Variance components for survival of piglets at farrowing using a reduced animal model

Farrowing survival is usually analysed as a trait of the sow, but this precludes estimation of any direct genetic effects associated with individual piglets. In order to estimate these effects, which are particularly important for sire lines, it is necessary to fit an animal model. However this can be computationally very demanding. We show how direct and maternal genetic effects can be estimated with a simpler analysis based on the reduced animal model and we illustrate the method using farrowing survival information on 118 193 piglets in 10 314 litters. We achieve a 30% reduction in computing time and a 70% reduction in memory use, with no important loss of accuracy. This use of the reduced animal model is not only of interest for pig breeding but also for poultry and fish breeding where large full-sib families are performance tested.     

Pejibaye palm (Bactris gasipaes,Arecaceae): Multi-use potential for the lowland humid tropics

Pejibaye (Bactris gasipaes) was domesticated and widely used in the lowland humid neotropics during pre-Colombian times. Several research programs are underway to study and improve the species for use by farmers in ecologically suitable regions. Five breeding programs are outlined, each for a use to which the pejibaye may be put: (1) palmito (heart of palm), (2) whole fruit for human consumption, (3) flour and meal production, (4) oil production, and (5) animal ration from residues or purposefully bred varieties. Yield estimates and breeding problems are discussed. It is certain that the pejibaye can again become an important crop for the humid tropics.     

Genomics for food safety and sustainable animal production

There is a growing concern in society about the safety of animal-derived food, the health and welfare of farm animals and the sustainability of current animal production systems. Along farm animal, breeding genomics may contribute to a solution for these concerns. The use of genomic analysis tools, to achieve genetic progress in typical out-bred populations of farm animals, seems to be more difficult compared to 'model' organisms or plants. However, identification of positional candidate genes may be accelerated by linkage disequilibrium (LD) mapping. Recording of sustainable traits requires a large financial and logistic input and the economic advantages for the market are not as clear as for traditional selection traits. Examples show that the major genes causing variability for similar traits in different species are rarely the same. Therefore, for breeding purposes genomic analysis of the species of interest is needed. The fundamental knowledge obtained on the genetic architecture of complex traits will open new perspectives for the use of DNA tests in selection schemes. For food safety and traceability, DNA-based techniques evolve for monitoring and early warning systems.     

A computational approach to animal breeding

We propose a computational model of mating strategies for controlled animal breeding programs. A mating strategy in a controlled breeding program is a heuristic with some optimization criteria as a goal. Thus, it is appropriate to use the computational tools available for analysis of optimization heuristics. In this paper, we propose the first discrete model of the controlled animal breeding problem and analyse heuristics for two possible objectives: (1) breeding for maximum diversity and (2) breeding a target individual. These two goals are representative of conservation biology and agricultural livestock management, respectively. We evaluate several mating strategies and provide upper and lower bounds for the expected number of matings. While the population parameters may vary and can change the actual number of matings for a particular strategy, the order of magnitude of the number of expected matings and the relative competitiveness of the mating heuristics remains the same. Thus, our simple discrete model of the animal breeding problem provides a novel viable and robust approach to designing and comparing breeding strategies in captive populations.     

The role of the veterinary staff in mouse breeding colony management

The rapid increase in the production and use of transgenic mice has been a boon for biomedical research and a challenge for the animal care and use programs responsible for providing housing and medical care to these animals. The authors suggest ways in which the veterinary staff can successfully organize and manage transgenic mouse breeding programs to reduce uncontrolled breeding and the problems associated with it.     

Factor analytic and reduced animal models for the investigation of additive genotype-by-environment interaction in outcrossing plant species with application to a Pinus radiata breeding programme

Key message

Modelling additive genotype-by-environment interaction is best achieved with the use of factor analytic models. With numerous environments and for outcrossing plant species, computation is facilitated using reduced animal models.

