Genetic variation in dieback resistance in Fraxinus excelsior confirmed by progeny inoculation assay

Ash dieback caused by the pathogenic fungus Hymenoscyphus fraxineus [previously known as H. pseudoalbidus (sexual stage) and Chalara fraxinea (asexual stage)] is a widespread problem in Europe. Here, we assess crown damage from natural infection and necrosis development following artificial controlled inoculations on full‐sib and half‐sib progeny from Danish Fraxinus excelsior clones with contrasting and well‐characterized levels of susceptibility to the disease. The inoculation assay was performed on a total of 123 offspring, and necrosis development monitored over two years. The offspring from low susceptible mother clones developed smaller necroses when compared to offspring from susceptible clones. Their crown damage due to natural infections was also significantly less. The correlation coefficient between average crown damages of mother clones and the average of their progeny was 0.85 (natural infections), while the correlation between crown damage of mother clones and the average necrosis development in their progeny after controlled inoculation was 0.73. The correlation between resistance of parent trees and crown damage/necrosis development on their offspring confirms the presence of heritable resistance and indicates that a bioassay based on controlled inoculations has the potential of becoming a fast and cost‐effective tool for estimation of dieback susceptibility in breeding programmes for resistance in ash trees.     

Analysis of moniliformin in maize plants using hydrophilic interaction chromatography

A novel HPLC method was developed for detection of the Fusarium mycotoxin, moniliformin in whole maize plants. The method is based on hydrophilic interaction chromatography (HILIC) on a ZIC zwitterion column combined with diode array detection and negative electrospray mass spectrometry (ESI(-)-MS). Samples were extracted using acetonitrile-water (85:15), and the extracts were cleaned up on strong anion exchange columns. By this procedure we obtained a recovery rate of 57-74% moniliformin with a limit of detection at 48 ng/g and a limit of quantification at 96 ng/g using UV detection at 229 nm, which is comparable to current methods used. Limit of detection and quantification using ESI(-)-MS detection was 1 and 12 ng/g, respectively. Screening of maize samples infected with the moniliformin producing fungi F. avenaceum, F. tricinctum, or F. subglutinans detected moniliformin levels of 1-12 ng/g in 15 of 28 samples using ESI(-)-MS detection. To our knowledge this is the first example of HILIC separation in mycotoxin analysis.     

The apparent prevalence of skin lesions suspected to be human-inflicted in Danish finishing pigs at slaughter

Skin lesions on pigs inflicted by humans compromise animal welfare and are the subject of increased public and political attention in Denmark. Systematic surveillance of such skin lesions was enforced in April 2010 at all Danish pig abattoirs, through the recording of meat inspection Code 904 for the presence of skin lesions suspected to be human inflicted. The objectives of the present study were to (a) estimate the apparent prevalence of Code 904s at the pig and herd owner level; (b) characterise the distribution of deliveries with pigs demonstrating a Code 904; (c) characterise the distribution of herd owners with repeated Code 904 recordings; and (d) determine the developments in Code 904 prevalence over time in Danish finishing pigs in the period from May 1, 2010 to September 30, 2013.     

Herd diagnosis of low pathogen diarrhoea in growing pigs – a pilot study

Background

The major indication for antibiotic use in Danish pigs is treatment of intestinal diseases post weaning. Clinical decisions on antibiotic batch medication are often based on inspection of diarrhoeic pools on the pen floor. In some of these treated diarrhoea outbreaks, intestinal pathogens can only be demonstrated in a small number of pigs within the treated group (low pathogen diarrhoea). Termination of antibiotic batch medication in herds suffering from such diarrhoea could potentially reduce the consumption of antibiotics in the pig industry. The objective of the present pilot study was to suggest criteria for herd diagnosis of low pathogen diarrhoea in growing pigs.Data previously collected from 20 Danish herds were used to create a case series of clinical diarrhoea outbreaks normally subjected to antibiotic treatment. In the present study, these diarrhoea outbreaks were classified as low pathogen (<15% of the pigs having bacterial intestinal disease) (n =5 outbreaks) or high pathogen (≥15% of the pigs having bacterial intestinal disease) (n =15 outbreaks). Based on the case series, different diagnostic procedures were explored, and criteria for herd diagnosis of low pathogen diarrhoea were suggested. The effect of sampling variation was explored by simulation.

Results

The diagnostic procedure with the highest combined herd-level sensitivity and specificity was qPCR testing of a pooled sample containing 20 randomly selected faecal samples. The criteria for a positive test result (high pathogen diarrhoea outbreak) were an average of 1.5 diarrhoeic faecal pools on the floor of each pen in the room under investigation and a pathogenic bacterial load ≥35,000 per gram in the faecal pool tested by qPCR. The bacterial load was the sum of Lawsonia intracellularis, Brachyspira pilosicoli and Escherichia coli F4 and F18 bacteria per gram faeces. The herd-diagnostic performance was (herd-level) diagnostic sensitivity =0.99, diagnostic specificity =0.80, positive predictive value =0.94 and negative predictive value =0.96.

