Abstract
African livestock breeds are numerous and diverse, and typically well adapted to the harsh environment conditions under which they perform. They have been used over centuries to provide livelihoods as well as food and nutritional security. However, African livestock systems are dynamic, with many small- and medium-scale systems transforming, to varying degrees, to become more profitable. In these systems the women and men livestock keepers are often seeking new livestock breeds or genotypes – typically those that increase household income through having enhanced productivity in comparison to traditional breeds while maintaining adaptedness. In recent years genomic approaches have started to be utilized in the identification and development of such breeds, and in this article we describe a number of examples to this end from sub-Saharan Africa. These comprise case studies on: (a) dairy cattle in Kenya and Senegal, as well as sheep in Ethiopia, where genomic approaches aided the identification of the most appropriate breed-type for the local productions systems; (b) a cross-breeding program for dairy cattle in East Africa incorporating genomic selection as well as other applications of genomics; (c) ongoing work toward creating a new cattle breed for East Africa that is both productive and resistant to trypanosomiasis; and (d) the use of African cattle as resource populations to identify genomic variants of economic or ecological significance, including a specific case where the discovery data was from a community based breeding program for small ruminants in Ethiopia. Lessons learnt from the various case studies are highlighted, and the concluding section of the paper gives recommendations for African livestock systems to increasingly capitalize on genomic technologies.
Highlights
INTRODUCTIONThe livestock sector plays a key role in the provision of livelihoods as well as food and nutrition security
In developing countries, the livestock sector plays a key role in the provision of livelihoods as well as food and nutrition security
These include: savings and insurance, food security, income, livelihood diversification and risk reduction, inputs to crop production, transportation, various uses of hides and skin, allowing households to benefit from common-property resources, and fulfilling social obligations, amongst other (Herrero et al, 2013; Marshall, 2014; Marshall et al, 2014; ILRI, 2019)
Summary
The livestock sector plays a key role in the provision of livelihoods as well as food and nutrition security. There are an increasing number of examples of African livestock populations being used in studies aimed at identifying the genes or gene-pathways and genomic variants underpinning economically or ecologically important traits These include a number of studies that have detected putative signatures of selection for a variety of traits including feeding/drinking behavior, heat tolerance/thermoregulation, tick resistance, milk production under harsh environments, immune response, meat quality, and reproductive performance, amongst others (Makina et al, 2015; Mwacharo et al, 2017; Taye et al, 2017; Bahbahani et al, 2018). It is not yet clear whether existing SNP assays provide sufficient information to track inheritance of segments of the genome back to their diverse origins with sufficient accuracy to undertake GWAS that separates the different forms of LD in the population Assuming that it will prove possible, the between population LD is potentially of greatest interest given the very large genetic differences between ancestral breeds and the potential to apply gene-based selection for suitable combinations of productivity and adaptation traits. Such studies are useful in understanding their evolutionary history as well as identifying appropriate populations for the identification of genomic variants
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