Abstract

The development of efficient plant breeding strategies requires a knowledge of the magnitude and structure of genotype-by-environment interaction. This information can be obtained from appropriate linear mixed model analyses of phenotypic data from multi-environment trials. The use of factor analytic models for genotype-by-environment effects is known to provide a reliable, parsimonious and holistic approach for obtaining estimates of genetic correlations between all pairs of trials. When breeding for outcrossing species the focus is on estimating additive genetic correlations and effects which is achieved by including pedigree information in the analysis. The use of factor analytic models in this setting may be computationally prohibitive when the number of environments is moderate to large. In this paper, we present an approach that uses an approximate reduced animal model to overcome the computational issues associated with factor analytic models for additive genotype-by-environment effects. The approach is illustrated using a Pinus radiata breeding dataset involving 77 trials, located in environments across New Zealand and south eastern Australia, and with pedigree information on 315,581 trees. Using this approach we demonstrate the existence of substantial additive genotype-by-environment interaction for the trait of stem diameter measured at breast height. This finding has potentially significant implications for both breeding and deployment strategies. Although our approach has been developed for forest tree breeding programmes, it is directly applicable for other outcrossing plant species, including sugarcane, maize and numerous horticultural crops.     

与医科学生谈实验动物标准化

实验动物标准化由实验动物生产条件的标准化、实验动物质量标准化、动物实验条件的标准化以及与之相适应的饲养管理规范化和动物实验规范化几个部分组成。实验动物法制化管理是实验动物标准化的保证。动物实验是医学生物学必需的是实验手段之一,用标准的实验动物进行标准的动物实验是科研实验的基本要求。     

Effects of housing density on nasal pathology of breeding mice housed in individually ventilated cages

The 2011 edition of the Guide for the Care and Use of Laboratory Animals includes new recommendations for the amount of floor space that should be provided to breeding mice. When pairs or trios of continuously breeding mice are housed in shoebox cages, they may have less than this recommended amount of floor space. High housing densities may adversely affect animal health, for example, by compromising air quality inside the cage. Hence, some institutions are carefully reevaluating the microenvironments of breeding cages. The use of individually ventilated cages (IVCs) to house research mice allows for greater control over the quality of the cage microenvironment. The authors evaluated the microenvironments of shoebox cages in an IVC rack system housing breeding and non-breeding Swiss Webster mice. Ammonia concentrations were significantly higher in cages housing breeding trios with two litters. Histopathologic lesions attributable to inhaled irritants such as ammonia were found in mice housed in breeding pairs and trios. The authors conclude that the microenvironments of cages in an IVC rack system housing breeding pairs and trios may be detrimental to animal health.     

Bayesian prediction of breeding values for multivariate binary and continuous traits in simulated horse populations using threshold-linear models with Gibbs sampling

Simulated data were used to determine the properties of multivariate prediction of breeding values for categorical and continuous traits using phenotypic, molecular genetic and pedigree information by mixed linear-threshold animal models via Gibbs sampling. Simulation parameters were chosen such that the data resembled situations encountered in Warmblood horse populations. Genetic evaluation was performed in the context of the radiographic findings in the equine limbs. The simulated pedigree comprised seven generations and 40 000 animals per generation. The simulated data included additive genetic values, residuals and fixed effects for one continuous trait and liabilities of four binary traits. For one of the binary traits, quantitative trait locus (QTL) effects and genetic markers were simulated, with three different scenarios with respect to recombination rate (r) between genetic markers and QTL and polymorphism information content (PIC) of genetic markers being studied: r = 0.00 and PIC = 0.90 (r0p9), r = 0.01 and PIC = 0.90 (r1p9), and r = 0.00 and PIC = 0.70 (r0p7). For each scenario, 10 replicates were sampled from the simulated horse population, and six different data sets were generated per replicate. Data sets differed in number and distribution of animals with trait records and the availability of genetic marker information. Breeding values were predicted via Gibbs sampling using a Bayesian mixed linear-threshold animal model with residual covariances fixed to zero and a proper prior for the genetic covariance matrix. Relative breeding values were used to investigate expected response to multi- and single-trait selection. In the sires with 10 or more offspring with trait information, correlations between true and predicted breeding values ranged between 0.89 and 0.94 for the continuous traits and between 0.39 and 0.77 for the binary traits. Proportions of successful identification of sires of average, favourable and unfavourable genetic value were 81% to 86% for the continuous trait and 57% to 74% for the binary traits in these sires. Expected decrease of prevalence of the QTL trait was 3% to 12% after multi-trait selection for all binary traits and 9% to 17% after single-trait selection for the QTL trait. The combined use of phenotype and genotype data was superior to the use of phenotype data alone. It was concluded that information on phenotypes and highly informative genetic markers should be used for prediction of breeding values in mixed linear-threshold animal models via Gibbs sampling to achieve maximum reduction in prevalences of binary traits.     

