Spatial and stochastic simulation to evaluate the impact of events and control measures on the 1997-1998 classical swine fever epidemic in The Netherlands. II. Comparison of control strategies

Using the spatial, temporal and stochastic simulation model InterCSF, several alternative pre-emptive slaughter strategies that could have been applied in the Dutch Classical Swine Fever (CSF) epidemic of 1997–1998 were evaluated. Furthermore, effects of changes in some disease-spread and disease-control parameters were studied. InterCSF simulates the spread of CSF between farms through local spread and contacts (animals, transport and persons). Disease spread is affected by control measures implemented through different mechanisms (e.g. depopulation of infected farms, pre-emptive slaughter, movement control). The starting point for the evaluation of strategies was a simulated basic scenario, which mimicked the real epidemic. Strategies were compared using epidemiological as well as economic results. Economic results were generated by a separate model (EpiLoss) that calculated the direct losses and consequential losses for farmers and related industries. The comparison of the different alternatives to the basic scenario led to some general conclusions on the Dutch CSF-epidemic. Pre-emptive slaughter seemed to be an effective strategy to reduce the size of an epidemic, if started at an early stage. Economically, pre-emptive slaughter was not as expensive as expected; the resulting smaller size of the epidemic, combined with less welfare slaughter, led to much lower overall losses. Furthermore, although large movement control areas seemed effective in reducing the size of the epidemic, the total losses were relatively high because of subsequent welfare slaughter. If infection probabilities could be reduced, for example by improved biosecurity, the resulting epidemics would be much smaller.     

The effect of adipocyte and heart fatty acid-binding protein genes on intramuscular fat and backfat content in Meishan crossbred pigs

Effects of genetic variation in porcine adipocyte and heart fatty acid-binding protein genes, A-FABP and H-FABP, respectively, on intramuscular fat (IMF) content and backfat thickness (BFT) were examined in F2 crossbreds of Meishan and Western pigs. The involvement of each FABP gene in IMF accretion was studied to confirm previous results for Duroc pigs. The F2 crossbred pigs were genotyped for various markers including microsatellite sequences situated within both FABP genes. Linkage analysis assigned the A-FABP and H-FABP genes to marker intervals S0001-S0217 (20 cM) on SSC4 and Sw316-S0003 (16.6 cM) on SSC6, respectively, refining previous chromosomal assignments. Next, the role of both chromosome regions/genes on genetic variation in IMF content and BFT was studied by 1) screening SSC4 and SSC6 for QTL affecting both traits by performing a line-cross analysis and 2) estimation of the effect of individual A-FABP and H-FABP alleles on both traits. In the first analysis, suggestive and chromosome-wise significant evidence for a QTL affecting IMF was detected on SSC6. The H-FABP gene is a candidate gene for this effect because it resides within the large region containing this putative QTL. The second analysis showed a considerable but nonsignificant effect of H-FABP microsatellite alleles on IMF content. Suggestive evidence for a QTL affecting BFT was found on SSC6, but H-FABP was excluded as a candidate gene. In conclusion, present and previous results support involvement of H-FABP gene polymorphisms in IMF accretion independently from BFT in pigs. Therefore, implementation of these polymorphisms in marker-assisted selection to control IMF content independently from BFT may be considered. In contrast to previous findings for Duroc pigs, no evidence was found for an effect of the A-FABP gene on IMF or BFT in this population.     

The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs

The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76 683 animals, of which 4933 animals are genotyped. The heritabilities for front leg conformation, stayability, osteochondrosis and arched back, estimated using the traditional pedigree, were found to be between 0.12 and 0.29. When using the combined genomic and pedigree relationship matrix, the heritabilities were between 0.14 and 0.36. The results show that the combined relationship matrix can be used for the estimation of (co)variance components, and that the predictive ability of the model in this study marginally increases with the inclusion of genomic information.     

Risk factors affecting metaphyseal irregularities in the radius and ulna of growing Newfoundland dogs

The main objective of this study was to study risk factors affecting metaphyseal irregularities (MI) in the distal radius and ulna of growing Newfoundland dogs. Risk factors studied included the genetic effects, effects of litters, BW, circumferences of the distal radius and ulna (CDRU), and total serum alkaline phosphatase (ALP) concentrations. The study included 118 Newfoundland dogs (60 females, 58 males), derived from 32 litters. Body weight, separated on sex and MI, was fitted to the Gompertz function. Occurrence of MI differed significantly between sexes, with 55% of males and 35% of females affected (P = 0.03). Growth curves for the 2 groups of dogs, with and without MI, diverged after 60 to 70 d, and dogs with irregularities were heavier at maturity than dogs of the same sex without irregularities. In univariate analysis, the litter effect was a significant predictor of MI, explaining 32% of total variability of the MI incidence, but the genetic effects were not significant. However, the latter were significant in bivariate analysis of MI and BW. In the bivariate analysis, the effects of litter on MI and BW were significantly correlated at all observational points except at birth, 180 d, and 536 d. Total ALP concentrations decreased with increasing age, and differences between groups diminished with increasing age, indicating a negative effect of total ALP on MI. Correlation between MI and total ALP concentrations of litters was estimated in a bivariate analysis. This correlation was significant and ranged between -0.34 and -0.62. Similarly, the genetic relationship between total ALP and MI from 120 d of age onward varied between -0.31 to -0.60. However, correlations were only significant at 356 d of age (genetic correlation = 0.60; P = 0.01). The mean CDRU increased from 90 d of age toward a peak at 180 d. Thereafter, CDRU declined and stabilized at about 1 yr of age. The mean CDRU between the groups of dogs with and without MI diverged most at 90 d of age, then was nearly stable until 180 d and gradually declined until 356 d, when the CDRU began to equalize. Metaphyseal irregularities and CDRU levels of litter were significantly correlated. Litter effect was a significant predictor of MI. The effects of litters and the genetic effects on BW and MI were correlated at most phases of the growth of the dog. Similar, but lower, correlations were found for CDRU and MI, and total ALP and MI.     

