Identifying potential breeding sites for the stone curlew (Burhinus oedicnemus) in the UK

The stone curlew (Burhinus oedicnemus) is one of the rarest breeding birds in the UK with an estimated breeding population of under 300 pairs. In the UK a marked decrease in the numbers has occurred, mainly due to habitat change or loss, resulting in the bird no longer breeding on many of its traditional nesting grounds. Using a Geographic Information System we define potential breeding areas in a landscape known to historically support a stone curlew breeding population. With an understanding of the birds’ abiotic nesting requirements, we model optimal locations for potential breeding sites for the bird, using known historical breeding data to verify the selection process. In total, we identify 424 parcels of land (2866 hectares) providing the critical habitat requirements for the stone curlew in the overall study area, 323 (1958 hectares) of which correspond with the known historic breeding distribution of the bird. We conclude that the modelling approach outlined is valuable in the identification of potential breeding sites for the stone curlew and that the model could be operated in tandem with agri-environment payments such as those offered within the Countryside Stewardship Scheme, in an attempt to focus these payments upon areas which will deliver maximum nature conservation potential. In addition we suggest that, subject to appropriate data availability, the approach outlined be applied to other species of high-conservation concern, particularly those which are currently under consideration for introduction or re-introduction programmes.     

Pedigrees, MHC and microsatellites: an integrated approach for genetic management of captive African wild dogs (Lycaon pictus)

Captive breeding programmes aim to provide an insurance against extinction in the wild and a source for re-introductions making it essential to minimise genetic threats, and maximise representation of wild adaptive genetic diversity. As such, genetic assessments of captive breeding programmes are increasingly common. However, these rarely include comprehensive comparisons with wild populations and typically neutral, rather than adaptive, genetic diversity is assayed. Moreover, genetic data are rarely integrated with studbook information, which enables the most robust assessments. Here we use the European captive African wild dog (Lycaon pictus) population to demonstrate the utility of this combined approach. Specifically, we combined studbook pedigree information with genetic assessments of captive and wild samples at both neutral markers and a locus thought to be important for adaptation (a gene at the Major Histocompatibility Complex, MHC). With these data we were able to evaluate founder origin and representation, as well as the distribution and origin of genetic variation within the captive population. We found discrepancies between diversity metrics derived from neutral and adaptive markers and pedigree versus genetic derived inbreeding estimates. Overall, however, we found a large proportion of genetic diversity from wild populations to be conserved in the captive population, much of which can be attributed to recent imports from outside of the European breeding programme. Nonetheless, we also found a high incidence of inbreeding and very skewed founder contributions. Based on these results, we proposed and implemented a genetic management plan to prevent further losses of diversity and reduce inbreeding.     

Captive breeding—a useful tool in the preservation of biodiversity?

Within the next decades species extinction may eliminate between 20 and 50% of the Earth's species. Captive breeding has often been claimed to be a useful tool in preservation of biodiversity. The role of zoos in conservation work and the value of captive breeding are discussed; the latter exemplified by the Peregrine Falcon (Falco peregrinus) Programme and the Arabian oryx (Oryx leucoryx) Programme. Captive breeding programmes are very resource demanding and can only be afforded for a very small number of species, which limits their value significantly. Zoos deal mainly with vertebrates, but these comprise less than 3% of the described species, and although the 878 zoos considered hold more than 20 000 specimens of 140 threatened mammal species, they probably only contribute to the conservation of 20 full species. The situation for birds, reptiles and amphibians is even worse. Zoos face serious problems with minimum viable population sizes and hybridization. However, zoos can make a major contribution to preservation of biodiversity through educating and informing the public. Today, where the crisis of extinction of species has reached such daunting dimensions, captive breeding and otherex situ conservation tools should be the last resort for preserving biodiversity, and captive breeding must not become an excuse to avoid dealing with preservation of habitats.     

