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.     

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.     

Small ruminant production in smallholder and pastoral/extensive farming systems in Kenya

A survey was conducted by way of personal interviews with 562 respondents comprising 459 farmers and 103 butchers/traders in selected districts in the central and western parts of Kenya, consisting of three predominantly smallholder and four predominantly pastoral/extensive districts. The study aimed to provide a better understanding of smallholder and pastoral/extensive sheep and goat farming systems in the tropics, by taking Kenya as an example. The results showed that 58% of the pastoral/extensive farmers and 46% of the smallholders indicated livestock as their main activity. Small ruminants ranked closely behind cattle in their importance. Thirty-four percent of the households kept only sheep, 18% only goats and 48% both species. The survey demonstrated the relative importance to the farmers of tangible benefits of farming sheep and goats (e.g., regular cash income, meat, manure and, in the case of goats, milk) versus intangible benefits (e.g., the role of small ruminants as an insurance against emergencies). Regular cash income and an insurance against emergencies were the highest priorities. Seventy-eight percent of the farmers reported animal sales over the previous 12 months of the survey date. Of these sales, the income was spent on school fees (32%), purchase of food (22%), farm investment (18%), medical expenses (10%), off-farm investment (9%), social activities (5%) and re-stocking (4%). Indigenous genotypes were predominant among the pastoralists and mixed crosses predominant among the smallholders. A range of traits: growth rate, body size, body shape, drought tolerance, meat quality, fertility, disease and heat tolerance, prolificacy and temperament were all considered important for both sheep and goats in both farming systems and across the different genotypes. Compared with other pure breeds, the Red Maasai sheep and the Small East African goats were rated poorly in terms of body size, body shape, growth and fertility, but highly in terms of drought and (for the Red Maasai) heat tolerance by both smallholder and pastoralist farmers. In general, crosses were perceived less favourably than indigenous pure breeds. Body size and performance ranked as the most important traits in the choice of breeding males. Approximately half the farmers inherited their males, reared them on the farm and kept them for an average of 2–3 years. Uncontrolled mating within the household's flock was predominant in both farming systems. Over 98% of the farmers reported incidence of disease, especially pneumonia (in pastoral/extensive areas), helminthosis, tick-borne diseases, diarrhoea and foot-rot. Over 95% of the farmers fed supplements in both dry and wet seasons. Pure exotic and indigenous × exotic genotypes fetched higher prices than indigenous genotypes due to their heavier body weight. In conclusion, the foregoing issues need attention in genetic improvement programmes, with more emphasis on the conservation and utilisation of indigenous small ruminant genotypes.     

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Buša breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.     

Importance of adaptation and genotype × environment interactions in tropical beef breeding systems

This paper examines the relative importance of productive and adaptive traits in beef breeding systems based on Bos taurus and tropically adapted breeds across temperate and (sub)tropical environments. In the (sub)tropics, differences that exist between breeds in temperate environments are masked by the effects of environmental stressors. Hence in tropical environments, breeds are best categorised into breed types to compare their performance across environments. Because of the presence of environmental stressors, there are more sources of genetic variation in tropical breeding programmes. It is therefore necessary to examine the genetic basis of productive and adaptive traits for breeding programmes in those environments. This paper reviews the heritabilities and genetic relationships between economically important productive and adaptive traits relevant to (sub)tropical breeding programmes. It is concluded that it is possible to simultaneously genetically improve productive and adaptive traits in tropically adapted breeds of beef cattle grazed in tropical environments without serious detrimental consequences for either adaptation or production. However, breed-specific parameters are required for genetic evaluations. The paper also reviews the magnitude of genotype × environment (G × E) interactions impacting on production and adaptation of cattle, where 'genotype' is defined as breed (within a crossbreeding system), sire within breed (in a within-breed selection programme) or associations between economically important traits and single nucleotide polymorphisms (SNPs - within a marker-assisted selection programme). It is concluded that re-ranking of breeds across environments is best managed by the use of the breed type(s) best suited to the particular production environment. Re-ranking of sires across environments is apparent in poorly adapted breed types across extreme tropical and temperate environments or where breeding animals are selected in a temperate environment for use in the (sub)tropics. However, G × E interactions are unlikely to be of major importance in tropically adapted beef cattle grazed in either temperate or (sub)tropical environments, although sex × environment interactions may provide new opportunities for differentially selecting to simultaneously improve steer performance in benign environments and female performance in harsher environments. Early evidence suggests that re-ranking of SNPs occurs across temperate and tropical environments, although their magnitude is still to be confirmed in well-designed experiments. The major limitation to genetic improvement of beef cattle over the next decade is likely to be a deficiency of large numbers of accurately recorded phenotypes for most productive and adaptive traits and, in particular, for difficult-to-measure adaptive traits such as resistance to disease and environmental stressors.     

