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Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa

Dorper sheep was developed for meat production in arid and semi-arid regions under extensive production systems in South Africa. Two variants with distinct head and neck colors were bred during their development process. White Dorper have a white coat while Dorper have a black head and neck. Both variants have grown in popularity around the world. Therefore, understanding the genomic architecture between South African Dorpers and Dorper populations adapted to other climatic regions, as well as genomic differences between Dorper and White Dorper variants is vital for their molecular management. Using the ovine 50K SNP chip, this study compared the genetic architecture of Dorper variants between populations from South Africa and Hungary. The Dorper populations in both countries had high genetic diversity levels, although Dorper in Hungary showed high levels of inbreeding. White Dorpers from both countries were genetically closely related, while Dorpers were distantly related according to principal component analysis and neighbor-joining tree. Additionally, whereas all groups displayed unique selection signatures for local adaptation, Dorpers from Hungary had a similar linkage disequilibrium decay. Environmental differences and color may have influenced the genetic differentiation between the Dorpers. For their molecular management and prospective genomic selection, it is crucial to understand the Dorper sheep’s genomic architecture, and the results of this study can be interpreted as a step in this direction.

To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.

The focus of this review is to offer an overview of food and nutritional security, to identify associated constraints, and propose possible alternative solutions for improving the East African poultry sub-sector in the pursuit of food security, focusing on chicken breeding. To better understand the prospects of the poultry industry, we highlighted and combined confirming evidence of the phenotypic variability and genetic diversity of East African chicken genetic resources using both morphological and molecular tools, as well as performance traits. Furthermore, this work gives a detailed indication of what would be lost if indigenous chicken populations are left to suffer the ongoing massive genetic erosions due to various factors, not limited to indiscriminate crossbreeding. Previous and recent attempts to improve the productivity of indigenous chicken are highlighted, and possible future breeding plans and areas of immediate research are suggested as well. This review concludes that under the prevailing conditions, the village chicken production system appears to be the most imperious production system that needs to be extensively developed ; however, for the sustainability of the industry, the proposed improvement strategies should create a permanent balance between the competing needs of genetic improvement and the genetic diversity of the indigenous chicken genetic resource.