Successes and failures of small ruminant breeding programmes in the tropics: a review

Despite the large numbers and importance of adapted indigenous sheep and goats in the tropics, information on sustainable conventional breeding programmes for them is scarce and often unavailable. This paper reviews within-breed selection strategies for indigenous small ruminants in the tropics, highlighting aspects determining their success or failure. The aim is to better understand opportunities for genetic improvement of small ruminants by the resource-poor farmers in traditional smallholder and pastoral farming systems. Dismal performance of programmes involving breed substitution of exotics for indigenous breeds and crossbreeding with temperate breeds have stimulated a recent re-orientation of breeding programmes in tropical countries to utilize indigenous breeds, and most programmes are incipient. The success rate of some breeding programmes involving native breeds is encouraging. Definition of comprehensive breeding objectives incorporating the specific, immediate, and long-term social and economic circumstances of the target group as well as ecological constraints was found lacking in some projects that failed. To achieve success, it is necessary to look at the production system holistically, and involve the producer at every stage in the planning and operation of the breeding programme, integrating traditional behaviour and values.     

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.     

The application of reproductive technology to endangered species breeding programmes

Captive breeding plays an increasingly important role in species conservation, but special problems are encountered in achieving the ideal of a demographically stable but genetically diverse population. Breeding programmes involving co-operation among a number of centres are now being developed which will overcome some of these difficulties by identifying individual animals, genetic lineages or age cohorts from which to breed. Application of techniques such as artificial insemination, embryo transfer and semen collection and storage, as well as the monitoring of reproductive status will contribute to the success of such programmes. The usefulness of these procedures for various population problems is discussed and criteria for their appropriate implementation within breeding programmes is outlined.     

Accounting for competition in genetic analysis, with particular emphasis on forest genetic trials

Available experimental evidence suggests that there are genetic differences in the abilities of trees to compete for resources, in addition to non-genetic differences due to micro-site variation. The use of indirect genetic effects within the framework of linear mixed model methodology has been proposed for estimating genetic parameters and responses to selection in the presence of genetic competition. In this context, an individual’s total breeding value reflects the effects of its direct breeding value on its own phenotype and its competitive breeding value on the phenotype of its neighbours. The present study used simulated data to investigate the relevance of accounting for competitive effects at the genetic and non-genetic levels in terms of the estimation of (co)variance components and selection response. Different experimental designs that resulted in different genetic relatedness levels within a neighbourhood and survival were other key issues examined. Variances estimated for additive genetic and residual effects tended to be biased under models that ignored genetic competition. Models that fitted competition at the genetic level only also resulted in biased (co)variance estimates for direct additive, competitive additive and residual effects. The ability to detect the correct model was reduced when relatedness within a neighbourhood was very low and survival decreased. Selection responses changed considerably between selecting on breeding value estimates from a model ignoring genetic competition and total breeding estimates using the correct model. Our results suggest that considering a genetic basis to competitive ability will be important to optimise selection programmes for genetic improvement of tree species.     

Integrating genomic selection into dairy cattle breeding programmes: a review

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.     

Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world?

Improved management and use of estimated breeding values in breeding programmes, have resulted in rapid genetic progress for small ruminants (SR) in Europe and other developed countries. The development of single nucleotide polymorphisms chips opened opportunities for genomic selection (GS) in SR in these countries. Initially focused on production traits (growth and milk), GS has been extended to functional traits (reproductive performance, disease resistance and meat quality). The GS systems have been characterized by smaller reference populations compared with those of dairy cattle and consisting mostly of cross- or multi-breed populations. Molecular information has resulted in gains in accuracy of between 0.05 and 0.27 and proved useful in parentage verification and the identification of QTLs for economically important traits. Except for a few established breeds with some degree of infrastructure, the basic building blocks to support conventional breeding programmes in small holder systems are lacking in most developing countries. In these systems, molecular data could offer quick wins in undertaking parentage verification and genetic evaluations using G matrix, and determination of breed composition. The development of next-generation molecular tools has prompted investigations on genome-wide signatures of selection for mainly adaptive and reproduction traits in SR in developing countries. Here, the relevance of the developments and application of GS and other molecular tools in developed countries to developing countries context is examined. Worth noting is that in the latter, the application of GS in SR will not be a ‘one-size fits all’ scenario. For breeds with some degree of conventional genetic improvement, classical GS may be feasible. In small holder systems, where production is key, community-based breeding programmes can provide the framework to implement GS. However, in fragile growth systems, for example those found in marginal environments, innovative GS to maximize adaptive diversity will be required. A cost-benefit analysis should accompany any strategy of implementing GS in these systems.     

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.     