Conclusions

The pilot study suggests criteria for herd diagnosis of low pathogen diarrhoea in growing pigs. The suggested criteria should now be evaluated, and the effect of terminating antibiotic batch medication in herds identified as suffering from low pathogen diarrhoea should be explored.

Electronic supplementary material

The online version of this article (doi:10.1186/2046-0481-67-24) contains supplementary material, which is available to authorized users.     

Approaches to formulating practical breeding objectives for animal production systems

Abstract

This review paper provides an overview of the role of breeding objectives in livestock industries. The analyst developing a breeding objective must use the many and varied tools available in an appropriate theoretical context to quantify the benefits of alternative trait changes. The development in tools for deriving economic values has been from simple profit equations to detailed bio-economic models simulating the whole production system or industry. The importance of including the perspective of the stakeholders is also stressed. Stakeholder perspectives can be considered by using stated preference methods such as choice experiments. Also desired gain index or selection indices can be used in combination with profit equations or bio-economic models to adjust for undesirable genetic changes in breeding objective traits. This review shows that defining appropriate breeding objectives to account for the perspectives of different key stakeholders requires a multi-disciplinary approach.     

In silico prediction of Gallibacterium anatis pan-immunogens

The Gram-negative bacterium Gallibacterium anatis is a major cause of salpingitis and peritonitis in commercial egg-layers, leading to reduced egg production and increased mortality. Unfortunately, widespread multidrug resistance and antigenic diversity makes it difficult to control infections and novel prevention strategies are urgently needed. In this study, a pan-genomic reverse vaccinology (RV) approach was used to identify potential vaccine candidates. Firstly, the genomes of 10 selected Gallibacterium strains were analyzed and proteins selected on the following criteria; predicted surface-exposure or secretion, none or one transmembrane helix (TMH), and presence in six or more of the 10 genomes. In total, 42 proteins were selected. The genes encoding 27 of these proteins were successfully cloned in Escherichia coli and the proteins expressed and purified. To reduce the number of vaccine candidates for in vivo testing, each of the purified recombinant proteins was screened by ELISA for their ability to elicit a significant serological response with serum from chickens that had been infected with G. anatis. Additionally, an in silico prediction of the protective potential was carried out based on a protein property prediction method. Of the 27 proteins, two novel putative immunogens were identified; Gab_1309 and Gab_2312. Moreover, three previously characterized virulence factors; GtxA, FlfA and Gab_2156, were identified. Thus, by combining the pan-genomic RV approach with subsequent in vitro and in silico screening, we have narrowed down the pan-proteome of G. anatis to five vaccine candidates. Importantly, preliminary immunization trials indicated an in vivo protective potential of GtxA-N, FlfA and Gab_1309.

Electronic supplementary material

The online version of this article (doi:10.1186/s13567-014-0080-0) contains supplementary material, which is available to authorized users.     

Amino acid digestibility of heat damaged distillers dried grains with solubles fed to pigs

The primary objective of this experiment was to determine the effects of heat treatment on the standardized ileal digestibility(SID) of amino acids(AA) in corn distillers dried grains with solubles(DDGS) fed to growing pigs. The second objective was to develop regression equations that may be used to predict the concentration of SID AA in corn DDGS. A source of corn DDGS was divided into 4 batches that were either not autoclaved or autoclaved at130°C for 10, 20, or 30 min. Four diets containing DDGS from each of the 4 batches were formulated with DDGS being the only source of AA and CP in the diets. A N-free diet also was formulated and used to determine the basal endogenous losses of CP and AA. Ten growing pigs(initial BW: 53.5 ± 3.9 kg) were surgically equipped with a T-cannula in the distal ileum and allotted to a replicated 5 × 4 Youden square design with 5 diets and 4 periods in each square. The SID of CP decreased linearly(P 0.05) from 77.9% in non-autoclaved DDGS to 72.1, 66.1, and 68.5% in the DDGS samples that were autoclaved for 10, 20, or 30 min, respectively. The SID of lysine was quadratically reduced(P 0.05) from 66.8% in the non-autoclaved DDGS to 54.9, 55.3, and 51.9% in the DDGS autoclaved for 10, 20, or30 min, respectively. The concentrations of SID Arginine, Histidine, Leucine, Lysine, Methionine, Phenylalanine, or Threonine may be best predicted by equations that include the concentration of acid detergent insoluble N in the model(r2= 0.76, 0.68, 0.67, 0.84, 0.76, 0.73, or 0.54, respectively). The concentrations of SID Isoleucine and Valine were predicted(r2= 0.58 and 0.54, respectively) by the Lysine:CP ratio, whereas the concentration of SID Tryptophan was predicted(r2= 0.70) by the analyzed concentration of Tryptophan in DDGS. In conclusion, the SID of AA is decreased as a result of heat damage and the concentration of SID AA in heat-damaged DDGS may be predicted by regression equations developed in this experiment.