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Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Chronic simultaneous exposure of common carp (Cyprinus carpio) from embryonic to juvenile stage to drospirenone and gestodene at low ng/L level caused intersex
Šauer, Pavel ; Tumová, Jitka ; Steinbach, Christoph ; Golovko, Oksana ; Komen, Hans ; Maillot-Maréchal, Emmanuelle ; Máchová, Jana ; Grabic, Roman ; Aït-Aïssa, Selim ; Kocour Kroupová, Hana - \ 2020
Ecotoxicology and Environmental Safety 188 (2020). - ISSN 0147-6513
Adverse effects - Hormones - Pollutants - Progestogens - Reproduction

Synthetic progestins are emerging contaminants of the aquatic environment with endocrine disrupting potential. The main aim of the present study was to investigate the effects of the synthetic progestins gestodene, and drospirenone on sex differentiation in common carp (Cyprinus carpio) by histological analysis. To gain insights into the mechanisms behind the observations from the in vivo experiment on sex differentiation, we analyzed expression of genes involved in hypothalamus–pituitary–gonad (HPG) and hypothalamus–pituitary–thyroid (HPT) axes, histology of hepatopancreas, and in vitro bioassays. Carp were continuously exposed to concentrations of 2 ng/L of single progestins (gestodene or drospirenone) or to their mixture at concentration 2 ng/L of each. The exposure started 24 h after fertilization of eggs and concluded 160 days post-hatching. Our results showed that exposure of common carp to a binary mixture of drospirenone and gestodene caused increased incidence of intersex (32%) when compared to clean water and solvent control groups (both 3%). Intersex most probably was induced by a combination of multiple modes of action of the studied substances, namely anti-gonadotropic activity, interference with androgen receptor, and potentially also with HPT axis or estrogen receptor.

Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs
Chu, Thinh T. ; Bastiaansen, John W.M. ; Berg, Peer ; Komen, Hans - \ 2019
Genetics, Selection, Evolution 51 (2019)1. - ISSN 0999-193X - 12 p.

Background: Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships. Results: Using genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5% for full-sibs and ~ 11.5% for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5% compared to random grouping of full-sibs, and by 14.7% compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes. Conclusions: The use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.

Using phenotypic distribution models to predict livestock performance
Lozano-Jaramillo, M. ; Alemu, S.W. ; Dessie, T. ; Komen, H. ; Bastiaansen, J.W.M. - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Livestock production systems of the developing world use indigenous breeds that locally adapted to specific agro-ecologies. Introducing commercial breeds usually results in lower productivity than expected, as a result of unfavourable genotype by environment interaction. It is difficult to predict of how these commercial breeds will perform in different conditions encountered in e.g. sub-Saharan Africa. Here, we present a novel methodology to model performance, by using growth data from different chicken breeds that were tested in Ethiopia. The suitability of these commercial breeds was tested by predicting the response of body weight as a function of the environment across Ethiopia. Phenotype distribution models were built using machine learning algorithms to make predictions of weight in the local environmental conditions based on the productivity for the breed. Based on the predicted body weight, breeds were assigned as being most suitable in a given agro-ecology or region. We identified the most important environmental variables that explained the variation in body weight across agro-ecologies for each of the breeds. Our results highlight the importance of acknowledging the role of environment in predicting productivity in scavenging chicken production systems. The use of phenotype distribution models in livestock breeding is recommended to develop breeds that will better fit in their intended production environment.