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.     

Breeding goats for meat production: 2. Crossbreeding and formation of composite population

This review, the second in the series on breeding goats for meat production, examines the role of crossbreeding and composite population in improving economically important traits necessary for commercial production of meat goats. In general, the crossbreeding of indigenous goats or established breeds with one or more breeds (Alpine, Beetal, Boer, Jamunapari, Nubian and Saanen) that have demonstrated genetic merit in the performance traits of economical importance rely on specific cross and back cross to achieve increased productivity. Concurrently, the combining of desirable morphological characteristics and production performance of two or more breeds in composite populations has had considerable success in other livestock and poultry species, invigorating interest in the breeding of meat goats for commercial production. There have been a number of studies, world-wide, on evaluation of indigenous goats or established breeds and their crosses, including crossbreds derived from exotic breeds that are summarized. Furthermore, the Boer breed developed in South Africa has considerable potential for rapid and permanent improvement of meat production from goats, and studies on the Boer-sired crossbred offspring are highlighted.     

Genetic diversity and population structure of 20 North European cattle breeds

Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history and geographical divisions of native breeding regions of indigenous cattle. Divergence estimates between Icelandic cattle and indigenous breeds suggested a separation time of more than 1,000 years between Icelandic cattle and Norwegian native breeds, a finding consistent with historical evidence.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

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.     

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.     

Breeding biology of Sabine’s gull (Xema sabini) in the Canadian high Arctic

The Sabine’s gull (Xema sabini) is a small seabird that breeds in select locations across the circumpolar Arctic, but there have been few studies on its breeding biology, particularly from the high Arctic. We studied nesting phenology, breeding effort, and breeding success of Sabine’s gulls over 5 years at a colony on a small island (Nasaruvaalik) in the Canadian high Arctic. Compared to studies in the low Arctic, nest initiation dates and adult body mass were more consistent across years, and reproductive success was typically higher at Nasaruvaalik Island. These differences may be related to the more predictable food sources available in the nearby polynya upon arrival from migration, as well as the lower predation pressure at our site.     

Genotype-environment interactions for growth and carcass traits in different pig breeds kept under conventional and organic production systems

The demand for special breeding programmes for organic pig meat production is based on the assumption that pigs kept under organic conditions need different biological properties compared with conventionally kept pigs in order to achieve a good performance. This would mean that genotype-environment interactions exist. Therefore, 682 pigs of seven different genotypes were tested for growth performance and carcass quality under conventional and organic environments at two testing stations to verify genotype-environment interactions. All genotypes achieved significantly better results within the conventional environment and there were significant interactions between genotype and environment for all the criteria of growth performance and carcass quality. The interactions are mainly caused by varying differences between organic and conventional systems within genotypes, but for all traits, except weight gain, no major shift of the ranking order within environment between genotypes. Although statistically significant genotype-environment interactions exist, the modern genotypes selected under conventional conditions are also superior to indigenous breeds under organic conditions in economically important traits. Hence, it can be concluded from these results that no special breeding programme is necessary for organic production systems.     

Herders’ Perceptions on Ruminant Livestock Breeds and Breeding Management in Southwestern Niger

This study documents indigenous knowledge of breeds of cattle, sheep and goats in southwestern Niger, and includes both pastoralists and agropastoralists. Our study included sheep and goats in view of the increasing importance of small ruminants in livestock production systems in the Sahel since the drought of the 1970s and 1980s. This study was carried out under the Desert Margins Program (DMP) project on arresting land degradation and the conservation of biodiversity in desert margins of sub-Saharan Africa, partly funded by the Global Environment Facility (GEF).     

山羊群体遗传多样性的微卫星分析

为了保护和合理利用我国地方山羊品种遗传资源提供理论基础,本研究利用国际农粮组织和国际家畜研究所推荐的10对微卫星引物,结合荧光标记PCR,检测了中国9个地方山羊品种和1个引进山羊品种的遗传多样性。所研究的10个品种中7个呈现出高度多态,3个呈现出中度多态。并共检测到119个等位基因,有效等位基因数在1.4641~9.2911之间,座位平均杂合度在0.2618~0.7672之间,品种平均杂合度在0.5196~0.7024之间,其中SRCRSP23位点和河西绒山羊(HXR)平均杂合度最高。聚类关系(NJ和UPGMA)和主成分分析结果与其起源、育成历史及地理分布基本一致。     

The captive rearing of threatened Orthoptera: a comparison of the conservation potential and practical considerations of two species' breeding programmes at the Zoological Society of London

The development of ex situ conservation work for Orthoptera is demonstrated by examples of two captive-breeding programmes at the Zoological Society of London. The field cricket Gryllus campestris and wart-biter bush cricket Decticus verrucivorus are both species that have been bred in captivity and reintroduced to field sites in attempts to strengthen dwindling wild populations. Despite a similar approach to both programmes, we have encountered significant differences in the practical applications of the captive management process for the two species. By reviewing these breeding programmes, we examine some of the practical considerations associated with ex situ orthopteran programmes and compare some of the different elements that can influence programme success.     

