Landscape Genomics as a Response to Genetic Dilution  

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Many people have praised artificial insemination as a tool to help improve genetic and productive performance of African livestock including dairy beef poultry with mixed results but not many people have observed the sad loss to many of our African genetic pool highly priced for disease, parasites and pests, and the harsh African environmental tolerance gained throughout millennia.

Many marginalised smallholder farmers have lost productivity and resilience in their better suited and adapted African animals when they adopted the so called better suited genetically improved animals.

The debate is raging on whether African smallholder farmers should be allowed to continue to keep their adapted and resistant breeds rather than abandon them for imported or improved animals. There is inadequate research and breeding programmes focussing on improving the productivity and performance of the indigenous livestock as an alternative to the imported or improved breeds.

African livestock breeds are on a daily basis at risk of extinction and the breeds that are increasing getting threatened include the Nguni, Zebu, Hard Mashona and the Kuri cattle that have distinctive traits unmatched by the imported breeds.

The long horned Kuri cattle are found in Chad and parts of Nigeria are good swimmers that are generally unfazed by insect bites, and well suited for very hot environments.

In Livestock Genomics for Developing Countries – African Examples in Practice, by Karen Marshall et al, as part of the Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya and other institutions, “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 adaptation.

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;

  1. 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 some 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.

In developing countries, the livestock sector plays a key role in the provision of livelihoods as well as food and nutrition security.

The majority of livestock are kept by the rural poor, where they serve multiple functions. These include: savings and insurance, food security (meat and milk), income, livelihood diversification and thus risk reduction (such as in mixed crop-livestock systems), inputs to crop production (draft power, manure as fertilizer), transportation, various uses of hides and skin (such as for housing), allowing households to benefit from common-property resources (such as communal grazing areas), and fulfilling social obligations (such as being used in special ceremonies or for dowry), amongst other.

The livestock sector also benefits other actors in the associated value chains, such as input providers, traders, processors and retailers, through the provision of employment and income. Critically, animal source foods – consumed in even small amounts – play a key role toward food and nutritional security of the poor, as they provide quality protein and micronutrients essential for normal development and good health.

The demand for animal source foods is rapidly increasing in developing countries: for example, in low income countries the demand in 2030 for beef, milk, poultry and eggs is predicted to be a 124, 136, 301, and 208% increase over that in 2000, respectively.

This demand increase has been largely attributed to population growth, income growth and increasing urbanization. To ensure this demand is met, large increases in livestock production within developing countries will be required.

Achieving this in a sustainable manner is expected to be challenging, with a key component of this recognized to be increasing livestock productivity (output per unit of input).

Increasing livestock productivity in developing countries generally requires simultaneous interventions in the areas of animal feed, health and genetics. In many livestock development programs these interventions take the form of capacity building of the livestock keepers and other value chain actors, ensuring the availability and accessibility of inputs, provision of new technologies or customization of existing technologies, support to private and/or public sector involvement, and advocacy for supportive policies.

The provision of incentives for increased productivity can also be important, such as in some small-hold and pastoral sectors where livestock are primarily kept for savings and insurance purposes, so maintaining a livestock asset base is more important to the household than improving livestock productivity.

Such incentives could be provided by, for example, increasing livestock income through facilitating access to strong and stable markets, or ensuring that intra-household benefit from the livestock enterprise is equitable.

In addition, attention to other issues which can be affected through increased livestock productivity, such as equality, food safety and environmental sustainability, are also commonly part of livestock development programs. As livestock systems within developing countries are both diverse and dynamic, intervention packages typically need to be customized for each livestock sector.

To date, the majority of African livestock systems have not benefited from livestock technologies to the extent that developed countries have, including in relation to genetic improvement strategies.

Currently, there are few examples of sustainable breeding programs and the use of reproductive technologies, such as artificial insemination, is limited to specific livestock sectors. Contributing factors to this include: the lack of public and private sector investment; lacking or weak supportive policies and institutional arrangements; the heterogeneity of livestock systems, farm-scales, management practices, and needs and preferences of livestock keepers; poor infrastructure; and limited capacity in the field of animal breeding and reproduction, amongst others.

The potential of genetic improvement to increase livestock productivity is, however, increasingly being recognized by decision makers, with many African countries now explicitly including genetic improvement within their national livestock development plans.

The types of structured genetic improvement programs being implemented in Africa vary by system. These include: breed-substitution with other African breeds, breeds from other tropical countries such as India and Brazil, as well as breeds from elsewhere; cross-breeding, most commonly where a highly adapted but lowly productive indigenous breed is crossed with a poorly adapted but highly productive exotic breed; and less commonly within-breed improvement.

Increasingly, explicit attention is being paid to the development of working models to ensure sustainability of these programs, as it has been well demonstrated that the models implemented in developed countries cannot be directly applied.

The application of genomics – ranging from the determination of breed composition of animals in the absence of pedigree data for in situ comparison studies, or for the application of genomic selection in breed improvement programs – is just beginning to emerge, often overcoming a constraint that would otherwise exist, such as lack of recorded pedigree.