The Sub-Annual Breeding Cycle of a Tropical Seabird

Breeding periodicity allows organisms to synchronise breeding attempts with the most favourable ecological conditions under which to raise offspring. For most animal species, ecological conditions vary seasonally and usually impose an annual breeding schedule on their populations; sub-annual breeding schedules will be rare. We use a 16-year dataset of breeding attempts by a tropical seabird, the sooty tern (Onychoprion fuscatus), on Ascension Island to provide new insights about this classical example of a population of sub-annually breeding birds that was first documented in studies 60 years previously on the same island. We confirm that the breeding interval of this population has remained consistently sub-annual. By ringing >17000 birds and re-capturing a large sample of them at equivalent breeding stages in subsequent seasons, we reveal for the first time that many individual birds also consistently breed sub-annually (i.e. that sub-annual breeding is an individual as well as a population breeding strategy). Ascension Island sooty terns appear to reduce their courtship phase markedly compared with conspecifics breeding elsewhere. Our results provide rare insights into the ecological and physiological drivers of breeding periodicity, indicating that reduction of the annual cycle to just two life-history stages, breeding and moult, is a viable life-history strategy and that moult may determine the minimum time between breeding attempts.     

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.     

模型动物在动物流感病毒传播机制研究中的应用

动物流感（influenza）不仅会对畜禽养殖业造成巨大的经济损失,而且可以跨越种间障碍进入人群,引发全球性的公共卫生危机和灾难性后果.模型动物是研究流感传播机制的重要基础.模型动物的使用有助于我们对流感病毒传播机制的深入了解.本文从流感病毒的宿主范围、常用模型动物的宿主限制因素和模型动物在流感病毒跨种传播机制中的选择与应用等三个方面进行了综述.     

Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness

Tameness is a major element of animal domestication and involves two components: motivation to approach humans (active tameness) and reluctance to avoid humans (passive tameness). To understand the behavioral and genetic mechanisms of active tameness in mice, we had previously conducted selective breeding for long durations of contact and heading toward human hands in an active tameness test using a wild-derived heterogeneous stock. Although the study showed a significant increase in contacting and heading with the 12th generation of breeding, the effect on other behavioral indices related to tameness and change of gene expression levels underlying selective breeding was unclear. Here, we analyzed nine tameness-related traits at a later stage of selective breeding and analyzed how gene expression levels were changed by the selective breeding. We found that five traits, including contacting and heading, showed behavioral change in the selective groups comparing to the control through the generations. Furthermore, we conducted cluster analyses to evaluate the relationships among the nine traits and found that contacting and heading combined in an independent cluster in the selected groups, but not in the control groups. RNA-Seq of hippocampal tissue revealed differential expression of 136 genes between the selection and control groups, while the pathway analysis identified the networks associated with these genes. These results suggest that active tameness was hidden in the control groups but became apparent in the selected populations by selective breeding, potentially driven by changes in gene expression networks.     

The breeding and utilization of baboons for biomedical research.

The baboon (Papio cynocephalus) has been used extensively for biomedical research at the Southwest Foundation for Research and Education (SFRE) since 1958. This animal model has adapted well to captivity, has reproduced efficiently, and has proved to be very useful in many areas of medical research. Reproductive data from the SFRE baboon colony, the establishment of a breeding colony from imported animals, the present use of baboons as research models, and the predicted availability and use of these animals were discussed.     