Economic optimization of full-sib test group size and genotyping effort in a breeding program for Atlantic salmon
Janssen, Kasper ; Saatkamp, Helmut W. ; Calus, Mario P.L. ; Komen, Hans - \ 2019
Genetics, Selection, Evolution 51 (2019)1. - ISSN 0999-193X

Background: Breeding companies may want to maximize the rate of genetic gain from their breeding program within a limited budget. In salmon breeding programs, full-sibs of selection candidates are subjected to performance tests for traits that cannot be recorded on selection candidates. While marginal gains in the aggregate genotype from phenotyping and genotyping more full-sibs per candidate decrease, costs increase linearly, which suggests that there is an optimum in the allocation of the budget among these activities. Here, we studied how allocation of the fixed budget to numbers of phenotyped and genotyped test individuals in performance tests can be optimized. Methods: Gain in the aggregate genotype was a function of the numbers of full-sibs of selection candidates that were (1) phenotyped in a challenge test for sea lice resistance (2) phenotyped in a slaughter test (3) genotyped in the challenge test, and (4) genotyped in the slaughter test. Each of these activities was subject to budget constraints. Using a grid search, we optimized allocation of the budget among activities to maximize gain in the aggregate genotype. We performed sensitivity analyses on the maximum gain in the aggregate genotype and on the relative allocation of the budget among activities at the optimum. Results: Maximum gain in the aggregate genotype was €386/ton per generation. The response surface for gain in the aggregate genotype was rather flat around the optimum, but it curved strongly near the extremes. Maximum gain was sensitive to the size of the budget and the relative emphasis on breeding goal traits, but less sensitive to the accuracy of genomic prediction and costs of phenotyping and genotyping. The relative allocation of budget among activities at the optimum was sensitive to costs of phenotyping and genotyping and the relative emphasis on breeding goal traits, but was less sensitive to the accuracy of genomic prediction and the size of the budget. Conclusions: There is an optimum allocation of budget to the numbers of full-sibs of selection candidates that are phenotyped and genotyped in performance tests that maximizes gain in the aggregate genotype. Although potential gains from optimizing group sizes and genotyping effort may be small, they come at no extra cost.

Genetic correlations between growth performance and carcass traits of purebred and crossbred pigs raised in tropical and temperate climates1
Godinho, Rodrigo M. ; Bergsma, Rob ; Silva, Fabyano F. ; Sevillano, Claudia A. ; Knol, Egbert F. ; Komen, Hans ; Guimarães, Simone Eliza F. ; Lopes, Marcos S. ; Bastiaansen, John W.M. - \ 2019
Journal of Animal Science 97 (2019)9. - ISSN 0021-8812 - p. 3648 - 3657.
breeding program - correlated response - crossbred pigs - genotype by environment interactions - growing-finishing pigs

In pig breeding, selection commonly takes place in purebred (PB) pigs raised mainly in temperate climates (TEMP) under optimal environmental conditions in nucleus farms. However, pork production typically makes use of crossbred (CB) animals raised in nonstandardized commercial farms, which are located not only in TEMP regions but also in tropical and subtropical regions (TROP). Besides the differences in the genetic background of PB and CB, differences in climate conditions, and differences between nucleus and commercial farms can lower the genetic correlation between the performance of PB in the TEMP (PBTEMP) and CB in the TROP (CBTROP). Genetic correlations (rg) between the performance of PB and CB growing-finishing pigs in TROP and TEMP environments have not been reported yet, due to the scarcity of data in both CB and TROP. Therefore, the present study aimed 1) to verify the presence of genotype × environment interaction (G × E) and 2) to estimate the rg for carcass and growth performance traits when PB and 3-way CB pigs are raised in 2 different climatic environments (TROP and TEMP). Phenotypic records of 217,332 PB and 195,978 CB, representing 2 climatic environments: TROP (Brazil) and TEMP (Canada, France, and the Netherlands) were available for this study. The PB population consisted of 2 sire lines, and the CB population consisted of terminal 3-way cross progeny generated by crossing sires from one of the PB sire lines with commercially available 2-way maternal sow crosses. G × E appears to be present for average daily gain, protein deposition, and muscle depth given the rg estimates between PB in both environments (0.64 to 0.79). With the presence of G × E, phenotypes should be collected in TROP when the objective is to improve the performance of CB in the TROP. Also, based on the rg estimates between PBTEMP and CBTROP (0.22 to 0.25), and on the expected responses to selection, selecting based only on the performance of PBTEMP would give limited genetic progress in the CBTROP. The rg estimates between PBTROP and CBTROP are high (0.80 to 0.99), suggesting that combined crossbred-purebred selection schemes would probably not be necessary to increase genetic progress in CBTROP. However, the calculated responses to selection show that when the objective is the improvement of CBTROP, direct selection based on the performance of CBTROP has the potential to lead to the higher genetic progress compared with indirect selection on the performance of PBTROP.