In this article we describe several examples of the use of genomics in sub-Saharan African livestock systems, draw lessons learnt from these, and giving recommendations for African livestock systems to increasingly capitalize on genomic technologies.

The subsequent section ‘case studies’ describes the case studies grouped by application, namely the use of genomic information to:

  • to identify the most appropriate breed or cross-breed type for different livestock production systems;
  • to enable or enhance breeding programs;
  • create new breed-types; and
  • discover genetic variants of economic and ecological significance.

A discussion follows, first addressing current developments on livestock genomics in Africa, drawing on the case studies, and secondly describing the future outlook for livestock genomics in Africa.

Use of Genomic Approaches to Aid Identification of the Most Appropriate Breed or Cross-Breed for Different Livestock Production Systems

Identification of the most appropriate livestock breed or cross-breed type in a particular livestock production system is typically the starting point of a genetic improvement strategy.

To-date there are few studies to this end due to lack of investment in this area plus, in the case of cross-breeds, the inability to assign breed-type to animals in the field which is necessary for in situ comparisons.

The latter stems from the lack of pedigree information in most African livestock systems and the near impossibility of assigning breed-type based on phenotype, particularly in systems where unstructured cross-breeding is prevalent.

The use of genomic approaches to assign breed composition to individual animals can overcome this constraint. Here we discuss examples for dairy cattle systems in Senegal and Kenya, and sheep systems in Ethiopia.

Kenya Dairy Cattle

In Kenya the large majority of milk is produced by smallholder farmer who typically milk 1–5 cows. Smallholders mostly keep crosses between indigenous cattle and exotic dairy breeds such as Holstein, Friesian, Ayrshire, and Jersey.

There is no systematic breeding of crossbred cattle and farmers rarely keep pedigree or performance records. Most mating events involve local crossbred or indigenous bulls, where the crossbred bulls are of unknown breed composition.

Farmer production environments vary greatly and this translates into a wide range of production output per cow, from less than 1,000 l milk per annum to more than 5,000 l, with the large majority likely in the range 1,000 to 3,000 l milk.

There is no information about which breed composition works best for different production environments, other than the general observation that high grade exotics (cows with a very high proportion of exotic dairy breed composition) can do well in very good environments.

The likelihood is that the intermediate grades do better in poorer production environments but given the lack of evidence most advice provided to farmers is that they should upgrade to higher grade exotic animals by using AI.

The Dairy Genetics East Africa project set out to determine what grade of crossbred (i.e., what percentage of exotic dairy breed composition in a crossbred cow) worked best for different production environments.

The project worked with farmers to collect performance data, including on milk yields, reproduction events, and disease incidence, for 18–24 months. Further the recorded animals were genotyped using the Illumina bovine high density (HD, 780 k) single nucleotide polymorphism (SNP) assay with the HD SNP data used to perform admixture analyses, using the ADMIXTURE software, to generate an estimate of ancestral breed composition of each animal.

This allowed, for the first time, accurate information on breed composition to be combined with in situ performance data to determine what breed composition worked best in different smallholder environments.

By comparing farmer and enumerator (field staff) assessments of breed composition, based mostly on phenotypic appearance and farmer recollections on cows’ origins, with the admixture determinations of actual breed composition it was confirmed that phenotype-based assessments were very poor predictors of actual breed composition (R2 = 0.16).

The results showed that intermediate to low grade (<50% exotic breed ancestry) cows performed best in the majority of the smallholder farms, while animals with higher grades (>50%) only performed better than lower grades in the best environments (those supporting >1800 l/cow/annum.

are used globally because of their more limited use. Innovative applications of genomic technology or tools for breed composition and parentage determination, and genomic prediction, if accompanied by sound business models for their delivery hold great potential for impact in Africa.

Use of Genomic Approaches in the Creation of New Breed-Types

The most appropriate breed-type for African livestock systems are typically considered those which are both productive and adapted/resilient. Genomics and its associated technologies/techniques (transgenesis, cloning, gene/genome editing etc.) offer opportunities for creating such breed-types. The below case study is one example of this.

Trypanosome Resistant Cattle

Animal trypanosomias is caused by a group of extracellular protozoan parasites and transmitted by the tsetse fly is a major constraint to livestock production across much of the African continent with massive economic consequences. Attempts to develop vaccines against this pathogen have largely failed due to its ability to rapidly change its highly antigenic surface glycoprotein.

The alternative prevention measure, tsetse vector control has proved expensive and difficult to sustain with adverse environmental consequences. However, some African Bos taurus cattle breeds, such as N’dama, are tolerant of infection with trypanosomes, remaining healthy and productive and without the anemia that is characteristic of infection in susceptible breeds. This phenomenon has been termed trypanotolerance.

Because of the difficulty in conventional control methods, there has been significant research into a genetic approach to enabling livestock production under trypanosome challenge. In a series of studies, quantitative trait loci influencing response to trypanosome challenge were mapped in a mouse model and in N’dama cattle.

