP). This study, therefore, aimed to investigate AR pattern of bacterial isolates from SP in the Guinea Savanna agro-ecological zone of Nigeria. A total of 120 fresh poultry droppings were aseptically collected, randomly, from two tropically adapted (FUNAAB Alpha and Noiler) and local chickens. The chickens were raised either using ethnoveterinary medicines (n = 60) or antibiotics (n = 60). Bacterial isolates were characterized and analyzed using standard protocols, and appropriate statistical tools. Compared to Pseudomonas spp. (2.5%) and Klebsiella spp. (5.8%), Salmonella spp. (57.5%) and Escherichia coli (34.2%) were the most prevalent (χ2 = 96.67; p < 0.001). Prevalence of bacterial species was significantly (p = 0.024; Odds Ratio = 2.552) influenced by antibiotics usage. All four species were multi-drug resistant. In total, 30% of the isolates had a multiple AR index ≥ 0.2. Bacterial isolates from FUNAAB Alpha (58.0%) and Noiler (44.0%) were highly resistant to quinolones, while isolates from the local chickens (22.6%) were most resistant to aminoglycosides. Bacterial species isolated from FUNAAB Alpha and local chickens exhibited the lowest and highest percentage of AR, respectively. Clustering of isolates with similar antibiogram revealed inter-species dependence with possibility for inter-species gene transfer. These findings provide a background to investigate the metagenomics of local and improved chickens for AR.

Growth performance, survivability and profitability of improved smallholder chicken genetics in Nigeria: A COVID-19 intervention study.

The impact of COVID-19 pandemic on smallholder farming households (SFH) includes increased poverty, and loss of livelihoods. Provision of livestock to SFH is a helpful intervention to mitigate this impact. This study provided a total of 150 smallholder poultry farmers, randomly selected from three states (Kebbi, Nasarawa, and Imo) in Nigeria, with ten 5-week-old chickens (mixed sexes) each, of either FUNAAB Alpha or Noiler chicken genetics. The improved, dual-purpose chickens were evaluated for growth performance (GP), survivability and profitability. The birds were managed under semi-scavenging production system. Body weight, mortality, and cost of production (COP) were recorded every 4 weeks until 21 weeks of age. Profitability was a function of the COP, and the selling price for live-birds (cocks). Body weight of Noiler (1,927 g) birds was not significantly (p > .05) higher than FUNAAB Alpha (1,792 g) at 21 weeks. Agroecology and genetics had significant (p < .05) effects on GP and survivability. Survivability of FUNAAB Alpha was higher (p < .05) than Noiler, with Nasarawa (81%-96%), having the highest (p < .0001) survival rate compared to Imo (62%-81%), and Kebbi (58%-75%). At 21 weeks, the number of cocks and hens differed significantly (p < .05) within the states (Imo: 2.4 ± .2 and 5.4 ± .3; Kebbi: 2.6 ± .2 and 5.5 ± .3; and Nasarawa: 2.9 ± .2 and 5.8 ± .3). Nasarawa (NGN 7,808; USD 19) ranked best for profitability, followed by Kebbi (NGN 6,545; USD 16) and Imo (NGN 5,875; USD 14). Overall, this study demonstrates that provision of improved chickens to vulnerable SFH in Nigeria holds great potential for economic growth, and resilience during emergencies, such as the COVID-19 pandemic.

Antimicrobial Usage in Smallholder Poultry Production in Nigeria.

The indiscriminate use of antimicrobials in livestock production is of increasing concern due to the threat of antimicrobial resistance in both humans and animals. Much emphasis has been placed on intensively managed poultry production systems, which routinely use antimicrobials as against smallholder poultry production systems (SPPS). Therefore, this study investigated the use of antimicrobials among smallholder poultry farmers in Nigeria, and compared the prevalence of antimicrobial drug use against the practice of ethnoveterinary medicine (EVM). A cross-sectional study was conducted in five states (agroecologies) of Nigeria using structured questionnaires administered on a total of 350 farmers. The practice of EVM was prevalent among most of the farmers (39%). The western method (pharmaceuticals) was practiced by a large proportion of farmers (60%), either solely (25%) or in combination with EVM (35%). Antimicrobials were used primarily for treatment and prevention of diseases (78%). Semi-scavenging system of production had the highest proportion (49%) of farmers using antimicrobials, compared to semi-intensive (37%) and scavenging (14%) systems. Gender (χ 2 = 9.30, p = 0.01), and location (χ 2 = 216.86, p ≤ 0.001), influenced farmers' choice of methods for bird treatment. Education (odds ratio [OR] odds ratio [OR] 3.06, 95% CI 2.10-4.44), income (OR 1.99, 95% CI 1.10-3.59) and management system (OR 1.97, CI% 1.1-3.45) were most associated with antimicrobial use. Critically important antibiotics, with lower to higher risk of antimicrobial resistance, were used by farmers (40%). These findings showed the indiscriminate use of antimicrobials by farmers and the potential risk of antimicrobial resistance within the SPPS in Nigeria.

