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Groups of Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) hens were reared under helminth-free conditions and kept afterwards together in a free range system. Mortality rate, body weight development, laying performance and faecal egg counts (FEC) were recorded during a 12 month laying period. At the end of the laying period, 246 LSL and 197 LB hens were necropsied and worms counted following the World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.) guidelines. In addition adult Heterakis gallinarum and Ascaridia galli were sexed and measured for length. Significant (P 0.05) different between the genotypes. There was no significant phenotypic correlation between body weight and worm burden in LSL, whereas it was the case in LB (r = 0.17, P

Due to consistent increases of inbreeding of on average 0.95% per generation in layer populations, selection tools should consider both genetic gain and genetic relationships in the long term. The optimum genetic contribution theory using official estimated breeding values for egg production was applied for 3 different lines of a layer breeding program to find the optimal allocations of hens and sires. Constraints in different scenarios encompassed restrictions related to additive genetic relationships, the increase of inbreeding, the number of selected sires and hens, and the number of selected offspring per mating. All these constraints enabled higher genetic gain up to 10.9% at the same level of additive genetic relationships or in lower relationships at the same gain when compared with conventional selection schemes ignoring relationships. Increases of inbreeding and genetic gain were associated with the number of selected sires. For the lowest level of the allowed average relationship at 10%, the optimal number of sires was 70 and the estimated breeding value for egg production of the selected group was 127.9. At the highest relationship constraint (16%), the optimal number of sires decreased to 15, and the average genetic value increased to 139.7. Contributions from selected sires and hens were used to develop specific mating plans to minimize inbreeding in the following generation by applying a simulated annealing algorithm. The additional reduction of average additive genetic relationships for matings was up to 44.9%. An innovative deterministic approach to estimate kinship coefficients between and within defined selection groups based on gene flow theory was applied to compare increases of inbreeding from random matings with layer populations undergoing selection. Large differences in rates of inbreeding were found, and they underline the necessity to establish selection tools controlling long-term relationships. Furthermore, it was suggested to use optimum genetic contribution theory for conservation schemes or, for example, the experimental line in our study.

BackgroundSudden limb paresis is a common problem in White Leghorn flocks, affecting about 1% of the chicken population before achievement of sexual maturity. Previously, a similar clinical syndrome has been reported as being caused by inflammatory demyelination of peripheral nerve fibres. Here, we investigated in detail the immunopathology of this paretic syndrome and its possible resemblance to human neuropathies.MethodsNeurologically affected chickens and control animals from one single flock underwent clinical and neuropathological examination. Peripheral nervous system (PNS) alterations were characterised using standard morphological techniques, including nerve fibre teasing and transmission electron microscopy. Infiltrating cells were phenotyped immunohistologically and quantified by flow cytometry. The cytokine expression pattern was assessed by quantitative real-time PCR (qRT-PCR). These investigations were accomplished by MHC genotyping and a PCR screen for Marek's disease virus (MDV).ResultsSpontaneous paresis of White Leghorns is caused by cell-mediated, inflammatory demyelination affecting multiple cranial and spinal nerves and nerve roots with a proximodistal tapering. Clinical manifestation coincides with the employment of humoral immune mechanisms, enrolling plasma cell recruitment, deposition of myelin-bound IgG and antibody-dependent macrophageal myelin-stripping. Disease development was significantly linked to a 539 bp microsatellite in MHC locus LEI0258. An aetiological role for MDV was excluded.ConclusionsThe paretic phase of avian inflammatory demyelinating polyradiculoneuritis immunobiologically resembles the late-acute disease stages of human acute inflammatory demyelinating polyneuropathy, and is characterised by a Th1-to-Th2 shift.

1. Over twelve 28-d laying periods (almost one year), 272 laying hens of the Lohmann Silver strain, individually tagged with transponders, were monitored on their ranging behaviour and laying performance in an aviary system with an adjacent winter garden. 2. From laying periods 1 to 12, the daily frequency of passages between the barn and the winter garden of individual hens, showed an antagonistic trend compared to the average duration of single visits. While the frequency of passages decreased until the end of the recording period to 8 passages per hen and day, the average duration of single visits increased to a maximum of 32 min per hen. 3. The heritability estimates for the traits, length of stay in the winter garden and frequency of passages were higher for the last 5 laying periods than at the beginning of the recording period. For the last 5 laying periods, the estimates for the duration of stay in the winter garden varied between h(2) = 0.21 and 0.32 and for the frequency of passages, between h(2) = 0.30 and 0.49. 4. Most of the estimated heritabilities for the rate of lay were on an expected medium level (h(2) = 0.09 to 0.45). Deviant h(2)-values to a few laying periods were based on low additive genetic variances or high environmental variance. 5. Genetic correlations between both free range traits and the laying performance were negative (r(g length of stay) = -0.34 and r(g passage frequency) = -0.08). 6. Generally, there seems to be a possibility to influence the ranging behaviour through selection. Further investigations with different genotypes and varying dates of exposure to the laying environment, should be carried out to clarify possible influences on other traits and the negative correlation with laying performance.