Eventually, a combination of linkage mapping, expression analysis, candidate gene sequencing, population analysis and in vitro studies allowed candidate genes and variants to be identified with some confidence However, no genes of large effect were identified and the mechanism of tolerance remains unclear.

An alternative genetic-based approach is currently under investigation that attempts to exploit the resistance to infection with some trypanosome species shown by most primates. Resistance in primates is mediated by subset of high-density lipoproteins (HDLs) called trypanosome lytic factors (TLFs) which kill many trypanosome species.

The active component of TLF has been shown to be apolipoprotein (apoL-1) which, following endocytosis by the trypanosome, is activated within the acidic lysosome to form membrane pores, resulting in parasite swelling and lysis (Molina-Portela Mdel et al., 2005; Thomson and Finkelstein, 2015). Primate TLF has been shown to kill the cattle-infective trypanosome, Trypanosoma congolense as well as the human-infective trypanosomes, T. brucei rhodesiense.

Furthermore susceptible mice have been shown to become fully resistant to infection with these trypanosomes following transfection with primate-derived APOL1. There is thus good reason to believe that transgenic cattle could be constructed, which are fully resistant to trypanosomes.

This could potentially allow Bos indicus cattle breeds that are well adapted to the African environment, except for susceptibility to trypanosomes, to become sustainably resistant without the use of toxic drugs or environmentally damaging insecticides and research to explore this possibility in East Africa is currently underway.

African Indigenous Livestock as Resource Populations for Discovery of Genetic Variants of Economic and Ecological Significance

African livestock populations are rich resources for discovery of genetic variants, and many efforts are underway to this end. The first case study below describes a breeding program for small ruminants (sheep and goats) which, whilst currently not using genomics as part of the breeding program itself, is using the breeding program data for genetic variant discovery purposes.

Following this a second ‘case study’ illustrates other efforts toward genetic variant discovery: unlike the other cases described here which are specific initiatives/projects, this draws on numerous studies to showcase the various types of activities occurring in this space.

Other Initiatives on Genetic Variant Discovery

Post domestication, livestock genomes have continuously been modified through selective breeding for economically or otherwise important traits, and natural selection for adaptation to local agro-environments.

Africa has diverse agro-environments and a predominantly tropical environment that is characterized by harsh and extreme climatic conditions, seasonal feed and water scarcity, heat stress, high solar radiation, widespread pathogens, parasitic infections and disease epidemics. These present the main evolutionary forces shaping Africa’s livestock genomes.

Accordingly, African livestock display unique adaptive traits including enhanced disease resistance, superior innate immunity and greater ability to thrive, produce and reproduce in unfavorable environments. Some of the adaptive traits in African livestock, such as resistance to gastro-intestinal parasites in small ruminants, are of global significance.

There are numerous African livestock populations already identified as of interest for gene-discovery studies. These include, as examples: breeds that are highly resistant/tolerant to gastro-nematodes, such as the Red Maasai sheep and Small East African Goats of East Africa, West African Dwarf sheep and Goat.

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 behaviour, heat tolerance/thermoregulation, tick resistance, milk production under harsh environments, immune response, meat quality, and reproductive performance, amongst others.

There are additionally some reports of GWAS, such as for tick and gastrointestinal parasite resistance though these are rarer due to lack of datasets with both phenotypes and genotypes recorded on sufficient animals.

Some genetic mapping studies targeting QTL identification, such as for resistance to gastro-intestinal nematodes and trypanotolerance have also been reported. In cases candidate genes have also been identified within the genomic regions of interest, for instance genes likely associated with trypanotolerance.

Should this work be extended to the identification of refined genomic regions and/or validated functional mutations and variants, there is potential for it to be fed into genetic improvement strategies, either via breeding programs incorporating the use of genomic/genetic data or through the creation of new breeds via either introgression or genome modification approaches.

Building human capacity in animal breeding, genetics and genomics within Africa, such that appropriate expertise exists to design and support implementation of the genetic improvement strategies and linked genomic technologies, is required.

Suggestions on how to strengthen developing country higher education systems in animal breeding include concerted efforts in training of trainers, co-operation among higher education institutes within regions (South–South collaboration) in order to improve the quality of training offered, and collaboration with institutes in more developed countries.

Concluding Comments

In conclusion, genomic applications are currently benefiting African livestock systems in a variety of ways, including on genetic improvement and more broadly, such as assisting in system characterization. This has emerged relatively recently, largely within the last 5 years. The expectation for the future is that African livestock systems will increasingly benefit from genomics, particularly if the various issues constraining this (as discussed in this paper) are addressed. The rate at which this will occur will large depend on the level of investment in African livestock genetic improvement.

Adapted from Livestock Genomics for Developing Countries – African Examples in Practice, by Karen Marshall et al, as part of the Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya and Centre for Tropical Livestock Genetics and Health, Nairobi, Kenya and other institutions.

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