Estimation of quantitative genetic parameters

This paper gives a short review of the development of genetic parameter estimation over the last 40 years. The need to analyse genetic processes in both animal selection experiments and animal breeding improvement programmes motivated the majority of this work. The usage of animal model in conjunction with residual maximum likelihood (REML) techniques for mixed models has revolutionized the methods. These methods to estimate quantitative genetic parameters have recently been advocated for use in evolutionary studies of natural populations. Therefore, it is perhaps timely to discuss the development of REML methods and their application to the analysis of artificial selection experiments and breeding programmes in animals. This should give extra insight into the methods and hopefully lead to synergy between both the areas.     

Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits

 RAPD markers and agronomic traits were used to determine the genetic relationships among 32 breeding lines of melon belonging to seven varietal types. Most of the breeding lines were Galia and Piel de Sapo genotypes, which are currently being used in breeding programmes to develop new hybrid combinations. A total of 115 polymorphic reliable bands from 43 primers and 24 agronomic traits were scored for genetic distance calculations and cluster analysis. A high concordance between RAPDs and agronomic traits was observed when genetic relationships among lines were assessed. In addition, RAPD data were highly correlated with the pedigree information already known for the lines and revealed the existence of two clusters for each varietal type that comprised the lines sharing similar agronomic features. These groupings were consistent with the development of breeding programmes trying to generate two separate sets of parental lines for hybrid production. Nevertheless, the performance of certain hybrids indicated that RAPDs were more suitable markers than agronomic traits in predicting genetic distance among the breeding lines analysed. The employment of RAPDs as molecular markers both in germplasm management and improvement, as well as in the selection of parental lines for the development of new hybrid combinations, is discussed. Received: 25 July 1997 / Accepted: 6 October 1997     

Livestock QTLs — bringing home the bacon?

Markers have been used for some time to study the genetic control of economically important traits in livestock. The early work was based on single loci and detected some significant effects, but results were often inconsistent across studies. Now that complete microsatellite-based maps of the major species are becoming available, more complete and rigorous scans of the genome are possible. The first of these have detected some surprisingly large effects, both within breeds and in breed crosses. As research workers digest these results and their implications for livestock breeding programmes and ponder further research, commercial breeding companies have already started applying the first fruits of marker research to breed a better animal.     

Converting multi-trait breeding objectives into operative selection indexes to ensure genetic gains in low-input sheep and goat breeding programmes

Small ruminant breeding programmes in low-input production systems are best organised at the community level. Participant farmers have to agree on goal traits and their relative importance. When BLUP breeding values of goal traits are not available in time, appropriate selection indexes can be used to aid visual selection. Taking Ethiopian Abergelle goat and Bonga sheep community-based breeding programmes (CBBPs) as an example, breeding objective functions were defined and selection indexes were constructed and evaluated. Breeding goals for Abergelle goats included early sale weight, survival and milk production. Breeding goals for Bonga included the number of offspring born, sale weight and survival. Economic weights of objective traits can be used in several ways depending on measured traits and the reliability of their genetic parameters. Selection indexes included combinations of objective traits measured on candidates and their dams and situations when Abergelle communities prefer to restrict genetic changes in number of offspring born or adult weight and when Bonga communities prefer to restrict changes in adult weight. Genetic and economic gains were evaluated as well as sensitivity to feed cost assumptions and to repeated dam records. After independent culling on preponderant traits such as coat colour and horn/tail type, sires in Abergelle goat community breeding programmes should be selected on indexes including at least own early live weight and their dams average milk production records. Sires for Bonga sheep programmes should be selected on own early live weight and desirably also on their dam’s number of offspring born. Sensitivity to feed cost assumptions was negligible but repeated measurements of dam records improved index accuracies considerably. Restricting genetic changes in number of offspring born or adult weight is not recommended.     

Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or differences in the level of expression of genetic differences among environments. G×E can reduce heritability and overall genetic gain, unless breeding programmes are structured to address different categories of environments. Understanding the impact of G×E, the role of environments in generating G×E and the problems and opportunities is vital to efficient breeding programme design and deployment of genetic material. We review the current main analytical methods for identifying G×E: factor analytic models, biplot analysis and reaction norm. We also review biological and statistical evidence of G×E for growth, form and wood properties in forest species of global economic importance, including some pines, eucalypts, Douglas-fir, spruces and some poplars. Among these species, high levels of G×E tend to be reported for growth traits, with low levels of G×E for form traits and wood properties. Finally, we discuss possible ways of exploiting G×E to maximise genetic gain in forest tree breeding. Characterising the role of environments in generating interactions is seen as the basic platform, allowing efficient testing of candidate genotypes. We discuss the importance of level-of-expression interaction, relative to rank-change interaction, as being greater than in many past reports, especially for deployment decisions. We examine the impacts of G×E on tree breeding, some environmental factors that cause G×E and the strategies for dealing with G×E in tree breeding, and the future role of genomics.     