Functional evolution of the colony-stimulating factor 1 receptor (CSF1R) and its ligands in birds.

Macrophage colony-stimulating factor (CSF1 or M-CSF) and interleukin 34 (IL34) are secreted cytokines that control macrophage survival and differentiation. Both act through the CSF1 receptor (CSF1R), a type III transmembrane receptor tyrosine kinase. The functions of CSF1R and both ligands are conserved in birds. We have analyzed protein-coding sequence divergence among avian species. The intracellular tyrosine kinase domain of CSF1R was highly conserved in bird species as in mammals but the extracellular domain of avian CSF1R was more divergent in birds with multiple positively selected amino acids. Based upon crystal structures of the mammalian CSF1/IL34 receptor-ligand interfaces and structure-based alignments, we identified amino acids involved in avian receptor-ligand interactions. The contact amino acids in both CSF1 and CSF1R diverged among avian species. Ligand-binding domain swaps between chicken and zebra finch CSF1 confirmed the function of variants that confer species specificity on the interaction of CSF1 with CSF1R. Based upon genomic sequence analysis, we identified prevalent amino acid changes in the extracellular domain of CSF1R even within the chicken species that distinguished commercial broilers and layers and tropically adapted breeds. The rapid evolution in the extracellular domain of avian CSF1R suggests that at least in birds this ligand-receptor interaction is subjected to pathogen selection. We discuss this finding in the context of expression of CSF1R in antigen-sampling and antigen-presenting cells.

Production performance and survivability of six dual-purpose breeds of chicken under smallholder farmers' management practices in Nigeria.

Chickens kept under free-range, backyard or semi-intensive systems in the developing countries have more diverse use and benefits to rural households. Their use varies from region to region and from community to community within a region. The study investigated growth, laying performance and survivability of six improved dual-purpose breeds in five agroecologies of Nigeria represented by the following states: Kebbi (Sudan savanna/northern Guinea savanna); Kwara (northern Guinea savanna/southern Guinea savanna); Nasarawa (southern Guinea savanna/derived savanna); Imo (lowland rainforest/swamp); and Rivers (freshwater swamp/mangrove swamp). On-farm data were obtained from 2100 smallholder poultry farmers that received an average of 30 birds (mixed sexes) of any one of the following dual-purpose breeds (Fulani, FUNAAB Alpha, Kuroiler, Noiler, Sasso and Shika-Brown) randomly allocated to them. The farmers used the backyard, scavenging system of management. Body weight and mortality records for cocks were taken for 18 weeks, while body weight, mortality, egg production and egg weight data were collected for hens up to 72 weeks. Compared with the local cocks (680 g), Kuroiler (1391 g), Sasso (1398 g) and Noiler (1461 g) had over 200 % body weight at 18 weeks. Hen day egg production (HDEP) was higher in Shika-Brown (45.9 %), FUNAAB Alpha (45.8 %) and Kuroiler (45.7 %) compared with the other breeds. Fulani, FUNAAB Alpha and Shika-Brown had higher survivabilities ( p < 0.05 ) than Noiler, Sasso and Kuroiler. Ranking of the breeds for growth, laying performance and survivability was as follows: Shika-Brown/Sasso  >  FUNAAB Alpha/Noiler  >  Kuroiler  >  Fulani. The performance of the breeds was significantly ( p < 0.05 ) influenced by the agroecologies. The cock body weights for Fulani (1121.1 g), FUNAAB Alpha (1502.4 g) and Noiler (1459.2 g) were highest in Kebbi, while for Kuroiler (1561.0 g), Sasso (1695.9 g) and Shika-Brown (1131.6 g) cock body weights were highest in Imo. Across the states, Imo had the highest HDEP (62.8 %). Overall, the lowland rainforest/ freshwater swamp agroecologies supported the highest production performance of the breeds.