Animal breeding and genetics MOOC: Why and what initial results?

Bill & Melinda Gates Foundatio

A systematic literature review of the major factors causing yield gap by affecting growth, feed conversion ratio and survival in Nile tilapia (Oreochromis niloticus)

Abstract Productivity among small- and medium-scale tilapia farms varies considerably. The difference between the best performers and lower ones (yield gap), is affected by differences in growth rate and feed conversion ratio (FCR). FCR at the farm level is strongly influenced by survival of fish. In this study a systematic literature review of two databases (ASFA and CAB-Abstracts) identified 1973 potentially relevant articles. Data from 32 articles that met the inclusion criteria were analysed using linear mixed models for the most important factors with significant contributions to growth [investigated through analysis of the thermal growth coefficient (TGC)], survival and FCR of Nile tilapia. Increasing crude protein (CP), dissolved oxygen (DO) and pH significantly decreased FCR and increased TGC. Increasing stocking weight (SW) significantly improved both FCR and survival. Temperature had the largest effect on FCR followed by DO, pH and CP. DO had the largest effect on TGC followed by CP and pH. This study confirms that the optimal rearing temperature for Nile tilapia is between 27 and 32°C. Improving management to optimize DO (> 5 mg/L), stocking density (3–5 fish/m2), SW (> 10 g) and CP (25 − 30%) will improve performance and survival in small- and medium-scale tilapia farming. However, it is hard to influence temperature in ponds and cages while DO is largely influenced by aeration. Since many small- and medium-sized farms do not have aeration, these major tilapia farming systems could benefit from genetically improved strains selected for resilience to highly fluctuating diurnal temperature and DO levels

Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers) and current merits (economic, ecological and cultural merits). Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04) as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83). We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan

Characterization and conservation of indigenous sheep genetic resources: A practical framework for developing countries

Livestock characterization projects in developing regions are characterized by a mere physical description of traditionally recognized populations or a purely academic genetic description of populations. However, characterization of livestock resources is meant to serve the purpose of developing conservation and utilization programs. A national characterization project should be geared to the specific national livestock production objectives. Thus there is a need to adopt a more practical characterization approach to assist in the development of national conservation and utilization strategies. This report provides a practical methodological framework suited for characterization and conservation of sheep resources in developing regions. The report highlights current approaches and tools for characterization and conservation of sheep resources and presents a model approach synthesising results of a study on characterization and conservation of sheep resources of Ethiopia. The study is a collaborative project between Wageningen University and the International Livestock Research Institute. The methodological framework can be applied elsewhere in developing countries with similar characterization and conservation objectives. This report largely dwelt on the technical aspects of sheep genetic resource characterization and conservation in developing regions. Operational aspects of setting up national programs for characterization and conservation action may be country specific. However, some general aspects such as institutional setups and breeding policy and strategy formulation could be similar across countries. A proposed scheme for setting up a national livestock characterization and conservation program is presented, taking Ethiopia as a case study

Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method

Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens

Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes

Fluctuations in growth are heritable and a potential indicator of resilience in Nile tilapia (Oreochromis niloticus)

Resilience can be defined as the capacity of an animal to be minimally affected by perturbations or to quickly recover to the state it had before the perturbation. When applied to production animals, resilience is defined as consistency in production over time. This consistency can be quantified by the variance of deviations from the expected trait level measured at multiple time points. The objectives of this study were to estimate genetic parameters for resilience in Nile tilapia, measured as consistency in growth. We used log-transformed variance of deviations (LnVar) of body weight measured five times during grow-out in either an aerated or a non-aerated pond. The hypothesis was that fish grown in non-aerated ponds are more challenged by environmental conditions, such that heritable variation in LnVar of body weight is more expressed showing larger differences between more and less resilient fish. The heritability for LnVar was 0.10 in aerated pond and 0.12 in the non-aerated pond. In aerated ponds the genetic correlation (rg) of LnVar with harvest weight (HW) was 0.36 ± 0.26, and with thermal growth coefficient (TGC) it was 0.47 ± 0.21. In the non-aerated pond, the rg with HW and TGC were close to zero (−0.01 ± 0.29 and − 0.08 ± 0.22). The genetic correlation for LnVar between both environments was 0.80. These estimates suggest that selection for HW or TGC in aerated ponds will increase LnVar in both environments. Increased LnVar may decrease resilience and this will be detrimental to performance. Selecting for more resilient fish would lead to more constant growth rates, which makes biomass estimation more accurate and could therefore result in more optimal feeding regimes and less feed waste. This would have a favorable effect on the feed efficiency in production units and on the environmental impact of fish farming. To improve resilience together with growth we recommend that fish breeding programs collect repeated records on body weight, preferably in challenging environments

Agroecologies defined by species distribution models improve model fit of genotype by environment interactions to identify the best performing chicken breeds for smallholder systems

Animal performance is an outcome of genetic effects, environmental influences, and their interaction. Understanding the influences of the environment on performance is important to identify the right breeds for a given environment. Agroecological zonation is commonly used to classify environments and compare the performance of breeds before their wider introduction into a new environment. Environmental classes, also referred to as agroecologies, are traditionally defined based on agronomically important environmental predictors. We hypothesized that our own classification of agroecologies for livestock at a species level and incorporating the most important environmental predictors may improve genotype by environment interactions (GxE) estimations over conventional methodology. We collected growth performance data on improved chicken breeds distributed to multiple environments in Ethiopia. We applied species distribution models (SDMs) to identify the most relevant environmental predictors and to group chicken performance testing sites into agroecologies. We fitted linear mixed-effects models (LMM) to make model comparisons between conventional and SDM-defined agroecologies. Then we used Generalized Additive Models (GAMs) to visualize the influences of SDM-identified environmental predictors on the live body weight of chickens at species level. The model fit in LMM for GxE prediction improved when agroecologies were defined based on SDM-identified environmental predictors. Partial dependence plots (PDPs) produced by GAMs showed complex relationships between environmental predictors and body weight. Our findings suggest that multi-environment performance evaluations of candidate breeds should be based on SDM-defined environmental classes or agroecologies. Moreover, our study shows that GAMs are well-suited to visualizing the influences of bioclimatic factors on livestock performance