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Studies indicate that the evaluation of animal welfare in birds may be carried out with the measurement of the stress-related hormone corticosterone in feathers. However a standardized procedure for corticosterone measurements in feathers is lacking, a validation needs to be carried out for each new species before implementation. The aim of the present study was to establish a valid method to measure corticosterone concentrations in feathers of laying hens in a precise and repeatable manner using an established and commercially available ELISA. Validation was performed with feather pools of tail and interscapular feathers of commercial Lohmann Brown laying hens. Assessment groups, consisting of 5 replicates, were created. All replicates of an assessment group were processed at the same time. Each replicate was run in 4 repetitions by ELISA. Intra-assay and interassay CV was 7.5 and 6.4%, respectively. The serial dilution showed linearity and parallelism. Examining the hormone extraction efficiency by using different methanol volumes resulted in no statistical differences (P > 0.05). Pulverized feathers showed higher corticosterone values than minced feathers (P > 0.05). Differences were shown between 2 feather types (tail vs. interscapular feathers; P 0.05). With the present study, a valid protocol, feasible for analyzing feather pools of laying hens, was developed. It may provide fundamentals for further investigations on corticosterone in feathers as a noninvasive indicator to evaluate aspects of animal welfare.

The present study was conducted to examine effects of long-term graded L-arginine supply on growth development, egg laying and egg quality in four genetically diverse purebred layer lines. The study comprised a rearing trial from hatch to week 16 and a following laying performance trial from week 17 to 41. After hatch 150 one-day-old female chicks of each genotype were distributed to three diets. The experimental diets were equivalent to 70, 100 and 200% L-arginine of age-specific recommended level (National Research Council, 1994) and were offered ad libitum to chicks (hatch to week 7), pullets (week 8 to 16) and hens (week 17 to 41). However, hens' diets were quite low in crude protein. After a pre-laying period from week 17 to 21 thirty-six pullets of each group were used further in the laying performance trial. Independent of chicken's genetic background, insufficient L-arginine supply caused lower body weight, daily weight gain and daily feed intake during the rearing (p

Little information has been available about the influence of genetic background and dietary L-arginine (Arg) supply on organ growth of chickens. Therefore, the present study examined the effects of a graded ad libitum Arg supply providing 70, 100 and 200% of recommended Arg concentration on organ growth of female chickens from hatch to 18 weeks of age. The chickens derived from four layer lines of different phylogeny (white vs. brown) and laying performance (high vs. low). Based on residual feed and absolute body and organ weights recorded in six-week-intervals, feed consumption, changes of relative organ weights and allometric organ growth were compared between experimental groups. Surplus Arg caused higher feed intake than insufficient Arg (p

Results: Several single nucleotide polymorphisms on chromosome 1 between 104 and 110 Mb (galGal6) had highly significant associations with tibial breaking strength. The alternative genotypes of markers of large effect that flanked the region had tibial breaking strengths of 200.4 vs. 218.1 Newton (P < 0.002) and, in a subsequent founder generation, the higher breaking strength genotype was again associated with higher breaking strength. In a subsequent generation, cortical bone density and volume were increased in individuals with the better bone genotype but with significantly reduced medullary bone quality. The effects on cortical bone density were confirmed in a further generation and was accompanied by increased mineral maturity of the cortical bone as measured by infrared spectrometry and there was evidence of better collagen cross-linking in the cortical bone. Comparing the transcriptome of the tibia from individuals with good or poor bone quality genotypes indicated four differentially-expressed genes at the locus, one gene, cystathionine beta synthase (CBS), having a nine-fold higher expression in the genotype for low bone quality. The mechanism was cis-acting and although there was an amino-acid difference in the CBS protein between the genotypes, there was no difference in the activity of the enzyme. Plasma homocysteine concentration, the substrate of CBS, was higher in the poor bone quality genotype. Conclusions: Validated markers that predict bone strength have been defined for selective breeding and a gene was identified that may suggest alternative ways to improve bone health in addition to genetic selection. The identification of how genetic variants affect different aspects of bone turnover shows potential for translational medicine., The work was supported through an ERANET by the Biotechnology and Biological Sciences Research Council, UK grant ‘Better Bones’ BB/M028291/1, FORMAS 2014-01840, Investigación y Tecnología Agraria y Alimentaria 291815. The Roslin Institute is funded with a BBSRC Institute strategic programme grant BB/J004316/1.

