Farm animal genetic resources face a double challenge. On the one hand the demand for animal products is increasing in developing countries. The Food and Agriculture Organisation of the United Nations (FAO) has estimated that demand for meat will double by 2030 (2000 basis) and demand for milk will more than double in this 30-year period. On the other hand, animal genetic resources are disappearing rapidly worldwide. Over the past 15 years, 300 out of 6000 breeds identified by FAO have become extinct, and 1 to 2 breeds disappear every week. FAO has been requested by its member countries to develop and implement a global strategy for the management of farm animal genetic resources. It is important to conserve local breeds because many of them utilise lower quality feed, are more resilient to climatic stress, are more resistant to local parasites and diseases, and represent a unique source of genes for improving health and performance traits of industrial breeds. It is important also to develop and utilise local breeds that are genetically adapted to their environments. Genotype x environment interactions are important especially where extreme environments are involved. Most of these production environments are harsh, with very limited natural and managerial inputs, and they are not limited to developing countries. Animals genetically adapted to these conditions will be more productive at lower costs. They will support food, agriculture and cultural diversity, and will be effective in achieving local food security objectives. In many countries local communities depend on these adapted genetic resources. Their disappearance or drastic modification, for example by crossbreeding, absorption or replacement by exotic breeds, will have tremendous impacts on these human populations. Most breeds at risk are not supported by any established conservation activity or related policy, and breed extinction rates are increasing.

The paper provides an historical overview of conservation activities undertaken in Europe to maintain native livestock breeds, including the motivation and methods applied in conservation programmes and the contribution of various stakeholders. The current state of conservation activities is presented, based on reports provided by the National Coordinators on animal genetic resources (AnGR) during annual Workshops. These Workshops have been convened jointly by the Food and Agriculture Organisation of the United Nations (FAO) and the European Association for Animal Production since 1995, and are conducted within the framework of the FAO Global Strategy for Management of Farm Animal Genetic Resources. Analysis includes policy and legislation development, state and mode of financial support, conservation approaches and public awareness and education initiatives. The paper describes the establishment of the European Regional Focal Point for AnGR, its terms of reference, and ongoing and future activities. Questions regarding a vision of future needs and developments in AnGR are raised in this paper, both from a technical and policy context.

In 2003 the Rare Breeds Survival Trust (RBST) celebrated its 30th anniversary and is now widely recognised as the national non-governmental organisation responsible for rare breeds of farm livestock in the UK. No breed of farm animal has been lost since 1973 and there are now 72 breeds which meet the Trust's criteria for recognition as a rare breed. These criteria, which are regularly reviewed, take into consideration how long the breed has existed, the number of adult females and geographic distribution. With one or two notable exceptions, the breeds listed by the Trust have built up numbers and have become well distributed. However, all rare breeds still face an uncertain future but their greatest enemy is no longer immediate extinction but extinction by stealth. The sustained downward pressure on livestock farming in the UK, National and European government legislation, loss of genetic diversity and public indifference make a dangerous combination.

So what can an organisation like the RBST do, funded entirely by membership subscriptions, donations and legacies? The answer is a great deal! Firstly, we need to make people care, so that Governments and legislators listen and consider the implications of new (and existing) legislation on rare breeds. There is strong evidence that where people are seen to care, then government does listen to ‘umbrella’ organisations like the RBST lobbying on behalf of a small and sometimes fragmented sector of the industry. Widespread concern during the early days of the recent Foot and Mouth Disease (FMD) epidemic in the UK enabled the Trust to secure unprecedented exemption for rare breeds of sheep and pigs from contiguous culls. However, unlike captive zoo collections or wild populations, the individual cattle, horse/ponies, pigs, poultry and sheep/goats belong to individual breeders! Without their support, co-operation and participation, progress can be difficult and slow.