Learn how to set up a breeding programme | WURcast
Komen, J. - \ 2019
Wageningen :
animal breeding - animal breeding methods - breeding programmes
Deterministic simulations to determine the impacts of economic and non-economic breeding objectives on sustainable intensification of developing smallholder dairy farms
Kariuki, C.M. ; Arendonk, J.A.M. van; Kahi, A.K. ; Komen, H. - \ 2019
Livestock Science 226 (2019). - ISSN 1871-1413 - p. 7 - 12.
Breeding objectives - Developing dairy cattle systems - Non-market weights - Sustainability

Dairy cattle farming in developing countries is mainly by resource poor smallholder farmers. Intensification of production within smallholder production systems is being driven by increasing demand for animal products. Current intensification is driven by importation of high-input high-output genotypes. This puts in question the sustainability of these resource constrained systems under harsh environmental conditions. Sustainability of production systems can be defined as long-term resilience and productivity. We use deterministic simulations to compare the impacts of three criteria to define breeding objectives i.e., economic, desired gains and non-market value, on annual genetic and monetary gains in production (market) and functional (non-market) traits for a small-sized nucleus genomic selection breeding program under developing country conditions. Market traits considered were milk yield (MY) and mature body weight (MBW). Non-market traits were calving interval (CI) and production lifetime (PLT). Fat yield (FY) was also considered a non-market trait as it had no market value. With the economic objective, traits were weighted on economic values. Weights for desired gains and non-market (NM) values were derived iteratively. Economic objectives placed highest emphasis on MY with very little gains in non-market traits but had the highest returns on investment. For desired gains objective, maximal achievable gains in PLT, CI and FY were lower than the indicated desired gains. The non-market value objective achieved the best compromise between gains in MY and other traits. We conclude that non-market value objectives can be applied to direct selection towards more robust genotypes but with loss in monetary gain. Breeding robust genotypes can contribute to sustainable intensification in developing small-holder dairy systems. However, for such objectives to be satisfactory, a sound criterion is required to determine declines in genetic gains for market traits that are acceptable by producers.

Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones
Lozano-Jaramillo, M. ; Bastiaansen, J.W.M. ; Dessie, T. ; Komen, H. - \ 2019
Animal 13 (2019)7. - ISSN 1751-7311 - p. 1536 - 1543.
agro-ecology - breeding programs - distribution models - livestock - local adaptation

Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.

