Some considerations when designing a breeding programme

Approaches better adapted to consider the potential of indigenous livestock breeds must be developed. Realistic ways of improving these breeds must be chosen and applied in the context of environmental constraints and socio-economic demands and within the resources available. Aspects of sustainability and provision of future genetic diversity are critical. A basic principle to follow should be based on the assumption that there is no better way to conserve a breed for future generations than to consistently keep the breed or population viable by using an efficient, demand-driven long-term breeding programme suitable to commercial or cultural needs of livestock owners. In certain cases, it may be important to conserve the desired genes and not the genotype. Well designed crossbreeding and synthetic breed formation programmes can achieve this. Where applicable, especially with regard to genes responsible for adaptation such as disease and parasite resistance, marker-assisted introgression (MAI) would also contribute to sustainable conservation of desirable genes. However, MAI would have to be preceded by identification of such genes and a thorough characterization and understanding of their functions in well-designed functional genomic studies. Such an introgression may also be an effect of long-term crossing between breeds within an area and where traits of both breeds are favoured in the crossbred population.

An important feature of a genetic improvement programme, contrasting to an external input effect, is that the effects of selection accumulate over time (Figure 1). The economic benefits of selection also accumulate. Breeding programmes should, therefore, be seen as investments for sustainable improvements of the animal stock and the potential to produce food or other goods. To realize the benefits of a breeding programme, the breeding objectives must be appropriately defined for the species or breeds, communities and environments concerned, and the strategies laid out can be followed in practice.

Many important circumstances determine the scope of opportunities for and constraints to the breeding programme. Agricultural and land use policies, market information and access, environmental conditions, characteristics of animal populations and infrastructure available are examples of such factors.Basic questions concerning the choice of an overall breeding strategy include the emphasis on improving indigenous breeds vs. the use of tropical breeds from other areas or ‘exotic’ breeds. This section highlights some of these key elements which need to be considered before the final design of a breeding programme at breed level.

Figure 1.Genetic improvement from selection


The agriculturaldevelopment policy

Animal breeding programmes should be seen in the context of long-term development programmes contributing to both more food and other livestock commodities produced and to improved resource utilization and livelihood of the livestock owners (FAO, 2010; Mueller, 2006; Mueller, 2002). Thus, livestock breeding programmes may be seen as important parts of national agricultural policies, aiming at improving the food and income of a country, region or locality and of livestock keepers. Indeed, in most cases the agricultural development policy sets the scene. The long-term vision of the national interests and the breeding objectives must coincide, although there might be some discrepancies between short-term political goals and the more long-term breeding goals. Some compromises might be necessary and interim solutions applied, while maintaining the long-term goals [CS 1.12 by Chagunda]. Food imports may, for example, be necessary while awaiting the domestic production to increase through whatever means.

Environment, production system and the market

Any breeding programme is totally dependent on environmental conditions, the production system, the culture of the people for whom the animals are bred, and the market to which the animals and animal products are sold. Village breeding programmes for smallholder farmers, (Mueller, 2006; Wurzinger et al., 2010) [CS 1.19 by Yapi-Gnaore] will be different from those of large-scale farming systems[CS 1.16 by Mpofu]; [CS 1.26 by Ramsay et al]. Intensive crop–livestock systems, with good feed and health care facilities available, enable more opportunities for rapid improvement programmes than harsh rangeland systems do. Whatever the environment, to be sustainable the breeding programme must be market-oriented, i.e., demand-driven, yet considering the multi-purpose use of the animals and the long-term benefits to the farmer. To develop a programme that considers both the present circumstances and possible future situations, including market conditions, is a challenging task. This is because there is a considerable time lag between implementation of the programme and when the benefits of genetic gains are realized. Therefore, breeding programmes should be somewhat flexible and responsive to variable scenarios for the future needs of the programmes.