This national role, to be effective and comprehensive, must be grounded in sound science, reliable technical data and impartial information. The Trust now has the expertise and the tools to quantify the genetic diversity in rare breeds while offering practical solutions to some of the problems facing rare breeds. The RBST is doing a great deal but there is still much to do. The next 30 years promise to be as important in securing the future of the UK's rare breeds of farm livestock as the first 30 years were in rescuing them from extinction.

The Foot and Mouth Disease (FMD) epidemic of 2001 clearly illustrated the fragility of the UK's farm animal genetic resources. In particular, millions of sheep were killed by the disease and by the ‘stamping out’ policy chosen for disease control. Loss of genetic resources was not evenly spread throughout the UK, nor throughout the many different sheep breeds that are native to the UK and for which the UK has a formal responsibility for protection to the United Nations. In fact, the FMD epidemic demonstrated for the first time that sheep breeds comprising large numbers of individuals which are commercially farmed, can nevertheless be at considerable risk of extinction. The breeds most affected were those restricted to geographical regions of the UK into which the FMD spread. These regionally important breeds are adapted to their particular regional environments, represent an important living heritage for the UK and are a key component in sustaining the rural economies of sheep farming communities.

The events of 2001 provided clear proof that there are two components of the UK's farm animal genetic resources demanding protection. One component is already recognised as a priority and is composed of the numerically rare breeds of all domesticated species: these are already under the protection of the Rare Breeds Survival Trust (RBST). The second component has not previously been recognised as a priority for protection. The FMD crisis proved that sheep breeds could exist as large numbers of individuals, but nevertheless face extinction due to their regional location. Urgent attention must be focussed on our Heritage Breeds of sheep. The UK has one of the greatest number of native sheep breeds of any country in the world. The Heritage Breeds provide potentially valuable genetic resources for environmental, low-input farming systems.

Heritage GeneBank was founded during the FMD epidemic specifically to protect sheep breeds at threat of extinction from the disease. A group of academic research scientists established a genetic salvage programme: collecting semen and embryos for protection in a gene bank. Germplasm from seven breeds is in long-term storage. Following the crisis, the scientists involved in the gene bank made a commitment to continue their conservation work in recognition that the Heritage Breeds of sheep in the UK continue to require protection.

This paper describes: (1) the work of Heritage GeneBank (HGB); (2) the threefold mission of The Sheep Trust, the new national charity that evolved from HGB (http://www.thesheeptrust.org); and (3) the ongoing urgent need for conservation of the UK's Heritage Breeds of sheep threatened by genetic erosion.

Historically the UK has not had or needed a defined Government policy on the conservation and utilisation of farm animal genetic resources. However, this situation has changed recently, partly as a result of international efforts, stimulated by the Convention on Biological Diversity, and led by the Food and Agricultural Organisation of the United Nations, to co-ordinate national strategies for conservation and utilisation of farm animal genetic resources. As part of this international effort, a National Consultative Committee was set up in the UK in 2001. This committee produced the UK Country Report on farm animal genetic resources, which was published in 2002 and submitted to FAO. This paper outlines the structure and recommendations of this report, and discusses government policy on farm animal genetic resources.

Factors that influence variability between and within populations at levels ranging from the molecular to quantitative traits are reviewed. For quantitative traits, models of how levels of variation are determined and how they change have to be based on simplifying assumptions. At its simplest, variation is maintained by a balance between gain by mutation and loss by sampling due to finite population size. Rates of response in commercial breeding programmes and long-term selection experiments are reviewed. It is seen that rates of progress continue to be high in farmed livestock, but not in race horses, and that continuing responses have been maintained for 100 generations in laboratory experiments. Hence variability can be maintained over long periods despite intense selection in populations of limited size. The potential role of conserved populations is reviewed, and it is suggested that their role is unlikely to be as a useful source of variation in commercial populations but mainly to preserve our culture and to fill particular niches.

The procedures outlined by the Food and Agriculture Organisation of the United Nations (FAO) guidelines for managing small populations at risk are reviewed. These cover identification of breeds at risk, prioritising and deciding upon actions, managing in vivo populations at risk, and managing gene banks of cryoconserved material.