GENSTAT programs for performing Muir's alternative partitioning of genotype-by-environment interaction

Genotype-by-environment (GE) interaction exists when different cultivars or strains have different phenotypic responses to environmental variation (Merila and Fry 1998). The phenomenon is of major concern in plant breeding, as it can limit gains in selecting superior cultivars. In animal breeding, the problem is also an important issue because breeding stocks are developed by a few companies but are used worldwide (Lin and Togashi 2002).     

树鼩独立换气笼具的设计

目的设计研究一种满足于树鼩感染性疾病动物模型实验生物安全要求的独立换气专用隔离笼具。方法根据树驹的生物学特性、实验生物安全要求及有关实验动物笼具标准进行设计。结果该笼舍完全适用于感染性疾病实验树鼢的饲养和实验操作。结论该笼具能达到维护实验动物福利,保证实验动物质量,保障人身健康,保护环境的要求,对于使用树鼩开展人类重大传染病研究具有广泛的应用价值和市场前景。     

Endospore production of Bacillus spp. for industrial use

The increased occurrence of antibiotic resistance and the harmful use of pesticides are a major problem of modern times. A ban on the use of antibiotics as growth promoters in animal breeding has put a focus on the probiotics market. Probiotic food supplements are versatile and show promising results in animal and human nutrition. Chemical pesticides can be substituted by biopesticides, which are very effective against various pests in plants due to increased research. What these fields have in common is the use of spore-forming bacteria. The endospore-forming Bacillus spp. belonging to this group offer an effective solution to the aforementioned problems. Therefore, the biotechnological production of sufficient qualities of such endospores has become an innovative and financially viable field of research. In this review, the production of different Bacillus spp. endospores will be reviewed. For this purpose, the media compositions, cultivation conditions and bioprocess optimization methods of the last 20 years are presented and reflected.     

Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat

Microsatellites (SSRs) are widely used in cereal research, and their use in marker assisted breeding has increased the speed and efficiency of germplasm improvement. Central to the application of SSRs for many purposes are methodologies enabling the low-cost acquisition of large quantities of genetic information for gene and genotype identification. In this study, multiplex-ready PCR was evaluated in barley and bread wheat as an approach for rapid and more automated SSR genotyping on a fluorescence-based DNA fragment analyzer. Multiplex-ready PCR is a method that allows SSR genotyping to be performed using a standardized protocol. The method enables flexible fluorescence labeling of SSRs, generates a relatively constant amount of PCR product for each marker, and has a high amenability to multiplex PCR (the simultaneous amplification of several SSRs in the same reaction). A high (92%) compatibility of published SSRs with multiplex-ready PCR is demonstrated, and the usefulness of the method for large scale genotyping is shown by its application for whole genome marker assisted breeding in barley. A database of more than 2,800 barley and wheat SSRs, and a suite of bio-informatic tools were developed to support the deployment of multiplex-ready PCR for various genetic applications, and are accessible at . Multiplex-ready PCR is broadly applicable to cereal genomics research and marker assisted breeding, and should be transferable to similar analyses of any animal or plant 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.     

Application of Genomics Tools to Animal Breeding

The main goal in animal breeding is to select individuals that have high breeding values for traits of interest as parents to produce the next generation and to do so as quickly as possible. To date, most programs rely on statistical analysis of large data bases with phenotypes on breeding populations by linear mixed model methodology to estimate breeding values on selection candidates. However, there is a long history of research on the use of genetic markers to identify quantitative trait loci and their use in marker-assisted selection but with limited implementation in practical breeding programs. The advent of high-density SNP genotyping, combined with novel statistical methods for the use of this data to estimate breeding values, has resulted in the recent extensive application of genomic or whole-genome selection in dairy cattle and research to implement genomic selection in other livestock species is underway. The high-density SNP data also provides opportunities to detect QTL and to encover the genetic architecture of quantitative traits, in terms of the distribution of the size of genetic effects that contribute to trait differences in a population. Results show that this genetic architecture differs between traits but that for most traits, over 50% of the genetic variation resides in genomic regions with small effects that are of the order of magnitude that is expected under a highly polygenic model of inheritance.