Infrastructure and role of farmers

Breeding programmes usually assume some kind of cooperation between the participants, e.g., by common ownership of some valuable breeding stock for wide use, conducting testing schemes involving many herds or employing trained people for artificial insemination (AI) services and other activities [CS 1.2 by Mpofu]; [CS 1.6 by Mpofu & Rege]; [CS 1.14 by Olivier]. The initial developments of breeding programmes are generally made by the government in collaboration with bilateral organizations in most developing countries because of the national benefits of improving livestock for food production and other purposes. In that way, basic investments and structures can be put in place. However, experience shows that it is extremely important that farmers get involved early in the process to ensure that their needs are taken into account and that they provide the support needed for the programme to work (Ahuya et al., 2004; Ahuya et al., 2005; vander Westhuizen and Scholtz, 2005; Kosgey et al., 2006; Peacock, 2008; Peacock et al., 2011); [CS 1.14 by Olivier]; [CS 1.26 by Ramsay et al.]. Throughout the world breeding programmes in the hands of farmers’ cooperatives, often with government support, have been successful for several livestock species (Ahuya et al., 2004; Mueller et al., 2006). Specialized breeding companies, however, have evolved under certain commercial conditions, especially for poultry and pig breeding and to a lesser extent for cattle breeding. However, private pioneers have in some cases played important roles in developing breeds and breeding programmes, e.g., in Brazil. Private companies have often been able to produce high quality breeding stock for industrialized production systems. In these cases, it is important, from a farmer’s and government’s perspective, to ensure that the most suitable animals are developed in relation to the real needs, environmental, socio-economic and other resources given [CS 1.26 by Ramsay et al.]

Infrastructure includes a broad range of essential inputs, which must be available for the breeding programme to succeed. These include trained staff, facilities for breeding animals and logistics for dissemination of germplasm, methods and means for recording, handling of data and evaluation of animals, decision-making bodies, finances, etc. [CS 1.30 by Jensen]; [CS 1.6 by Mpofu & Rege]. One often over-looked assumption is the required integration of all activities constituting a breeding programme. This applies both at the government level and at the practical organizational level. Another potential problem in developing countries is lack of or an inadequate number of people with appropriate training or incentives to successfully run a breeding programme (see Ojango et al., 2010). Lack of required infrastructure is one of the most serious constraints to developing indigenous breeds in tropical countries.

Matching genotypes with the environment—Or the other way around?

Clearly, to improve any breed or population, one must understand both the inherent genetic constitution of the population and how this interacts with the environment, which itself should also be well understood. It is only then that meaningful genetic improvement programmes can be developed. Given that not all components of the environment can be changed, particularly in low-input tropical production systems, one needs to know which genotypes can be used under such environmental conditions, i.e., different types of production environments need different types of animals [Gibson and Cundiff in ICAR Tech. Series No. 3]. Specifically, specialized exotic breeds are unlikely to survive, let alone produce, in the typically harsh tropical environments[CS 1.26 by Ramsay et al.]; [CS 1.28 by Madalena]. However, continuous improvements and changes of some environmental factors, such as feed availability, veterinary services and development of new production systems, will also be necessary to meet future demands on animal agriculture. In doing so, the environmental stress will decrease and some exotic breeds or crosses may become relevant and valuable for parts of the tropics.

When establishing or planning a livestock improvement programme for a difficult environment, there are two main approaches: one is to alter the environment, making it less rigorous and the other is to select stock which is likely to be the most adaptable to local conditions, including climatic stresses, that also has potential for increased productivity. To what extent should efforts be made to modify production environments to accommodate animals of the highest genetic potential for production, as opposed to concentrating on the productivity of genotypes which withstand the rigours of the harsh environment, while neglecting the scope for its amelioration? There is need to balance efforts in the two areas by examining cost–benefit relationships; either option taken alone will not be optimal, both ways should be explored [CS 1.36 by Sartika and Noor]. In many traditional tropical livestock production systems, levels of animal management and nutrition cannot support the potential of the so-called improved breeds. At the same time, despite the absence of scientifically based knowledge, the levels of traditional knowledge have been thoroughly underestimated or forcibly eroded, leading to inadequate husbandry and, consequently, the observed current poor performance by indigenous livestock populations. The extent to which these environments can be freed of the limitations imposed by climate, disease, parasites and nutrition is often limited. However, where efficient infrastructure is in place, control of diseases and feed resources can improve the situation considerably. Thus, there is a strong case for utilization of the best locally available, adapted genotypes in combination with improvements in the environment, wherever feasible and economical, while also considering development of appropriate breeding programmes for further development of these breeds [CS 1.31 by Philipsson]; [CS 1.39 by Okeyo and Baker].