There is a long history in the UK of procuring and maintaining plant genetic resources for curiosity, novelty, taxonomic reference or direct utilisation. This paper describes the evolution, the current structures and the processes involved in plant genetic resource activities in the UK, and discusses similarities and differences in the issues in and approaches to plant and animal genetic resources conservation and utilisation.

Managing the rate of inbreeding (ΔF) provides a general framework for managing genetic resources in farmed breeding populations. Methods for managing ΔF have been developed over the last five years and they allow the attainment of the greatest expected genetic progress while restricting at the same time the increase in inbreeding. This is achieved by optimising the contribution that each candidate for selection must have to produce the next generation. The methods take into account all available performance and pedigree information and use Best Linear Unbiased Prediction (BLUP) estimates as a predictor of merit. Importantly, these tools give at least equal, but more often more gain than traditional selection based on truncation of BLUP estimated breeding values when compared at the same ΔF. Deterministic predictions for the expected gain obtained with optimised selection with ΔF restricted are now available. The optimisation tool can be also applied in a conservation context to minimise ΔF with restrictions to avoid loss in performance in valuable traits. Information on known quantitative trait loci or on markers linked to them can be incorporated into the optimisation process to further increase selection response. Molecular genetic information can also be incorporated into these tools to increase the precision of genetic relationships between individuals and to manage ΔF at specific positions or genome regions.

Molecular markers can be used to explore the diversity present in livestock populations. In cattle the diversity among breeds, revealed using molecular markers, is greater than the within breed diversity. Therefore both at the phenotypic and genetic level breeds form discrete populations, which could be used to conserve maximum diversity in the species. The best way to conserve breeds is to ensure their commercial utility; therefore selection of breeds for commercially advantageous phenotypes should be encouraged. Gene mapping studies suggest that, even for complex traits, there may be very few genes involved in controlling variation in the phenotype. Therefore selection for a particular trait does not necessarily affect the genetic base of the population, other than at the genes under selection. This seems to be the situation in the Hereford breed, where the phenotype has changed considerably over the past 50 years, while blood group data suggests that the genetic base of the population has not been greatly affected. Genome mapping approaches allow first the chromosomal location and ultimately the genes controlling traits to be identified. This information provides DNA markers for favourable alleles at trait genes that can be used in selective breeding programmes to improve breeds for a range of traits. Work on double muscling in Belgian Blue cattle has shown that a single gene, myostatin, can be responsible for an extreme phenotype, so selection for double muscling potentially only affects diversity around this gene. However, the examination of the phenotypes associated with this gene in other breeds suggests that genes in addition to myostatin are involved in the development of the extreme phenotype. Thus information on single genes is too narrow to be of value in making conservation decisions. With the current state of knowledge genetic information can aid the choice of individuals to use for breeding and for conservation of diversity, but the information should be used with caution and in conjunction with additional information, such as pedigree, phenotype or function data.

Analysis of molecular genetic diversity in livestock potentially allows for rational management of genetic resources experiencing the serious pressures now facing the livestock sector. The potentially damaging effects of genetic erosion are an ongoing threat, both through loss of breeding stock during the 2001 FMD crisis and potentially as a result of the ongoing National Scrapie Plan. These factors and an increasing focus through the Food and Agriculture Organisation of the United Nations (FAO) on the conservation of animal genetic resources force us to consider seriously how to measure, monitor and conserve diversity throughout the genomes of livestock. Currently debated ways to optimally conserve livestock diversity, particularly the ‘Weitzman Approach’, may fail to take into account the significance of within-breed genetic diversity and its structuring, and apply relatively simplistic models to predict the probability of extinction for breeds over defined periods of time under certain management scenarios. In this paper I argue, using examples from our work and that of others, that within-breed diversity, in particular, should not be ignored when conserving livestock diversity, since breeds may be genetically structured at a variety of scales and there is little evidence for a convincing relationship between effective population size and genetic diversity within rare UK breeds. Furthermore, until we understand the population genetic forces that shape diversity in breeds in more detail, using raw indices of genetic variation or distances to rank or prioritise breeds in terms of some notional threat of extinction has questionable conservation value.