Understanding the Effect of the Environmental Conditions on the Suitability of a Breed for Different Agro-Ecological Zones
Lozano Jaramillo, Maria ; Bastiaansen, J.W.M. ; Dessie, Tadelle ; Komen, J. - \ 2018
In: Proceedings of the World Congress on Genetics Applied to Livestock Production Auckland : IAVS / Massey University - 4 p.
Predicting suitability of breeds for a production system can be challenging in livestock. Most attempts to introduce exotic breeds in low input systems were unsuccessful mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to elucidate their suitability to different locations. Predictive habitat distribution models use the current climatic conditions of a breed to make
predictions of the potential distribution of the breed. A methodology was developed to predict breed suitability for different agro-ecological zones based on GIS tools and PHD models. This methodology was tested on distribution data of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Results from cross-validation based on the current distribution of the breeds showed this methodology to be effective in predicting breed specific environmental suitability. Furthermore, for both breeds the significant climatic factors that shape the breeds distribution
were similar between the suggested distribution area, and the environment from which the breeds originated in South Africa and Egypt. This novel methodology applied to livestock research, allows for better decisions in introduction programs and the design of testing schemes, and increases our understanding of the role of the environment in livestock productivity.
Genotype by environment interaction for growth and survival of Nile tilapia in aerated and non-aerated ponds
Mengistu, Samuel ; Komen, J. ; Benzie, John A.H. ; Khaw, H.L. ; Mulder, H.A. - \ 2018
In: Session abstracts ISGA 2018. - - 1 p.
The economic value of R0 for macroparasitic diseases
Janssen, K.P.E. ; Saatkamp, H.W. ; Bijma, P. ; Jong, M.C.M. de; Komen, J. - \ 2018
In: Proceedings of the World Congress on Genetics Applied to Livestock Production. - WCGALP - 8 p.
Economic values are used to balance the emphasis on breeding goal traits, and determine whether selection for a trait is worthwhile. The basic reproduction ratio (R0) determines transmission dynamics of a disease and, therefore, R0 is an appropriate breeding goal trait. This study presents an easy to use framework for the derivation of the economic value of R0 for macroparasitic diseases. An example for sea lice in salmon is provided, resulting in an estimate of R0 of 2.9 with an economic value of -0.072 €/unit R0/kg production. Keywords: Economic value, R0, epidemiology, disease
Derivation of the economic value of r0 for macroparasites: application to sea lice in salmon
Janssen, K.P.E. ; Komen, J. ; Saatkamp, H.W. ; Jong, M.C.M. de; Bijma, P. - \ 2018
Posternummer SBQ8
Derivation of the economic value of R0 for macroparasitic diseases and application to sea lice in salmon
Janssen, Kasper ; Komen, Hans ; Saatkamp, Helmut W. ; Jong, Mart C.M. de; Bijma, Piter - \ 2018
Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X

Background: Macroparasites, such as ticks, lice, and helminths, are a concern in livestock and aquaculture production, and can be controlled by genetic improvement of the host population. Genetic improvement should aim at reducing the rate at which parasites spread across the farmed population. This rate is determined by the basic reproduction ratio, i.e. R 0, which is the appropriate breeding goal trait. This study aims at providing a method to derive the economic value of R 0. Methods: Costs of a disease are the sum of production losses and expenditures on disease control. Genetic improvement of R 0 lowers the loss-expenditure frontier. Its economic effect depends on whether the management strategy is optimized or not. The economic value may be derived either from the reduction in losses with constant expenditures or from the reduction in expenditures with constant losses. Results: R 0 ≤ 1, the economic value of a further reduction is zero because there is no risk of a major epidemic. When R 0 > 1 and management is optimized, the economic value increases with decreasing values of R 0, because both the mean number of parasites per host and frequency of treatments decrease at an increasing rate when R 0 decreases. When R 0 > 1 and management is not optimized, the economic value depends on whether genetic improvement is used for reducing expenditures or losses. For sea lice in salmon, the economic value depends on a reduction in expenditures with constant losses, and is estimated to be 0.065€/unit R 0 /kg production. Discussion: Response to selection for measures of disease prevalence cannot be predicted from quantitative genetic theory alone. Moreover, many studies fail to address the issue of whether genetic improvement results in reduced losses or expenditures. Using R 0 as the breeding goal trait, weighed by its appropriate economic value, avoids these issues. Conclusion: When management is optimized, the economic value increases with decreasing values of R 0 (until the threshold R 0 = 1, where it drops to zero). When management is not optimized, the economic value depends on whether genetic improvement is used for reduced expenditures or production losses. For sea lice in salmon, the economic value is estimated to be 0.065 €/unit R 0 /kg production.