Utilization of frozen-thawed epididymal ram semen to preserve genetic diversity in Scrapie susceptible sheep breeds

The European Union has introduced transmissible spongiform encephalopathy (TSE) resistance breeding programmes for several sheep breeds to cope with the genetic susceptibility to Scrapie infections. Due to the different allele frequencies among breeds, strong selection for ARR alleles is associated with a loss of genetic diversity in small populations and in larger populations with unfavourable ARR allele frequencies. To ensure maintenance of genetic diversity, an adhoc cryopreservation programme was initiated employing epididymal sperm from 109 rams representing 16 different breeds within one breeding season. Epididymal semen was chosen for this adhoc programme because time consuming training of rams for ejaculated semen collection via an artificial vagina was not possible. Prior to freezing, average sperm motility was 79.7% and acrosome integrity was 93.7%. After freezing, these levels were decreased to 60.5 and 72.8%, respectively. An insemination trial using frozen-thawed epididymal semen resulted in a lambing rate of 87.5%. Results show that this semen preservation method is robust and efficient and associated with high fertility. It may also be useful for other animal species.     

Phylogeography and Origin of Sheep Breeds in Northern China

With the establishment of modern sheep production systems in China, various forms of hybridization with Western breeds and between native breeds have been utilized for genetic improvement. At the same time, the progressive destruction or deterioration of sheep habitat has accompanied urbanization in China. Together these factors have accelerated the loss of genetic diversity, or even resulted in the extinction of some indigenous breeds. It is therefore important that efficient strategies for surveillance, evaluation, conservation and utilization of available genetic resources are developed for this species. In this study, a total of 30 microsatellite markers were used to assess genetic diversity for 12 native breeds and one Western sheep breed in Northern China. The high polymorphism information contents at the 30 markers, varying from averages of 0.519 to 0.666 for the 13 breeds, imply the retention of natural variation from source populations in the domestic breeds from different geographic regions in China. Analysis of genetic differentiation revealed substantial divergence among these breeds. Neutrality tests indicated that more than one third of the 30 loci were in departure from neutrality, implying that some evolutionary forces (e.g. selection and migration) had acted on these populations. Phylogenetic and phylogeographic analyses displayed a remarkable degree of consistency between geographic origins, breeding histories and the pattern of genetic differentiation.     

Identification of smallholder farmers and pastoralists' preferences for sheep breeding traits: choice model approach

Identification of breeding objective traits pertinent to specific production environments with the involvement of target beneficiaries is crucial to the success of a breed improvement program. A choice experiment was conducted in four locations representing different production systems and agro-ecologies that are habitat to four indigenous sheep breeds (Afar, Bonga, Horro and Menz) of Ethiopia with the objective of identifying farmers'/pastoralists' preferences for sheep breeding traits. Following a synthesis of secondary information and diagnostic surveys, two communities per location consisting of 60 households each having at least four breeding ewes were identified. Producers' priority attributes used in the choice sets were identified through in-depth production system studies conducted from December 2007 to March 2008. On the basis of prior information, four to seven attributes were used to design choice sets with different profiles in order to capture results that mimic real life of the different communities. The attributes and levels chosen for the sheep profile were as follows: body size (large/small), coat color (brown/white/black), tail type (good/bad) for both rams and ewes; horn (polled/horned) and libido (active/poor) for rams; and lambing interval (three lambings in 2 years/two lambings in 2 years time), mothering ability (good mother/bad mother), twinning rate (twin bearer/single bearer) and milk yield (two cups per milking/one cup per milking) for ewes. A fractional factorial design was implemented to construct the alternatives included in the choice sets. The design resulted in a randomized selection of 48 sheep profiles (24 sets) for both sexes, which were grouped into four blocks with six choice sets each. An individual respondent was presented with one of the four blocks to make his/her choices. Results indicate that producers' trait preferences were heterogeneous except for body size in rams and mothering ability in ewes where nearly homogeneous preferences were investigated. In the pastoral production system, attention was given to coat color of both breeding rams and ewes, favoring brown and white colors over black. Ram libido influenced producers' decisions in Bonga, Horro and Menz areas. The influence of milk yield and twinning on respondents' decision making was high in Afar and Horro, respectively. Breeders in all areas attempt to combine production and reproduction traits as well as they can in order to maximize benefits from their sheep. The elicited measurable objective traits were used to design alternative community-based sheep breeding plans for the four indigenous sheep breeds in their production environments that have been implemented since.