Artificial Insemination (AI), the first generation of Reproductive Biotechnologies (RB), is widely used in cattle with more than 110 million females, accounting for 20% of the total global population of breeding females, inseminated annually. There is still great potential for expansion, but further increases will depend on improved conception rates on commercial premises. AI is also used in sheep and goats but to a much lesser extent. AI in pigs has become increasing popular in recent years (close to 50%) with further expansion (around 10% or more) expected in the next decade. The major challenge for AI in the years to come is to reduce the cost of the offspring that are produced. Irrespective of the species, the key element determining this cost is the percentage of inseminations that result in viable offspring. In vivo collected embryo transfer has also been widely used across the world but to a much lesser extent than AI. In cattle around 500,000 embryos are transferred annually, generating an active international exchange of germplasm. Technical limitations associated with variability in superovulatory responses between individuals will limit further uptake of this technology. In contrast, in vitro embryo production, particularly in the bovine, has greater potential for expansion due to its ability to (1) generate a large number of offspring, (2) reduce costs of embryo production, (3) facilitate adoption of nuclear transfer and transgenesis and (4) regulate and minimise potential hazards associated with disease transmission. A remaining factor limiting uptake of this technology is the achievement of satisfactory pregnancy rates following the transfer of cryopreserved embryos, although recent developments suggest these problems can be overcome. Nuclear transfer and transgenesis present numerous opportunities for genetic conservation, but are still very much at the experimental stage. Genetically modified animals may only be tolerated by society if they lead to benefits in human health or to the environment. Emphasis should be directed to disease resistance in relation to both animal and zoonotic diseases.

The establishment of repositories of frozen semen, for the conservation of agricultural genetic resources, is not a simple matter of collecting and freezing semen in the hope that one day it will be suitable for use in an artificial insemination procedure. Important genetic issues need to be considered; for example, how many samples should be stored and from how many individuals? Aside from these, many biological and logistic issues must be considered. Cryopreservation technology does not work equally well in all species, often because of anatomical differences in the female reproductive tract leading to significant variability in the number of spermatozoa needed in order to achieve an acceptable conception rate. Moreover, spermatozoa from different species are not equally susceptible to cryoinjury. However, it is also emerging that semen samples from individuals within a species are also of different quality; several studies have revealed that these differences reflect the quality of DNA within the spermatozoon itself and also the efficacy of biochemical functions, including metabolic and signalling systems, within individual cells. As new possibilities to select spermatozoa for insemination arise, especially the use of flowsorting for gender selection, these issues may become more significant. In this article we interpret the way in which some of this new information may impact upon the practical implementation of genetic resource conservation.

A number of methods can now be used to store the female germ plasm from farm species. New assisted reproductive techniques such as ultrasound guided oocyte pickup, followed by the in vitro maturation of oocytes together with cryopreservation enable the collection and storage of germinal vesicle or metaphase II secondary oocytes and more practically embryos after in vitro fertilisation. Following freezing using equilibration or vitrification protocols, oocytes and embryos can be stored at liquid nitrogen temperatures for as long as required. Despite much research interest, the efficiency of secondary oocyte freezing is low and the developmental potential of stored oocytes is directly affected by the local cellular and hormonal environment during maturation, fertilisation and extended culture in vitro. An alternative strategy which avoids many of the technical difficulties associated with mature oocyte freezing may be to cryopreserve primordial oocytes in situ within ovarian cortex. This approach has the added advantage that it may also provide a means of conserving the oocytes of rare species and it can be used to bank cells obtained from postmortem tissue samples or species for which IVF protocols may not have been fully optimised. Although the methodology is still in its infancy, when ovarian cryopreservation is combined with autografting, xenografting, or follicle culture, ovarian tissue freezing has the potential to restore or extend the fertility of domestic animals so maximising their genetic potential.