Towards genomic selection in apple (Malus ×domestica Borkh.) breeding programmes: Prospects, challenges and strategies

The apple genome sequence and the availability of high-throughput genotyping technologies have initiated a new era where SNP markers are abundant across the whole genome. Genomic selection (GS) is a statistical approach that utilizes all available genome-wide markers simultaneously to estimate breeding values or total genetic values. For breeding programmes, GS is a promising alternative to the traditional marker-assisted selection for manipulating complex polygenic traits often controlled by many small-effect genes. Various factors, such as genetic architecture of selection traits, population size and structure, genetic evaluation systems, density of SNP markers and extent of linkage disequilibrium, have been shown to be the key drivers of the accuracy of GS. In this paper, we provide an overview of the status of these aspects in current apple-breeding programmes. Strategies for GS for fruit quality and disease resistance are discussed, and an update on an empirical genomic selection study in a New Zealand apple-breeding programme is provided, along with a foresight of expected accuracy from such selection.     

Reduced genetic diversity and significant genetic differentiation after translocation: Comparison of the remnant and translocated populations of bridled nailtail wallabies (Onychogalea fraenata)

Loss of genetic diversity and increased population differentiation from source populations are common problems associated with translocation programmes established from captive-bred stock or a small number of founders. The bridled nailtail wallaby is one of the most endangered macropods in Australia, having been reduced to a single remnant population in the last 100 years. A translocated population of bridled nailtail wallabies was established using animals sourced directly from the remnant population (wild-released) as well as the progeny of animals collected for a captive breeding programme (captive-bred). The aims of this study were to compare genetic diversity among released animals and their wild-born progeny to genetic diversity observed in the remnant population, and to monitor changes in genetic diversity over time as more animals were released into the population. Heterozygosity did not differ between the translocated and remnant population; however, allelic diversity was significantly reduced across all released animals and their wild-born progeny. Animals bred in captivity and their wild-born progeny were also significantly differentiated from the source population after just four generations. Wild-released animals, however, were representative of the source population and several alleles were unique to this group. Both heterozygosity and allelic diversity among translocated animals decreased over time with the additional release of captive-bred animals, as no new genetic stock was added to the population. Captive breeding programmes can provide large numbers of animals for release, but this study highlights the importance of sourcing animals directly from remnant populations in order to maintain genetic diversity and minimise genetic drift.     

Using long-term ornithological studies in setting targets for conservation in Britain

Long-term studies are necessary in conservation work for two main purposes: monitoring of population parameters, and defining habitat requirements to set targets for conservation action. Apart from their intrinsic interest, birds may be of value also as a means of monitoring the wider environment. Current developments include the integration of measures of breeding performance and survival with those of population size. This will also aid early warning of changes. The range of normal variation in these measures needs assessment to identify limits beyond which action is needed. Monitoring studies need to be reported in appropriate habitat or geographical units, but cover as wide a geographical area as possible in a coordinated manner, to provide context. Long-term studies are required for defining requirements, as needs may vary with overall population size, weather conditions, and other features which differ between years. Population studies based on age-structures at a moment in time may not be a good approximation of the real performance as assessed by following age-cohorts through time. This may be especially so in rare species. For these, sample sizes also present problems in short studies. Long-term studies may be required also to identify the needs of less obvious components of populations, such as immature individuals.     

Characterization of six microsatellite loci in the Bermuda skink (Eumeces longirostris)

Conservation strategies for the critically endangered Bermuda skink will require knowledge of genetic variation and population structure. We describe the isolation of six polymorphic microsatellites for this species suitable for use in population genetics studies or for monitoring success of potential breeding programmes. Tissue sampling for DNA extraction involved no blood loss or tail autonomy. Three of these loci cross‐amplify and are polymorphic in a related North American skink (Eumeces fasciatus) and should also be informative for this species.     

