A running breeding program for indigenous chickens in Ethiopia: Evaluation of success

In 2008 a breeding program to increase production level in indigenous chickens was initiated at the Debre Zeit Agricultural Research Center in Ethiopia and is currently producing its 8th generation. Aim of this paper was to evaluate the success of the breeding program. Selection was on own performance for bodyweight at 16 weeks of age (BW16) and for the hens also on cumulative egg number at week 45 of laying (EN45). Heritability for BW16 in the 6th generation (G6) was 0.37, and for EN24 was 0.32. Phenotypic correlation between BW16 and EN24 was 0.36, but genetic correlation was -0.12. Genetic correlations of BW16 with cumulative egg production earlier in the laying series were 0.51 at 8 weeks of laying, decreasing to 0.22 at 16 weeks of laying. The genetic trends were positive for both traits under selection from generation 4 (G4) and G6

Population genetic structure of Sri Lankan backyard chicken flocks: Implication for conservation and genetic improvement programs

Traditional ‘random’ sampling strategy for molecular characterization has revealed low genetic differentiation and weak genetic structure among Asian and African indigenous, non-descript chicken populations although they carried high within-population phenotypic and molecular genetic diversity. In the present study, 192 backyard chickens collected following a nearly ‘complete’ sampling strategy for all adult birds within flocks of 75 households in five villages at two sites in Sri Lanka were genotyped using 20 microsatellite markers. The phenotypes and history of these birds were also recorded. A link of phenotypic composition and flock size with specific genetic structure of the backyard chicken populations was explored. The results suggest that the households who used to keep large flocks of indigenous backyard chickens of mixed genotypes should be included in in-situ conservation program to effectively maintain and sustainably utilize these important chicken genetic resources

Characterization and conservation of indigenous sheep genetic resources: A practical framework for developing countries

Livestock characterization projects in developing regions are characterized by a mere physical description of traditionally recognized populations or a purely academic genetic description of populations. However, characterization of livestock resources is meant to serve the purpose of developing conservation and utilization programs. A national characterization project should be geared to the specific national livestock production objectives. Thus there is a need to adopt a more practical characterization approach to assist in the development of national conservation and utilization strategies. This report provides a practical methodological framework suited for characterization and conservation of sheep resources in developing regions. The report highlights current approaches and tools for characterization and conservation of sheep resources and presents a model approach synthesising results of a study on characterization and conservation of sheep resources of Ethiopia. The study is a collaborative project between Wageningen University and the International Livestock Research Institute. The methodological framework can be applied elsewhere in developing countries with similar characterization and conservation objectives. This report largely dwelt on the technical aspects of sheep genetic resource characterization and conservation in developing regions. Operational aspects of setting up national programs for characterization and conservation action may be country specific. However, some general aspects such as institutional setups and breeding policy and strategy formulation could be similar across countries. A proposed scheme for setting up a national livestock characterization and conservation program is presented, taking Ethiopia as a case study

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Characterization of sheep populations of Kenya using microsatellite markers: Implications for conservation and management of indigenous sheep populations

Indigenous sheep of Kenya are very important to resource-poor farmers and pastoralists. They have over time adapted to the harsh environmental conditions of the arid and semi-arid lands where they are faced with challenges of persistent droughts, diseases, conflicts and poor nutrition, yet show resistance to gastrointestinal nematodes. In recent years, these indigenous sheep populations have been crossbred indiscriminately to exotic breeds particularly the Dorper. A study was undertaken to determine the level of genetic diversity and relatedness between the various sheep populations and breeds of Kenya. This paper reports results on the genetic diversity and admixture observed using microsatellite DNA markers

Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes

A simulation study was conducted to optimize a cooperative village-based sheep breeding scheme for Menz sheep of Ethiopia. Genetic gains and profits were estimated under nine levels of farmers' participation and three scenarios of controlled breeding achieved in the breeding programme, as well as under three cooperative flock sizes, ewe to ram mating ratios and durations of ram use for breeding. Under fully controlled breeding, that is, when there is no gene flow between participating (P) and non-participating (NP) flocks, profits ranged from Birr 36.9 at 90% of participation to Birr 21.3 at 10% of participation. However, genetic progress was not affected adversely. When there was gene flow from the NP to P flocks, profits declined from Birr 28.6 to Birr −3.7 as participation declined from 90 to 10%. Under the two-way gene flow model (i.e. when P and NP flocks are herded mixed in communal grazing areas), NP flocks benefited from the genetic gain achieved in the P flocks, but the benefits declined sharply when participation declined beyond 60%. Our results indicate that a cooperative breeding group can be established with as low as 600 breeding ewes mated at a ratio of 45 ewes to one ram, and the rams being used for breeding for a period of two years. This study showed that farmer cooperation is crucial to effect genetic improvement under smallholder low-input sheep farming systems

Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes

Village- and central nucleus-based schemes were simulated and evaluated for their relative bio-economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village-based 2-tier (Scheme-1) and 1-tier (Scheme-2) cooperative village breeding schemes, dispersed village-based nuclei scheme (Scheme-3), conventional 2-tier central nucleus-based scheme (Scheme-4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme-5) or in both central and village nuclei (Scheme-6). Among village-based schemes, Scheme-1 gave the highest genetic progress, while Scheme-2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme-4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus-based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village-based nuclei (Scheme-6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village-based breeding program is envisaged as should be the 1st step in most low-input systems, then Scheme-2 is the most efficient. To scale out to an entire Menz breed level, Scheme-3 would be recommended

Efficiency of selection for body weight in a cooperative village breeding program of Menz sheep under smallholder farming system

We evaluated the efficiency of selection for body weight in a cooperative village breeding program for Menz sheep of Ethiopia under smallholder farming system. The design of the program involved organizing villagers in a cooperative breeding group to implement selective breeding of their sheep. The program was jump-started through a one-time provision of elite rams from a central nucleus flock, but subsequent replacement rams were selected from within the village flocks. We also evaluated body weight trends in a village where cooperative breeding was not implemented and individual farmers managed their flocks under traditional breeding practices. Under traditional breeding practices, genetic progress over 8 years either stagnated or declined in all the weights recorded. In the cooperative villages, selection differentials of 2.44 and 2.45 kg were achieved in 2010 and 2011 selection seasons, respectively. Birth weight, 3-month weight and 6-month weight increased, respectively, by 0.49, 2.29 and 2.46 kg in the third-generation lambs over the base generation. Improved rams supplied from the central nucleus flock gave an initial genetic lift of 14.4% in the 6-month weight. This was higher than the gain achieved from selection in the village flocks, which was 5.2%. Our results showed that village-based genetic improvement in body weights under smallholder conditions could be feasible if appropriate designs are adopted and that commencing with elite central nucleus rams help jump-start village-based programs