International audience; Novel and traditional eggshell quality measurements were made from up to 2000 commercial pedigree hens for a candidate gene association analysis with organic eggshell matrix genes: ovocleidin-116, osteopontin (SPP1), ovocalyxin-32 (RARRES1), ovotransferrin (LTF), ovalbumin and ovocalyxin-36, as well as key genes in the maintenance and function of the shell gland [estrogen receptor (ESR1) and carbonic anhydrase II (CAII)]. Associations were found for (i) ovalbumin with breaking strength and shell thickness; (ii) ovocleidin-116 with elastic modulus, shell thickness and egg shape; (iii) RARRES1 with mammillary layer thickness; (iv) ESR1 with dynamic stiffness; (v) SPP1 with fracture toughness and (vi) CAII with egg shape. The marker effects are as large as 17% of trait standard deviations and could be used to improve eggshell quality.

Cracked eggshells result in economic loss and provide a route for pathogenic organisms to enter the egg. Genetic factors that contribute to shell strength are likely to decrease the risk that an egg will crack when subject to insult. A novel measurement, the dynamic stiffness of the eggshell (Kdyn) was examined to determine if it might be used in the genetic selection of hens with improved eggshell characteristics. The measurement is determined from acoustic resonance frequency analysis. The estimates of heritability for the novel measurement of Kdyn were moderately high and ranged from 0.33 to 0.53 depending on the model used for the estimation. The estimates of genetic correlation of Kdyn with eggshell breaking strength (0.49) and static stiffness (0.57) were positive and relatively large as expected. There was a small negative genetic correlation between Kdyn and egg production from 26 to 50 weeks of age (-0.19) and a moderate one from 58 to 74 weeks of age (-0.36). The moderate heritability and relative independence of Kdyn indicates that this measurement could be used successfully in a breeding programme to improve shell quality and to reduce the incidence of cracks.

In poultry breeding programs owned by private companies, selection is done within closed populations based on comprehensive phenotypic data recording in both pure and cross line birds under standardised housing conditions. Due to sex-limited data recording, male selection for egg quality and production traits is based mainly on female sibling tests. Early selection of the most promising male within full sib families will improve the rate of genetic progress and can substantially reduce the generation interval. Several past studies, based mainly on microsatellites, have identified quantitative trait loci (QTL) for production and quality traits with only limited use in commercial programs. Genome-wide selection is still in its initial stages in which 10–40-K single nucleotide polymorphism (SNP) chips have been used so far. Due to sequencing of all major pure lines from DNA pools, a customised 600-K SNP chip has been developed for comprehensive genotyping of all commercial lines. Small-scale line-specific SNP chips will be developed afterwards in order to reduce costs for genotyping of male progeny during rearing periods. Only the most promising young males will be transferred to the breeding farm for performance testing and pedigree reproduction. Parental generation will still be genotyped with the comprehensive SNP chip and used for retraining and for imputing. The first results using 30-K SNP chips were obtained from a commercial line used for training, validation and selection, which have shown improved accuracy of prediction at a young age and so resulted in increased genetic gain. Genome-wide marker-assisted selection must prove its advantages over traditional methods including cost benefits.

Background The predictive ability of genomic estimated breeding values (GEBV) originates both from associations between high-density markers and QTL (Quantitative Trait Loci) and from pedigree information. Thus, GEBV are expected to provide more persistent accuracy over successive generations than breeding values estimated using pedigree-based methods. The objective of this study was to evaluate the accuracy of GEBV in a closed population of layer chickens and to quantify their persistence over five successive generations using marker or pedigree information. Methods The training data consisted of 16 traits and 777 genotyped animals from two generations of a brown-egg layer breeding line, 295 of which had individual phenotype records, while others had phenotypes on 2,738 non-genotyped relatives, or similar data accumulated over up to five generations. Validation data included phenotyped and genotyped birds from five subsequent generations (on average 306 birds/generation). Birds were genotyped for 23,356 segregating SNP. Animal models using genomic or pedigree relationship matrices and Bayesian model averaging methods were used for training analyses. Accuracy was evaluated as the correlation between EBV and phenotype in validation divided by the square root of trait heritability. Results Pedigree relationships in outbred populations are reduced by 50% at each meiosis, therefore accuracy is expected to decrease by the square root of 0.5 every generation, as observed for pedigree-based EBV (Estimated Breeding Values). In contrast the GEBV accuracy was more persistent, although the drop in accuracy was substantial in the first generation. Traits that were considered to be influenced by fewer QTL and to have a higher heritability maintained a higher GEBV accuracy over generations. In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding populations.