The cumulative effects of management on the population dynamics of the Double‐crested Cormorant Phalacrocorax auritus in the Great Lakes

Wildlife species have been subject to control efforts throughout human history due to real or alleged human–wildlife conflicts. The Double‐crested Cormorant Phalacrocorax auritus in the interior of North America is no exception, with recent population growth leading to increased conflicts and consequently the development of many control programmes. These control programmes are usually conducted at local scales, often with little or no effort to assess their cumulative effects at the population level. We attempted the first comprehensive assessment of the cumulative effects of control at various spatio‐temporal scales, focusing on 199 colonies of Double‐crested Cormorant monitored during a 29‐year period. Linear models were used to assess the relationship between colony‐specific growth rates and a set of candidate factors using an information‐theoretic approach. Colony‐level density‐dependent effects and local control efforts had the greatest influences on population growth. We detected a cumulative effect of management, whereby (i) the reduction in population growth rate was generally stronger when different control activities such as culling or egg oiling were combined, and (ii) past control operations tended to have a pervasive impact on growth rates, especially egg oiling and nest destruction, which negatively affected local recruitment. However, our results also suggest that catastrophic events and the culling of breeding adults that occurred at least 2 years previously could fuel subsequent recruitment or natural immigration from nearby colonies, for instance if the breeding success of remaining pairs was increased through a diminution of density‐dependent regulatory processes. Density‐dependence at the metapopulation level constituted a third source of regulation, as local growth rates were reduced with increasing number or proximity of active neighbouring colonies. We also found evidence that the culling of Double‐crested Cormorants wintering in the southeastern USA could negatively impact the population growth of individual breeding colonies in the Great Lakes, although further research integrating models of migratory connectivity is needed to reach more definitive conclusions. Finally, despite previous studies emphasizing its importance, the net effect of management‐induced dispersal appeared small at large spatial scales. We show that this can be explained in part by control strategies (e.g. spatially clustered operations). The continuation of Cormorant management efforts will provide an opportunity to refine the present assessment of the relative importance of density‐dependence, breeding vs. non‐breeding season management and dispersal, particularly if population models are coupled with monitoring programmes within an adaptive management framework.     

Predicting the distribution of a suitable habitat for the white stork in Southern Sweden: identifying priority areas for reintroduction and habitat restoration

The loss of wetlands and semi-natural grasslands throughout much of Europe has led to a historic decline of species associated with these habitats. The reinstatement of these habitats, however, requires spatially explicit predictions of the most suitable sites for restoration, to maximize the ecological benefit per unit effort. One species that demonstrates such declines is the white stork Ciconia ciconia , and the restoration of habitat for this flagship species is likely to benefit a suite of other wetland and grassland biota. Storks are also being reintroduced into southern Sweden and elsewhere, and the a priori identification of suitable sites for reintroduction will greatly improve the success of such programmes. Here a simple predictive habitat-use model was developed, where only a small but reliable presence-only dataset was available. The model is based on the extent and relative soil moisture of semi-natural pastures, the extent of wetlands and the extent of hayfields in southern Sweden. Here the model was used to predict the current extent of stork habitat that is suitable for successful breeding, and the extent of habitat that would become suitable with moderate habitat restoration. The habitat model identifies all 10 occupied nesting sites where breeding is currently successful. It also identifies ∼300 km² of habitat that is predicted to be suitable stork habitat, but that is presently unused; these sites were identified as potential areas for stork reintroduction. The model also identifies over 100 areas where moderate habitat restoration is predicted to have a disproportionate effect (relative to the restoration effort) on the area of suitable habitat for storks; these sites were identified as priorities for habitat restoration. By identifying areas for reintroduction and restoration, such habitat suitability models have the potential to maximize the effectiveness of such conservation programmes.     