Successful matching of genotypes with environments assumes availability of a wide range of genotypes. The tropical world is endowed with numerous genotypes. What is required is knowledge of their relative merits and appropriate exploitation of these merits [Breed information]; [DAGRIS]; [DAD–IS]. Developing countries should look at what is available locally or in other tropical areas before importing exotic breeds. Even when some sort of crossbreeding is opted for, the countries must maintain parallel programmes of evaluation, improvement and conservation of the indigenous parental breeds.

Unfortunately, many national governments in the tropical world lack appropriate livestock policies and have not given due consideration to development of indigenous livestock breeds [CS 1.12 by Chagunda]. Indeed, there is a tendency to focus on the imported breeds and often neglect desirable characteristics of indigenous breeds [CS 1.2 by Mpofu]. However, in some tropical situations, e.g., in highlands and in peri-urban production systems with improved environments, there are successful examples of introducing exotic breeds and their crosses with indigenous breeds [CS 1.31 by Philipsson]. The previously FAO-driven State of the World participatory reporting process and the various country reports on farm animal genetic resources (AnGR) [DAD-IS] contain a comprehensive inventory of AnGR at individual country level, with each country identifying its respective priorities and immediate actions that should be taken. The Global Strategy for the Management of farm AnGR provides a technical and operational framework for assisting countries, comprising:

  1. An intergovernmental mechanism for direct government involvement and policy development.
  2. A country-based global infrastructure to help countries cost-effectively plan, implement and maintain national strategies for the management of AnGR.
  3. A technical programme aimed at supporting effective action at the country level in the sustainable intensification, conservation, characterization and access to AnGR.
  4. A system to guide the Strategy’s implementation, facilitate collaboration, coordination and policy development, and maximize cost-effectiveness of activity.

In tandem with the recently revised FAO Breeding Guidelines [see FAO, 2010], most developed and some developing countries have outlined how each of these would be facilitated and the supportive policy and legal frameworks needed to achieve these. Turning these good intentions into actions and tangible outcomes and impacts must be the main focus of all stakeholders. This means that effective breeding strategies should be applied to better exploit the genetic potentials for increased productivity and other values to ensure future availability of adapted species and breeds.

What breeds are or may be available?

The current distribution of indigenous breeds in most tropical developing regions is mostly a result of history, tradition and local convenience, sometimes even prejudice. There are only isolated cases where deliberate measures have been taken by national governments to implement programmes to select and breed animals specially suited physiologically for each region [CS 1.26 by Ramsay et al.]; [CS 1.28 by Madalena] or to import suitable indigenous germplasm from other tropical developing countries [CS 1.6 by Mpofu & Rege]; [CS 1.31 by Philipsson]. The kind of strategy which is needed to effectively utilize these indigenous livestock genetic resources is a key question for which answers must be provided.

A basic question is which breeds or genotypes to use or target for use and improvement. As there is a natural stratification of livestock breeds by climatic zones, there should be little difficulty in making choices. A good understanding of the environment in addition to knowledge of available breed resources is required to make appropriate decisions on breed choice and necessary improvement interventions [see van der Werf in ICAR Tech Series No. 3], [Nitter in ICAR Tech Series No. 3] and [Gibson and Cundiff in ICAR Tech Series No. 3].

Where opportunity exists for improving the production environment, a shift towards more commercialized meat (e.g., beef) or dairy production or both, may be desirable. In such cases, there are two options. One is to identify a suitable breed from the wide range of indigenous breeds. For example, in Africa beef operations in tsetse-free regions of the south may consider use of well-selected breeding animals from the Nguni, Afrikaner, Tuli or even Boran populations. Conversely, beef production in tsetse-infested parts of eastern Africa may consider using the Orma Boran or introducing the Ethiopian Sheko breeds, considered to be less trypano-susceptible than most ‘beef-type’ cattle breeds in the sub-region. Alternatively, crossing Boran and N’Dama or Sheko and selecting the resultant crosses so as to retain and use them for further breeding of individuals which possess the right combination of the quantitative trait loci (QTL) responsible for trypanotolerance from both breeds through introgression and selection is also promising (Hanotte et al., 2003; Orenge, 2010). These examples illustrate the need for systematic characterization of the breeds presently used in the actual area (Module 2, Section 2). Such a characterization must include both population structure andphenotypic trait descriptions, with emphasis on production, reproduction and adaptive traits to ensure that both the potential of the breed and what makes it a unique resource in its cultural and socio-economic environment is considered. The population structure describes the number of breeding animals by age and sex and its changes in the past. The dynamics in numbers of animals of a breed is important for the level of efforts in conserving the breed and in demonstrating its future potential for food production [DAGRIS]; [DAD–IS].