Cost-benefit analysis of aquaculture breeding programs
Janssen, Kasper ; Saatkamp, Helmut ; Komen, Hans - \ 2018
Genetics, Selection, Evolution 50 (2018)1. - ISSN 0999-193X
Background: Profitability of breeding programs is a key determinant in the adoption of selective breeding, and can be evaluated using cost-benefit analysis. There are many options to design breeding programs, with or without a multiplier tier. Our objectives were to evaluate different breeding program designs for aquaculture and to optimize the number of selection candidates for these programs. Methods: The baseline was based on an existing breeding program for gilthead seabream, where improvement of the nucleus had priority over improvement of the multiplier tier, which was partly replaced once every 3 years. Alternative breeding programs considered were annual multiplier tier replacement, annual multiplier tier replacement with priority on improvement of the multiplier tier, and a program without a multiplier tier. Cost-benefit analyses were performed to compare breeding programs. The outcomes were used to describe relationships between profitability and the number of selection candidates, length of the time horizon, and production output, and to estimate the optimum numbers of selection candidates. Results: The baseline breeding program was profitable after 5 years and reached a net present value of 2.9 million euro in year 10. All alternative programs were more profitable up to year 17. The program without a multiplier tier was the most profitable one up to year 22, followed by the program with annual multiplier tier replacement and nucleus priority. The optimum number of selection candidates increased with the length of the time horizon and production output. Conclusions: The baseline breeding program was profitable after 5 years. For a short time horizon, putting priority on improvement of the multiplier tier over the nucleus is more profitable than putting priority on nucleus improvement, and vice versa for a long time horizon. Use of a multiplier tier increases the delay between costs made for selection and resulting benefits. Thus, avoiding the use of a multiplier tier will increase the profitability of the breeding program in the short term. The optimum number of selection candidates increases with the length of the time horizon and production output. Using too many selection candidates relative to the optimum leads to less reduction in profitability than using too few selection candidates.
Improving feed efficiency in fish using selective breeding : A review
Verdal, Hugues de; Komen, Hans ; Quillet, Edwige ; Chatain, Béatrice ; Allal, François ; Benzie, John A.H. ; Vandeputte, Marc - \ 2018
Reviews in Aquaculture 10 (2018)4. - ISSN 1753-5123 - p. 833 - 851.
Feed conversion ratio - Feed efficiency - Feed intake - Fish - Genetics - Selection

Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30-70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE. Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.

A systematic review of management factors affecting growth, feed conversion ratio and survival in Nile tilapia
Mengistu, Samuel ; Mulder, H.A. ; Benzie, John A.H. ; Komen, J. - \ 2017
In: International Conference and Exposition EAS. - - p. 753 - 754.
Currently many small and medium sized tilapia farms in developing countries underperform in terms of feed conversion ratio (FCR), despite the use of genetically improved strains of tilapia such as GIFT. The variable and often lower production in commercial environments compared to nucleus selection environments is a major bottleneck to increase productivity in tilapia farming. Feed cost is the major variable cost in fish farming (El-Sayed, 1999, Craig, 2009) and therefore this underperformance affects the profitability of fish farms negatively. This so-called yield gap has severe consequences for the effectiveness of breeding programs. The objective of this review was to analyse the most important environmental and management factors with significant contributions to growth, increased mortality and reduced feed efficiency of Nile tilapia.

Materials and methods
We conducted a systematic literature search on two data bases ASFA and CAB-Abstract on the 7th of July 2016. The search resulted in 1973 potentially relevant articles from which 59 articles met the inclusion criteria. After categorizing the studies based on the factors they investigated, we extracted data on the following variables: stocking density, photoperiod, culture unit, strain, whether aerated or not, feeding rate, feeding frequency, level of crude protein (CP), stocking weight (IBW) and harvest weight, water temperature, pH, salinity, feed conversion ratio (FCR) here defined as the ratio of total feed given / total biomass of fish harvested, dissolved oxygen (DO), survival and calculated thermal growth coefficient (TGC).