Conservation of deer: contributions from molecular biology, evolutionary ecology, and reproductive physiology

Molecular phylogenetics, interspecific comparisons, and assisted reproductive techniques are recent approaches to understanding and facilitating conservation of endangered species. This paper reviews the contribution of these approaches to a small but well-studied group of mammals, deer, many of which are endangered in the wild. Conservation efforts require a comprehensive understanding of the biology and history of these animals. The value of assisted reproductive technologies for conservation of deer has received increased awareness especially for captive populations. Such breeding programmes are designed to assist propagation of threatened species and to maximize genetic diversity within populations through the movement of genetic material across the globe, but will only be successful if we understand the genetic and reproductive potential of various lineages. Here we discuss the phylogenetic status of deer, the distinctiveness and evolution of their reproductive patterns, and current approaches for improving the success of controlled breeding programmes for the conservation of endangered lineages. Only by combining both theoretical and practical approaches to conservation efforts can we hope to salvage the remaining organismal diversity of our planet.     

Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach

Quantitative trait locus (QTL) mapping is often conducted in line-crossing experiments where a sample of individuals is randomly selected from a pool of all potential progeny. QTLs detected from such an experiment are important for us to understand the genetic mechanisms governing a complex trait, but may not be directly relevant to plant breeding if they are not detected from the breeding population where selection is targeting for. QTLs segregating in one population may not necessarily segregate in another population. To facilitate marker-assisted selection, QTLs must be detected from the very population which the selection is targeting. However, selected breeding populations often have depleted genetic variation with small population sizes, resulting in low power in detecting useful QTLs. On the other hand, if selection is effective, loci controlling the selected trait will deviate from the expected Mendelian segregation ratio. In this study, we proposed to detect QTLs in selected breeding populations via the detection of marker segregation distortion in either a single population or multiple populations using the same selection scheme. Simulation studies showed that QTL can be detected in strong selected populations with selected population sizes as small as 25 plants. We applied the new method to detect QTLs in two breeding populations of rice selected for high grain yield. Seven QTLs were identified, four of which have been validated in advanced generations in a follow-up study. Cloned genes in the vicinity of the four QTLs were also reported in the literatures. This mapping-by-selection approach provides a new avenue for breeders to improve breeding progress. The new method can be applied to breeding programs not only in rice but also in other agricultural species including crops, trees and animals.     

Realities in breed improvement programmes for dairy goats in East and Central Africa

Increasing population pressure, land scarcity and diminishing production resources are promoting goat production in the tropics. Dairy goat breeding (DGB) projects have been implemented by development agencies, governments and the private sector with the objective of improving the dairy merits genetically through crossbreeding with exotic genotypes. The performance of these projects is still a cause for concern. Therefore, sustainable dairy goat breeding forces various stakeholders to re-orient their breeding goals, strategies and design of breeding programmes towards a sustainability perspective. This paper highlights a set of key requirements for establishing sustainable dairy goat breeding programmes. Conclusions are drawn based on the lessons learnt from numerous examples of DGB projects in East and Central Africa keeping sustainability concerns insight to inform on-going and future projects.     

Parks or arks: where to conserve threatened mammals?

Growing deterministic and stochastic threats to many wild populations of large vertebrates have focused attention on the conservation significance of captive breeding and subsequent reintroduction. However, work on both gorillas and black rhinos questions this shift in emphasis. In these species, field-based conservation can be effective if properly supported and, although this is not cheap, per capita costs may still be considerably lower than for ex situ propagation in captivity. Here we attempt to broaden the scope of this debate by contrasting the breeding success and costs of in situ and captive programmes for a range of threatened mammals. Data are scarce, but we find that across nine large-bodied genera, in situ conservation achieves comparable rates of population growth to those seen in established captive breeding programmes. Moreover, comparing budgets of well-protected reserves with zoos' own estimates of maintenance costs and the costs of zoo adoption schemes, we find that per capita costs for effective in situ conservation are consistently lower than those of maintenance in captivity. Captive breeding may be more cost-effective for smaller-bodied taxa, and will often remain desirable for large mammals restricted to one or two vulnerable wild populations. However, our results, coupled with the fact that effective in situ conservation protects intact ecosystems rather than single species, lead us to suggest that zoos might maximize their contribution to large mammal conservation by investing where possible in well-managed field-based initiatives, rather than establishing additional ex situ breeding programmes.     