If there is a choice among indigenous breeds to be selected for an improvement scheme, the facts revealed through the breed characterization form the basis for decision together with an analysis of the relationships between the breeds. Methodologies applying molecular genetics offer new opportunities to measure genetic relationships and diversity. Additionally, the economic analysis of the best options (Simianer et al. 2003) needs to be explored and refined (Module 2, Section 3.3). Among the breeds with good potential for food production and other desired products and use, it may be wise to conserve the least related breeds. It may be equally wise to merge small closely related breeds into a common more efficient selection programme than otherwise would be possible to enable the best opportunities to save important genes for future exploitation. Otherwise such breeds may suffer from serious inbreeding and become extinct.

As germplasm in several species can be moved easily around the world today, it means that there is a huge global livestock gene pool to draw from. Breeding programmes have, over time, become more international. This requires more knowledge than previously understood to evaluate what is marketed or made available on a global scale. Although one must always be open to investigate any advantages of bringing in new genetic material into a breed or area, the process to do so requires a critical review of all aspects of the breeding programme (later in this module) [see Gibson and Cundiff in ICAR Tech Series No. 3].

Are small sized breeds less productive than larger ones?

A specific and crucial question to raise in the context of choice of breeds for extensive production systems in the tropics relates to the desirable size of the animals. Under conditions of sparse feeding or low nutritional levels, small animals obviously have an advantage over large ones (Taylor and Murray, 1988). More energy is left for production when the maintenance requirements have been met. In such situations, selecting for body weight above certain optimum levels might result in animals becoming less adapted. In addition to the lower maintenance requirements and other related adaptive attributes already alluded to, an advantage of small body size, often overlooked, is the resulting convenient carcass size for rapid disposal in environments with inadequate transport network and freezing facilities. That is why poultry and small ruminants are relatively more common in such environments. Furthermore, there is no evidence indicating that the quality of beef from the small sized indigenous cattle is inferior to similarly reared large framed exotic stock [CS 1.2 by Mpofu]; [CS 1.8 by Mpofu]. However, with improved nutrition and general management, selection for increased growth rate or body weight may be justified.

Ample documented evidence indicates that under conditions in which indigenous tropical livestock are currently predominantly kept, specialized large sized imported breeds would be unsuitable, especially for meat production. To date, most studies—mainly under station or improved (commercial) production conditions in tropical and sub-tropical countries (e.g., Bonsma, 1949; Buck et al., 1982; Trail, 1984; Vilakati, 1990; Moyo, 1996) have shown that smaller sized indigenous breeds can be as productive as, if not more productive than, European breeds, especially if account is taken of viability and maintenance requirements. Additionally, the low risk factor of adapted breeds is an important consideration where market values are unstable, while production costs continue to increase, or where the probability of death from environmental stresses is high (Frisch, 1984).

It is a universally accepted fact thatindigenous African cattle produce less milk (on a per animal basis) than European dairy cattle. However, when adjusted for animal size, the productivity of some breeds is quite considerable[CS 1.31 by Philipsson], even without considering the harshness of the production environment and the input requirements for indigenous livestock relative to those for specialized exotic breeds. The variation among the indigenous breeds is, however, substantial [Breed information].

Unfortunately, few systematic breed evaluation studies have been carried out in the tropics in which indigenous and exotic breeds have been comprehensively and fairly compared under typical production conditions. However, there have been some interesting studies where small sized breeds were consistently superior in the productivity indices considered, mainly because of the low maintenance requirements, superior calving rate and low calf mortality (Madalena, 1984; Madalena, 1993; Madalena, 2005) [CS 1.8 by Mpofu; CS 1.39 by Okeyo and Baker].

Whereas the relationship between body weight and requirements for maintenance may be well established, the actual cost implications of this relationship in production systems where animals are entirely dependent on pasture is not clear. Nonetheless, figures indicate that where feed availability is a constraint the smaller sized indigenous breeds are superior. However, this situation also applies to temperate climates. In grazing systems, for example as practised in New Zealand, the smaller sized Jersey cows or their crosses do relatively well as regards production in relation to metabolic weight compared to the large sized Holstein cattle, whereas the opposite may be true in intensive feeding systems.