Using linear regression we found significant effects of strains (Abassa, FaST, GIFT, Imaela, Maryut and unspecified strain), culture unit, study length, IBW and feeding rate on FCR, survival and growth, calculated as TGC. The effect of strain was also significant on FCR and survival. FCR, survival and TGC increased with higher levels of dissolved oxygen (DO) and with higher levels of CP in the diet. Increased water temperature (range 21.5 to 28.5oC) favourably reduced FCR and improved survival (range 10 - 37oC). Higher salinity (range 0 to 30 ppt) reduced the survival of fish and growth (range 0 - 24ppt). Increased feeding rate improved survival and TGC while FCR was negatively affected by increased feeding rate. Increased dark photoperiod had a significant negative effect on TGC. The effect of stocking density on FCR, survival and TGC was not significant for the range of densities reported in the literature.

We found that the strains Abassa, FaST, GIFT, Imaela and Maryut were better in FCR than the unspecified strain. The probable reason could be that FaST, GIFT, Abassa, Maryut and Imaela strains have been selected for growth, which may have improved FCR as well. Ridha (2006) reported FaST and GIFT strains performed significantly better than unselected strains in terms of FCR. Furthermore, the strong negative genetic correlation of close to minus one between growth and FCR (Thoa et al., 2016) reported for Nile tilapia indicates that selecting for growth improves FCR. Selection for improved growth in Atlantic salmon also resulted in better FCR (Thodesen et al., 1999). In agreement with our study, stocking density was not significant in rainbow trout (Boujard T. et al. (2002) and in Oreochromis spilurus Cruz and Ridha (1989), while in African catfish (Clarias gariepinus) FCR was found to improve significantly with increasing stocking density from 4 fish m-3 to 8 fish m-3 (Toko et al., 2007).

In line with our result Abdel-Tawwab (2012) found fish fed with a higher CP level dealt better with stress than fish fed with a lower CP level. The effect of salinity on survival and the effect of salinity and dark photoperiod on TGC was negative and significant. The effect of salinity could be explained by high energy cost of osmoregulation (Prunet and Bornancin, 1989) which reduces available energy for growth. The negative effect of dark photoperiod could be explained by the fact that tilapias are diurnal feeders and an increased dark photoperiod could affect the feed intake negatively. We found also the effect of feeding rates was significant. Survival and TGC were improved with increased feeding rate, while the best FCR was at lowest feeding rate.