Role of inbreeding depression and purging in captive breeding and restoration programmes

Inbreeding depression is a major force affecting the evolution and viability of small populations in captive breeding and restoration programmes. Populations that experience small sizes may be less susceptible to future inbreeding depression because they have been purged of deleterious recessive alleles. We review issues related to purging, as they apply to the management of small populations, and discuss an experiment we conducted examining purging in populations of mosquitofish (Gambusia affinis). Purging is an important process in many small populations, but the literature contains a diversity of responses to purging both within and among studies. With the exception that slow inbreeding results in more purging and less threat to population viability, there seem to be few consistent trends that aid in prediction of how a purging event will affect a population. In our examination of purging on population viability in mosquitofish, single or multiple bottlenecks do not appear to have resulted in any purging of the influence of genetic load on population growth. Rather, serial bottlenecks resulted in a marked decline in population growth and an increase in extinction. Our results, taken together with those of reviewed studies, suggest that in small populations there is great uncertainty regarding the success of any single purging event in eliminating inbreeding depression, together with the high likelihood that purging will depress population viability through the fixation of deleterious alleles. In management of captive breeding and restoration programmes, the common practice of avoiding inbreeding and small population sizes should be followed whenever possible.     

Advanced phenotyping offers opportunities for improved breeding of forage and turf species

Background and Aims

Advanced phenotyping, i.e. the application of automated, high-throughput methods to characterize plant architecture and performance, has the potential to accelerate breeding progress but is far from being routinely used in current breeding approaches. In forage and turf improvement programmes, in particular, where breeding populations and cultivars are characterized by high genetic diversity and substantial genotype × environment interactions, precise and efficient phenotyping is essential to meet future challenges imposed by climate change, growing demand and declining resources.

Scope

This review highlights recent achievements in the establishment of phenotyping tools and platforms. Some of these tools have originally been established in remote sensing, some in precision agriculture, while others are laboratory-based imaging procedures. They quantify plant colour, spectral reflection, chlorophyll-fluorescence, temperature and other properties, from which traits such as biomass, architecture, photosynthetic efficiency, stomatal aperture or stress resistance can be derived. Applications of these methods in the context of forage and turf breeding are discussed.

Conclusions

Progress in cutting-edge molecular breeding tools is beginning to be matched by progress in automated non-destructive imaging methods. Joint application of precise phenotyping machinery and molecular tools in optimized breeding schemes will improve forage and turf breeding in the near future and will thereby contribute to amended performance of managed grassland agroecosystems.     

Beyond landraces: developing improved germplasm resources for underutilized species – a case for Bambara groundnut

The potential for underutilized crops (also known as minor, neglected or orphan crops) to improve food and nutrition security has been gaining prominence within the research community in recent years. This is due to their significance for diversified agricultural systems which is a necessary component of future agriculture to address food and nutritional security concerns posed by changing climate and a growing world population. Developing workable value chain systems for underutilized crop species, coupled with comparative trait studies with major crops, potentially allows us to identify suitable agricultural modalities for such species. Bambara groundnut (Vigna subterranea L. Verdc.), an underutilized leguminous species, is of interest for its reported high levels of drought tolerance in particular, which contributes to environmental resilience in semi-arid environments. Here, we present a synopsis of suitable strategies for the genetic improvement of Bambara groundnut as a guide to other underutilized crop species. Underutilized crops have often been adapted over thousands of years in particular regions by farmers and largely still exist as landraces with little or no genetic knowledge of key phenotypic traits. Breeding in these species is fundamentally different to breeding in major crops, where significant pedigree structures and history allow highly directed improvement. In this regard, deploying new integrated germplasm development approaches for variety development and genetic analysis, such as multi-parent advance generation inter-crosses (MAGIC), within breeding programmes of underutilized species will be important to be able to fully utilize such crops.     