The extraintestinal pathogen, avian pathogenic E. coli (APEC), known to cause systemic infections in chickens, is responsible for large economic losses in the poultry industry worldwide. In order to identify genes involved in the early essential stages of pathogenesis, namely adhesion and colonization, Signature-tagged mutagenesis (STM) was applied to a previously established lung colonization model of infection by generating and screening a total of 1,800 mutants of an APEC strain IMT5155 (O2:K1:H5; Sequence type complex 95). The study led to the identification of new genes of interest, including two adhesins, one of which coded for a novel APEC fimbrial adhesin (Yqi) not described for its role in APEC pathogenesis to date. Its gene product has been temporarily designated ExPEC Adhesin I (EA/I) until the adhesin-specific receptor is identified. Deletion of the ExPEC adhesin I gene resulted in reduced colonization ability by APEC strain IMT5155 both in vitro and in vivo. Furthermore, complementation of the adhesin gene restored its ability to colonize epithelial cells in vitro. The ExPEC adhesin I protein was successfully expressed in vitro. Electron microscopy of an afimbriate strain E. coli AAEC189 over-expressed with the putative EA/I gene cluster revealed short fimbrial-like appendages protruding out of the bacterial outer membrane. We observed that this adhesin coding gene yqi is prevalent among extraintestinal pathogenic E. coli (ExPEC) isolates, including APEC (54.4%), uropathogenic E. coli (UPEC) (65.9%) and newborn meningitic E. coli (NMEC) (60.0%), and absent in all of the 153 intestinal pathogenic E. coli strains tested, thereby validating the designation of the adhesin as ExPEC Adhesin I. In addition, prevalence of EA/I was most frequently associated with the B2 group of the EcoR classification and ST95 complex of the multi locus sequence typing (MLST) scheme, with evidence of a positive selection within this highly pathogenic complex. This is the first report of the newly identified and functionally characterized ExPEC adhesin I and its significant role during APEC infection in chickens.

Background The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be found in the analyst’s toolbox and hence are only rarely applied. Results We present a modern dimension reduction method called ’Invariant Coordinate Selection’ (ICS) and its application to high-throughput genotype data. The more commonly known Independent Component Analysis (ICA) is in this framework just a special case of ICS. We use ICS on both, a simulated and a real dataset to demonstrate first some deficiencies of PCA and how ICS is capable to recover the correct subgroups within the simulated data. Second, we apply the ICS method on a chicken dataset and also detect there two subgroups. These subgroups are then further investigated with respect to their genotype to provide further evidence of the biological relevance of the detected subgroup division. Further, we compare the performance of ICS also to five other popular dimension reduction methods. Conclusion The ICS method was able to detect subgroups in data where the PCA fails to detect anything. Hence, we promote the application of ICS to high-throughput genotype data in addition to the established PCA. Especially in statistical programming environments like e.g. R, its application does not add any computational burden to the analysis pipeline. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1589-9) contains supplementary material, which is available to authorized users.

The present study, involving 972 laying hens divided into 162 groups (n = 6), was aimed at the development of an immunisation protocol for laying hens to produce specific egg yolk antibodies. Recombinant bovine somatotropin (rbst), Escherichia coli pilus antigen K88 (K88), human serum immunoglobulin G (IgG), and low density lipoprotein (LDL) were used as antigens, each at four different doses (rbst, K88, LDL: 1μg, 10μg, 100μg, 1mg; IgG: 0.5μg, 5μg, 50μg, 0.5mg). Three subcutaneous or intramuscular immunisations were performed at intervals of four weeks. The adjuvant used was either the lipopeptide Pam3Cys-Ser-(Lys)4 (PCSL) or Freund's incomplete adjuvant (FIA), in two different doses (PCSL: 0.1 and 0.25mg; FIA: 0.1 and 0.25ml). In the four antigen control groups, hens were immunised without any adjuvant. In two negative control groups, only physiological saline was injected. The mean egg weight and egg yield were not influenced by the immunisation procedures. An antigen dose of 10–100g per injection was sufficient to induce high specific antibody titres in the egg yolk. The adjuvant efficacy of PCSL and FIA was proved to be the same (p < 0.05 versus antigen control). With PCSL as adjuvant, some groups showed a tendency to produce even higher specific antibody titres than did FIA groups. A second booster often caused a further significant increase in the amounts of specific antibodies, especially with PCSL. Subcutaneous administration of the antigen together with 250μg PCSL, resulted in a significantly higher immune response than when FIA was used.

Background High density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species. Results We report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P