Aquaculture farms should give emphasis to the major environmental and management factors to minimize or avoid the yield gap. This could be achieved by optimizing management and optimizing breeding programs for the environments in which commercial fish will perform, especially if some variables are beyond management control and subject to genotype by environment interaction.
Benefit cost analysis of aquaculture breeding programs
Janssen, K.P.E. ; Saatkamp, H.W. ; Komen, J. - \ 2017
In: Book of Abstracts of the 68th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 23) - ISBN 9789086863129 - p. 429 - 429.
Benefit cost analysis of aquaculture breeding programs
Janssen, K.P.E. ; Saatkamp, H.W. ; Komen, J. - \ 2017
Economic values of growth rate, feed intake, feed conversion ratio, mortality and uniformity for Nile tilapia
Omasaki, S.K. ; Janssen, K. ; Besson, M. ; Komen, H. - \ 2017
Aquaculture 481 (2017). - ISSN 0044-8486 - p. 124 - 132.
Breeding objective - Economic values - Feed conversion ratio - Growth - Nile tilapia - Smallholder production
The aim of the study was to derive the economic value (s) (EVs) of growth rate, feed intake, feed conversion ratio, mortality and uniformity for Nile tilapia (Oreochromis niloticus). A smallholder production system where fish are cultured in earthen ponds and oxygen is a limiting factor for production, was simulated using a deterministic bio-economic model. Traits of interest were: thermal growth coefficient (TGC), thermal feed intake coefficient (TFC), feed conversion ratio (FCR), mortality rate (M) and uniformity of harvest body weight (U). Two breeding objectives were considered: a breeding objective with TGC, TFC, M and U (H1 model), and a breeding objective with TGC, FCR, M and U (H2 model). Gross margin (GM) was simulated before and after one genetic standard deviation improvement (σa) on a trait while other breeding objective traits were kept unaltered. EVs (US$/kg/σa) were derived as: change in GM/(farm production before genetic improvement). Results show that EVs of TGC differ depending on the definition of the breeding objective. The EV of TGC was 1.19 when TFC was in the breeding objective. In contrast, EV was only 0.02 when FCR was in the breeding objective. This difference is caused by the way EVs are calculated: the increase in gross margin resulting from a marginal increase in TGC while keeping other traits (FCR or TFC) constant. EV of TFC was 1.25 and the EV for FCR was 0.41. EVs for M and U were 0.06 and 0.02, irrespective of the model used. Improving TGC reduced the overall grow-out period, increasing the number of production cycles in the farm. In H1 model, reduced grow-out period was accompanied by a decrease in the amount of feed used in the farm (− 272.24 kg/year) and in individual fish oxygen consumption (− 1.67 g/fish/year), resulting in an increase in gross margin. In H2 model, increasing TGC resulted in a reduced grow out period but also increased feed used in the farm (5.73 kg/year) and increased individual fish oxygen consumption (0.57 g/fish/year). We conclude that the EV of TGC depends on which breeding objective is used. Faster growing fish consume more oxygen, and unless faster growth is accompanied by improved FCR, this will lead to oxygen limitations, necessitating lower stocking densities. Our results thus strongly confirm the economic importance of reducing FCR, irrespective of the model used. Statement of relevance This is the first study that presents the economic values for breeding objective traits for Nile tilapia farmed in earthen ponds using a bio-economic model.
Optimization of Nile tilapia breeding schemes for monosex culture conditions in smallholder production systems
Omasaki, S.K. ; Janssen, K. ; Komen, H. - \ 2017
Aquaculture 481 (2017). - ISSN 0044-8486 - p. 8 - 15.
Genetic gain - Genotype by environment interaction - Growth - Monosex - Nile tilapia - Smallholder production
The aim of this study was to optimize the design of a nucleus Nile tilapia breeding program for harvest weight, growth rate and survival in the presence of genotype by environment interaction with monosex (MS) culture of all-male fish. A nucleus breeding program was deterministically simulated using pseudo-BLUP selection index theory, implemented in SelAction. First, we investigated the rates of genetic gain for growth rate, expressed as TGCms using different selection indexes with varying degrees of genotype by environment interaction (G × E), expressed as the genetic correlation (rg) between the nucleus and a monosex production environment. Selection strategies were (1) mass selection in nucleus only, (2) Best Linear Unbiased Prediction (BLUP) with full/half sib information from the nucleus fish only, and (3) BLUP with information from full and half sibs in the nucleus and in the monosex production environment. In the second step, we extended the breeding goal to include harvest weight (HWms) and survival (Sms) to derive desired weights and genetic gains for these breeding goal traits. Finally, we maximized genetic gains in Sms while restricting the loss in TGC to 5%. Results: the presence of G × E lowered accuracy of selection (rIH) which led to a loss in genetic gain for TGCms. At rg of 0.7 and less, incorporating half sib information from monosex sibs into the selection index resulted in higher genetic gains of TGCms. Using 8 offspring in the nucleus as selection candidates and 32 offspring in monosex production environment, resulted in highest accuracy with lowest rates of inbreeding. This index had the highest relative genetic gains in all rg tested, implying that this index is least sensitive to G × E. Phenotypic variance ratio had no effects on rIH but had effects on predicted genetic response. Maximizing gains for HWms and Sms caused a large reduction of genetic gain in TGCms. However, allowing a 5% loss of genetic gain in both TGCms and HWms resulted in a 33% increase in genetic improvement of Sms. A breeding goal that maximizes survival while restricting loss in TGC to 5% had the highest response in US$. Statement of relevance This is the first study that presents optimization of Nile tilapia breeding schemes for monosex culture conditions in smallholder production systems of the tropics.
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