Measuring farmers' attitude towards breeding tools: the Livestock Breeding Attitude Scale

Under-use of genetic improvement tools and low participation in breeding programmes are key drivers of breeding programmes under-performance. Both aspects are heavily influenced by farmers attitudes which, to date, have not been analysed in an objective and systematic manner. A key factor constraining the implementation of attitudinal studies towards livestock breeding tools is the lack of a reference scale for measuring attitudes. In this research, we provide the livestock breeding sector with such a reference measure. We developed the scale following the standardized psychometric methodologies and statistical tools. Then, as a case study, we used the scale to explore the attitudes of beef and dairy sheep farmers in Australia, New Zealand and Spain and analysed farmer and farming system factors related to those attitudes. Fourteen sheep and beef breed associations facilitated the implementation of a survey of 547 farmers, generating data that was used for the scale evaluation. The relationship between attitudinal factors and farmer and farming system factors was analysed using generalized linear models across and within breeds. The results suggest that the 8-item definitive scale we have developed is appropriate to measure farmer attitudes. We found that attitudes towards genetic improvement tools have two components; i) traditional selection and ii) genetic and genomic selection combined. This means that positive attitudes towards traditional phenotypic selection do not necessarily imply a negative attitude towards genetic and genomic selection tools. Farmer attitudes varied greatly not only across the studied breeds, species and countries, but also within them. High-educated farmers of business-oriented farms tend to have the most negative attitude towards traditional selection. However, attitudes towards genetic and genomic selection tools could not be linked to these factors. Finally, we found that the breed raised had a large effect on farmer attitude. These findings may help in the evolution of breeding programmes by identifying both the farmers most inclined to uptake breeding innovations in the early stages of its establishment and the farmers who would be more reluctant to participate in such programmes, thus informing where to focus extension efforts.     

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)

Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application of marker‐assisted selection (MAS) in breeding programmes. A crucial step in the successful application of MAS in breeding programmes is the development of cheap and easy to use molecular markers, such as single‐nucleotide polymorphisms. To mine selected elite wheat germplasm for intervarietal single‐nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next‐generation sequencing of normalized wheat complementary DNA libraries, in combination with a novel sequence alignment and assembly approach. Here, we describe the development and validation of a panel of 1114 single‐nucleotide polymorphisms in hexaploid bread wheat using competitive allele‐specific polymerase chain reaction genotyping technology. We report the genotyping results of these markers on 23 wheat varieties, selected to represent a broad cross‐section of wheat germplasm including a number of elite UK varieties. Finally, we show that, using relatively simple technology, it is possible to rapidly generate a linkage map containing several hundred single‐nucleotide polymorphism markers in the doubled haploid mapping population of Avalon × Cadenza.     

Review: Towards the agroecological management of ruminants,pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies

Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could be used more effectively if they benefited from the scientific and technical resources currently available for more common breeds. Last but not least, public policies need to enable improved information concerning the genetic resources and breeding tools available for the agroecological management of livestock production systems, and facilitate its assimilation by farmers and farm technicians.     

21st century wheat breeding: plot selection or plate detection?

The publicly reported limited application of marker-assisted selection (MAS) in wheat breeding programmes to date is reviewed and contrasted with the current situation, in which it has increasingly become technically feasible to tag almost any gene with a microsatellite assay. Although this capability is starting to have an impact on the conduct of large breeding programmes, a much more profound change in breeding strategy will become possible when single nucleotide polymorphism (SNP) technology has matured sufficiently so that the throughput of molecular marker-based genotyping is able to keep pace with the numbers of plants that breeders routinely handle in the field. We explore the extent to which the genomics revolution might generate a change in the conventional breeding paradigm, which has operated with such success for the best part of the 20th century, and identify the need for a substantial reduction in assay price before MAS is likely to make more than a marginal impact on present practice.