Cloning mammals from somatic cells by nuclear transfer has the potential to assist with the preservation of genetic diversity. An increasing number of species have been successfully cloned by this approach; however, present methods are inefficient with few cloned embryos resulting in healthy offspring. In those livestock species that have already been cloned, it is clearly feasible to use cloning to preserve endangered breeds (e.g. the last surviving Enderby Island cow). The opportunity exists to recover oocytes from these cloned heifers and use frozen Enderby Island sperm from deceased bulls for in vitro fertilisation and thus, expand the genetic diversity of this breed. Where there exists an adequate understanding of the reproductive biology and embryology of the species concerned and adequate sources of females to supply both recipient oocytes and surrogates to gestate the pregnancies, intra-specific nuclear transfer and embryo transfer can be utilised. However, when these requirements cannot be met, as is common for most endangered species, cloning technology invariably involves the use of inter-species nuclear transfer and embryo transfer. Even in intra-specific cloning the source of oocyte for nuclear transfer is an important consideration. Typically, cloned animals are only genomic copies of the founder if they possess mitochondrial DNA which differs from the original animal. Different maternal lineages of oocytes both within and between breeds significantly affect cloning efficiency and livestock production characteristics. Cloning should not distract conservation efforts from encouraging the use of indigenous livestock breeds with traits of adaptation to local environments, the preservation of wildlife habitats or the use of other forms of assisted reproduction. Whilst it is often difficult to justify cloning in animal conservation at present, the appropriate cryo-preservation of tissues and cells from a wide selection of biodiversity is of paramount importance. This provides an insurance against further losses of genetic variation from dwindling populations, disease epidemics or even possible extinction. It would also complement the gene banking of gametes or embryos and can be performed more easily and cheaply. Future cloning from preserved somatic cells can reintroduce lost genes back into the breeding pool. With greater appreciation of the heritable attributes of traditional livestock breeds there is the desire to identify superior animals within these local populations and the genetic loci involved. Through clonal family performance testing, nuclear transfer can aid the selection of desirable genotypes and then the production of larger numbers of embryos or animals for natural breeding to more widely disseminate the desirable traits. With the identification of alleles conferring desirable attributes, transgenesis could be utilised to both improve traditional and industrial livestock breeds. This further emphasizes the importance of preserving global farm animal genetic resources.

The foot-and-mouth disease (FMD) epidemic in the U.K. in 2001 highlighted the threat of infectious diseases to rare and valuable livestock and stimulated a renewed interest in biosecurity. Not all diseases resemble FMD, however; transmission routes and pathological effects vary greatly, so biosecurity strategies must take this into account. Realism is also needed as to which diseases to exclude and which will have to be tolerated. The aim should be to minimise disease generally and to exclude those diseases that threaten existence of the livestock, or preclude their national or international movement. Achieving this requires a team effort, bearing in mind the livestock species involved, the farming system (‘open’ or ‘closed’) and the premises. Effective biosecurity demands that practically every aspect of farm life is controlled, including movements of people, vehicles, equipment, food, manure, animal carcasses and wildlife. Above all, biosecurity strategies must cover the disease risks associated with moving the livestock themselves, and this will require quarantine if adult or juvenile animals are imported into the herd or flock. Reproductive technologies such as artificial insemination and embryo transfer offer much safer ways for getting new genetic materials into herds/flocks for breeding than bringing in live animals. Embryo transfer is especially safe when the sanitary protocols promoted by the International Embryo Transfer Society (IETS) and advocated by the Office International des Epizooties (OIE: the ‘World Organisation for Animal Health’) are used. It can also allow the full genetic complement to be salvaged from infected animals. Cryobanking of genetic materials, especially embryos, is another valuable biosecurity strategy because it enables storage for contingencies such as epidemic disease or other catastrophes.