Combined detection and introgression of quantitative trait loci underlying desirable traits

This study presents a new method that combines QTL mapping and gene introgression. The effectiveness of this method for simultaneous detection and introgression of a desirable QTL from a donor line into a recipient line was evaluated by simulation. For evaluation, we used the fourth backcross generation of 2 inbred lines. The difference between the 2 lines for the trait of interest was described entirely by 1 QTL, with the donor line carrying the superior allele. Nine scenarios, combinations of 3 heritabilities (h(2) = 0.10, 0.05, or 0.01) and 3 population sizes (N = 100, 500, or 1,000) were considered in the simulation. Selection of parents for the next backcross was based solely upon the estimated probability of carrying the superior allele after a QTL analysis. Estimates of the QTL location and allele substitution effect in most scenarios were comparable to the true values. However (with either small h(2) or N) the QTL allele substitution effect was underestimated, and location was also biased. The SE of the estimates decreased with increasing N. The retained donor chromosome segment and linkage drag were close to the expected values from other published work. In general, combined detection and introgression of genes underlying desirable traits not only saves at least 1 generation, but also it ensures that the desirable QTL is introgressed where its function is simultaneously tested in a planned environment and recipient genome structure.     

Applying weather index insurance to agricultural pest and disease risks

In this paper, we explore the application of weather index insurance to plant pest and disease management strategies using two distinct models: (1) insuring crop loss due to disease incidence (“Crop Insurance”) and (2) insuring the use of pesticides (“Pesticide Insurance”). We find that despite the seeming ease of applying weather-based pest incidence models to an insurance product, insuring plant disease incidence models is presently unsuitable for the insurance market for both scientific and behavioral reasons. However, derivative-like applications of weather index insurance to insure pesticide use offer a means to introduce financial leverage into pesticide usage decisions. Risk management with weather index insurance would thus function as a complement to existing risk management strategies using pesticides, and offer a market-based mechanism for pesticide abatement. We conclude that more interdisciplinary collaboration is needed to develop weather index insurance for remuneration of losses due to plant pests and diseases, but weather index insurance offers a potential mechanism to reduce inefficiencies and negative externalities in agricultural markets if pesticide expenditures are insured instead of crop losses.     

Economic feasibility of recirculating aquaculture systems in pangasius farming

This study aims to analyze the economic feasibility of recirculating aquaculture systems (RAS) in pangasius farming in Vietnam. The study uses a capital budgeting approach and accounts for uncertainty in key parameters. Stochastic simulation is used to simulate the economic performance of medium and large farms operating with a traditional system or RAS. Data are obtained through structured surveys and a workshop in the Mekong River Delta. Results show that for large farms, net present value increases from an average of 589,000 USD/ha to 916,000 USD/ha after implementing RAS. Overall, the probability that RAS is a profitable investment is found to be 99% for both farm sizes. With RAS, the crucial parameters determining profitability are price, yield, costs of fingerling, feed, and initial investment. Findings on the robustness of the economic performance of RAS are useful to support public and private decision making towards increasing the sustainability of pangasius production.     

Revealing genetic relationships between compounds affecting boar taint and reproduction in pigs

Boar taint is characterized by an unpleasant taste or odor in intact male pigs and is primarily attributed to increased concentrations of androstenone and skatole and to a lesser extent by increased indole. The boar taint compounds skatole and indole are produced by gut bacteria, metabolized in the liver, and stored in the fat tissue. Androstenone, on the other hand, is synthesized in the testis along with testosterone and estrogens, which are known to be important factors affecting fertility. The main goal of this study was to investigate the relationship between genetic factors involved in the primary boar taint compounds in an attempt to discover ways to reduce boar taint without decreasing fertility-related compounds. Heritabilities and genetic correlations between traits were estimated for compounds related to boar taint (androstenone, skatole, indole) and reproduction (testosterone, 17β-estradiol, and estrone sulfate). Heritabilities in the range of 0.47 to 0.67 were detected for androstenone concentrations in both fat and plasma, whereas those for skatole and indole were slightly less (0.27 to 0.41). The genetic correlations between androstenone in plasma and fat were extremely high (0.91 to 0.98) in Duroc and Landrace. In addition, genetic correlations between androstenone (both plasma and fat) and the other sex steroids (estrone sulfate, 17β-estradiol, and testosterone) were very high, in the range of 0.80 to 0.95. Furthermore, a genome-wide association study (GWA) and a combined linkage disequilibrium and linkage analysis (LDLA) were conducted on 1,533 purebred Landrace and 1,027 purebred Duroc to find genome regions involved in genetic control of the boar taint compounds androstenone, skatole, and indole, and sex hormones related to fertility traits. Up to 3,297 informative SNP markers were included for both breeds, including SNP from several boar taint candidate genes. From the GWA study, we found that altogether 27 regions were significant at a genome-wide level (P < 0.05) and an additional 7 regions were significant at a chromosomal level. From the LDLA study, 7 regions were significant on a genome-wide level and an additional 7 regions were significant at a chromosomal level. The most convincing associations were obtained in 6 regions affecting skatole and indole in fat on chromosomes 1, 2, 3, 7, 13, and 14, 1 region on chromosome 6 affecting androstenone in plasma only, and 5 regions on chromosomes 3, 4, 13, and 15 affecting androstenone, testosterone, and estrogens.