Fostering molecular breeding in developing countries

Molecular breeding (MB) increases genetic gain per crop cycle, stacks favourable alleles at target loci and reduces the number of selection cycles. In the last decade, the private sector has benefitted immensely from MB, which demonstrates its efficacy. In contrast, MB adoption is still limited in the public sector, and it is hardly used in developing countries. Major bottlenecks in these countries include shortage of well-trained personnel, inadequate high-throughput capacity, poor phenotyping infrastructure, lack of information systems or adapted analysis tools or simply resource-limited breeding programmes. The emerging virtual platforms aided by the information and communication technology revolution will help to overcome some of these limitations by providing breeders with better access to genomic resources, advanced laboratory services and robust analytical and data management tools. Apart from some advanced national agricultural research systems (NARS), the implementation of large-scale molecular breeding programmes in developing countries will take time. However, the exponential development of genomic resources, including for less-studied crops, the ever-decreasing cost of marker technologies and the emergence of platforms for accessing MB tools and support services, plus the increasing public–private partnerships and needs-driven demand for improved varieties to counter the global food crisis, are all grounds to predict that MB will have a significant impact on crop breeding in developing countries. These predictions are supported by some preliminary successful examples presented in this paper.     

Theory of nucleus breeding schemes with overlapping generations

Summary Explicit methods are derived for estimating steady-state genetic responses and genetic differences between nucleus and base progeny crops in open nucleus breeding schemes which utilize genetic differences between progeny groups with parents of different ages or between age groups. Explicit methods are also given for estimating proportions which should be selected from the different nucleus and base selection groups so as to maximise genetic responses under each of a range of selection methods. Some basic differences between selection programmes utilizing genetic differences between progeny groups with parents of different ages and those utilizing genetic differences between age groups in nucleus breeding schemes are summarized.     

Temporal flux in the morphological and molecular diversity of UK barley

Genetic-diversity assessments, using both phenotypic and molecular-marker data, were made on a collection of 134 barley varieties (both winter and spring types), chosen on the basis of their representation on the NIAB "Recommended List" over the period 1925-1995. Genotypic (AFLP and SSR) and phenotypic (UPOV characters) data were analysed to determine short- and long-term temporal trends in diversity over the period. A consistent pattern emerged demonstrating that only a minor proportion of the overall variance appears to be the result of any temporal drift, although there were strong indications of qualitative shifts in diversity, probably related to the changing relative acreage of winter and spring barleys over the study period. Our overall conclusions are that systematic plant breeding does not inevitably lead to a reduction in the genetic diversity of agricultural crops, and that diverse breeding programmes and the variety delivery systems in place in the UK have generally been successful in maintaining sufficient genetic diversity to allow the steady rise in genetic potential that has been a feature of 20th century crop breeding. The concentration of breeding effort into a smaller number of independent programmes is likely to be prejudicial to the maintenance of the genetic diversity of a crop.     

Quantitative genetic analysis of natural populations

Quantitative genetic studies in natural populations have been rare because they require large breeding programmes or known pedigrees. The relatedness that has been estimated from molecular markers can now be used to substitute for breeding, allowing studies of previously inaccessible species. Many behavioural ecologists have a sufficient number of markers and study species with characteristics that are amenable to this approach. It is now time to combine studies of selection with studies of genetic variation for a more complete understanding of behavioural evolution.     

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.     

Genetic monitoring of the Amazonian fish matrinchã (Brycon cephalus) using RAPD markers: insights into supportive breeding and conservation programmes

The importance of genetic evaluations in aquaculture programmes has been increased significantly not only to improve effectiveness of hatchery production but also to maintain genetic diversity. In the present study, wild and captive populations of a commercially important neotropical freshwater fish, Brycon cephalus (Amazonian matrinchã), were analyzed in order to evaluate the levels of genetic diversity in a breeding programme at a Brazilian research institute of tropical fish. Random Amplified Polymorphic DNA fingerprinting was used to access the genetic variability of a wild stock from the Amazon River and of three captive stocks that correspond to consecutive generations from the fishery culture. Although farmed stocks showed considerably lower genetic variation than the wild population, a significantly higher level of polymorphism was detected in the third hatchery generation. The results seem to reflect a common breeding practice on several hatchery fish programmes that use a small number of parents as broodstocks, obtaining reproductive success with few non‐identified mating couples. The obtained data were useful for discussing suitable strategies for the genetic management and biodiversity conservation of this species.     

Evaluating ex situ conservation projects: Genetic structure of the captive population of the Arabian sand cat

Ex situ conservation plays an increasingly important role in the conservation of endangered species. Molecular genetic markers can be helpful to assess the status of captive breeding programmes. We present the first molecular genetic analysis of the captive population of the Arabian sand cat (Felis margarita harrisoni) using microsatellites. Our data indicates that the captive population of F. m. harrisoni comprises three genetic clusters, which are based on different founder lineages. Genetic diversity was relatively high, the effective population size even exceeded the number of founders. This was presumably caused by subsequently integrating unrelated, genetically diverse founders into the captive population and a careful management based on minimizing kinship. However, we detected an error in the studbook records, which might have led to incestuous matings and underlines the usefulness of molecular evaluations in captive breeding programmes for endangered species.