The landscape of the UK has been largely determined by past agricultural practices that have given rise to a range of anthropogenic habitats much valued by conservationists. Many of these have been created by, or for, grazing livestock. The suggestion that grazing and browsing animals were instrumental in ‘cyclical succession’ in the preagricultural period is also gaining ground. For these reasons the use of grazing animals in the management of conservation sites has become more common. Since its foundation in 1997 the Grazing Animals Project (GAP) has promoted and facilitated the use of grazing livestock in management of habitats for conservation.

In 2001 GAP produced, in consultation with animal welfare organizations, A Guide to Animal Welfare in Nature Conservation Grazing. The practical advice in, and approach of, this document is potentially invaluable not only to conservation managers and graziers but also to all keepers of livestock. Another GAP publication, the Breeds Profiles Handbook, gives brief descriptions of 55 breeds of livestock known, or anticipated, to be of value in conservation grazing. Many of these are rare or traditional breeds, as these have the characteristics that enable the stock to thrive on the nutritionally relatively poor forage afforded by many conservation sites. These characteristics are often identified as ‘hardiness’ and ‘thriftiness’, but are poorly defined except through the practical experience of conservation managers.

Conservation grazing is a relatively new niche, and one that cannot be filled by modern breeds or strains adapted to high-input, high-output systems. It is, therefore, a great opportunity for rare and traditional breeds, many of which developed in parallel with habitats now appreciated for their conservation value. This applies not only in the UK but also in other European countries. Moreover, recent developments, such as English Nature's Traditional Breeds Incentive for Sites of Special Scientific Interest, several grazing projects funded by the Heritage Lottery Fund and the Limestone Country Life Project, suggest that this niche is no longer confined to nature reserves.

Conservation grazing can contribute to genetic conservation by:

• • Enabling an increase in numbers and wider distribution of rare and traditional breeds.

• • Allowing breeders to identify, and select, those individuals that fare best under relatively austere conditions.

• • Providing an outlet, or providing additional grazing, for stock that could not otherwise be kept.

• • Providing a market for good animals without reference to the showring.

• • Providing a refuge for rare breeds from threats such as that posed by the National Scrapie Plan.

The usefulness of molecular genetic markers as a tool for the conservation, characterisation and differentiation of domestic animal populations are shown in the following text, that summarises diverse applications to Iberian pigs.

Since the establishment of the Rare Breeds Survival Trust (RBST) in 1973, rare breed genetic conservation has only gradually emerged as a major key to the continued success and survival of populations. Thus, although basic population and demographic data have been recorded for all breeds listed by the Trust and most rare breeds have kept detailed pedigrees, there is still little information available about current population genetic structure and dynamics over time. Consequently, the majority of rare breed population meta-analyses based upon pedigree data are yet to be carried out. Transfer of rare breed records onto a computer database is therefore a current priority for the RBST, in addition to making available software to provide rare breed organisations with breed profiles to describe founder effects, effective population size (Ne), rate of inbreeding (ΔF), and kinship patterns. Results from rare breed pedigree analyses using this software can now be used to a) illustrate where and how loss of genetic diversity has taken place in rare breeds and b) enable decision processes concerning conservation strategy in future. Conservation strategy informed by such analyses can only be successfully implemented if due regard is given to the realities imposed by the need to maintain rare breed populations within an agricultural context, however. In light of these recent improvements to data recording and access to studies of population genetic structure, some of the traditional limitations to advances to rare breed conservation strategy may now need to be re-examined.

The Longhorn cattle breed has a long and prestigious history, dating back prior to the livestock pioneers of the 18th century. It was, for a period, the improved breed of choice in the Midland Counties. But the breed gradually fell from favour and, by the early 1970s, only 6 significant Longhorn herds remained in the UK. However, the Longhorn was one of many rare breeds to benefit from the growth of the rare breeds movement in the 1970s, led by the Rare Breeds Survival Trust. A number of factors have helped the breed to recover, including: an active breed society providing registrations and analyses based on these, promoting the breed, organising sales and shows and providing an important social framework for breeders and supporters; creation of a semen bank; niche marketing of meat and hides and the use of the breed in conservation grazing.