The genotype of chickens is assumed to be associated with variable immune responses. In this study a modern, moderate performing dual-purpose chicken line (DT) was compared with a high-performing layer-type (LT) as well as a broiler-type (BT) chicken line. One group of each genotype was vaccinated in ovo with a recombinant herpesvirus of turkeys expressing the virus protein VP2 of the infectious bursal disease virus (HVT-IBD) while one group of each genotype was left HVT-IBD unvaccinated (control group). Genotype associated differences in innate and adapted immune responses between the groups were determined over five weeks post hatch. HVT-IBD vaccination significantly enhanced humoral immune responses against subsequently applied live vaccines compared to non-HVT-IBD vaccinated groups at some of the investigated time points (P < 0.05). In addition HVT-IBD vaccination had depending on the genotype a significant impact on splenic macrophage as well as bursal CD4+ T-cell numbers (P < 0.05). On the other hand, the detectable genotype influence on Interferon (IFN) γ and nitric oxide (NO) release of ex vivo stimulated spleen cells was independent of HVT-IBD vaccination. The results of our study suggest considering a genotype specific vaccination regime in the field.

Measuring corticosterone concentrations in feathers of poultry may be suitable to determine birds' exposure to stress. It is thinkable, that in laying hens such information could be helpful as an animal welfare indicator to evaluate adverse husbandry conditions and to predict the risk of developing behavioral disorders, such as feather pecking and cannibalism. Yet, there are some fundamental issues which remain unclear. Therefore, the objective of the current pilot study was to examine the inter- and intraindividual variation of pullets at the end of the rearing period, when most of the feathers are fully grown and animals are reaching sexual maturity. Flight feathers from both wings (n = 4), the tail (n = 2 – 3), and body feathers (n = 1 pool of 3 – 5 feathers) were taken from pullets (n = 10), genetics Lohmann Brown, at an age of 19 weeks who were reared in the same flock (N = 728). Corticosterone analysis was performed applying a validated protocol for laying hens. Results indicate not only high intraindividual, but also high interindividual variation. Mean over all samples was 75.2 pg/mg (± 38.58 pg/mg, n = 76), showing higher intraindividual variation (between feather types; SD: 23.75 pg/mg – 49.38 pg/mg; n = 10 pullets) than interindividual variation (within feather types; SD: 11.91 pg/mg – 49.55 pg/mg; n = 6 feather types). The variation between different feather types within one bird was higher than the variation within one feather type between different birds, indicating that birds a) may respond differently when exposed to stressors and b) corticosterone measurements should be done with the same feather type.

To evaluate the effect of selection for high laying performance on the capacity to respond to an infection with avian influenza virus (AIV), four different chicken lines were tested: A white layer and a brown layer breed originating from a commercial breeding program, and a white layer and a brown layer line maintained as a conservation flock for decades without any selection. The different chicken breeds were infected with AIV of different pathotypes (low pathogenic to high pathogenic) to evaluate and compare their immunological competence. Morbidity and mortality rates, as well as viral shedding, were investigated as parameters of virus infection. Immune cells in blood samples collected after different time points following inoculation were identified. In general, the chickens of the two phylogenetically related brown layer lines (irrespective of the performance type) were more resistant to infection with the selected AIVs, reflected by a lower mortality rate (low virulent AIV) or a prolonged length of survival before succumbing to the disease (highly virulent AIV). Corresponding to these results, CD8-positive cell counts were reduced in both white layer lines. This observation was also confirmed in an in vivo allogenic transfer experiment, in which brown layers eliminated the transferred cells in a shorter time period. In conclusion, our results do not support the theory of reduced immunological competence of high-performance layer breeds, at least against AIV infection. Instead, brown layer strains had a faster CD8-positive immune cell response after viral or allogenic stimulus than the phylogenetically distant white layers, resulting in better resistance against AIV infection.

Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker-assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F2 population to include 1599 F2 females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n = 692 females) and a Hy-Line White Plymouth Rock line (n = 290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4-13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F2 population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker-assisted selection for improved eggshell quality.

Title of the paper: Genetic analysis of the laying pattern in floor management in terms of new performance parameters for breeding In order to facilitate a specific selection of laying hens which are suitable for alternative housing systems, it will be of advantage if the individual hens were tested in their later husbandry environment. Therefore, a new technology has been developed, the »Weihenstephan Funnel Nest Box«, which enables the automatic recording of these essential performance and nesting behaviour parameters of the individual hens in a group housing system. The exact oviposition times of 263 laying hens of Lohmann Silver line were recorded and used to analyse the laying pattern. Some results which were already pointed out in literature were thus confirmed, other brought new cognitions in terms of the oviposition pattern and about the pause following a laying sequence. A positive genetic correlation between the length of a laying sequence and the subsequent pause durations (rg=+0.49) confirmed the tendency to longer breaks following an increasing laying sequence. The duration of a break was, however, not such an essential criteria for the productivity of a hen. More important in this context was the number of pauses which rises constantly with the number of laying sequences over the whole observation period. When the hens laid in shorter sequences, it was observed that the proportion of sequences grew, which was reflected as smaller number of registered eggs per hen (rg =−0.73). The logical conclusion was the highly positive correlation between the length of a laying sequence and the number of registered eggs (rg =+0.82). Closely associated with the length of a laying sequence, as well as the laying performance, was the parameter time interval between two laid eggs. The time interval between two laid eggs was significant shortened from the first to the third egg within one laying sequence and eventually reached for more than 24 h for most of the hens. The phenotypic and genetic correlation between the time interval and the laying performance was negative (rp =−0.46 and rg =−0.46). The heritability for the time interval was estimated at h²=0.17 which was similar to the heritability for number of eggs (h²=0.20). Slightly higher heritabilities were estimated for the indirect parameter of the time interval, the oviposition time of the third to the fifth egg in a laying sequence (h²=0.25, h²=0.34 and h²=0.29). Valuations in this range would be in regard of new performance testing parameter competitive to the parameter number of eggs and therefore, be tested in further investigations.

Enterococcus faecalis is the major causative agent of amyloid arthropathy in chickens. Given the difficulty of estimating the risk from field strains, the embryo lethality assay (ELA) is proposed in this study as a model to predict the virulence of 68 avian E. faecalis strains. Additionally, Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was used to characterize the genetic diversity of the E. faecalis strains. The ELA was performed 10 times with subsets of 7-8 E. faecalis strains each on a sample of 9987 eggs, including control groups. An estimated 3-24 colony-forming units were inoculated into the allantoic cavity of 10-day-old embryos. The embryonic mortality rate (EMR) was determined by means of candling the eggs over a period of seven days. The ELA was able to distinguish the virulence of the E. faecalis strains. Twenty-six strains were considered as avirulent strains with an EMR of below 40%. Five strains were highly virulent with an EMR above 80%. The remaining 37 strains were classified as strains of moderate virulence, causing an EMR between 40% and 80%. The highest EMR occurred three and four days post-inoculation (p.i.). From the fourth day p.i., almost no embryonic mortality was observed. Therefore, the ELA could be optimized by reducing experiment duration to four days p.i. ERIC-PCR did not cluster the strains according to its virulence, although ERIC banding patterns revealed a considerable genetic diversity. In conclusion, the ELA can be considered a reliable and useful tool to predict the virulence of avian E. faecalis strains.

1. In commercial layer breeding, extensive gene pools are tested and selected for market requirements which must be anticipated at least 5 years ahead. Field results confirm a continuous positive genetic trend in egg output and better feed efficiency which can be converted into land savings. 2. Animal welfare and cage-free housing dominate future needs of the market. Nesting behaviour and minimal tendency to develop feather-pecking or cannibalism without beak treatment are key trait complexes. Stronger shells for longer production cycles without moulting have to be combined with better bones. 3. No single big gene effect can be expected to control the multifactorial problem of feather-pecking. Adjusting the shape of the beak, with a heritability of .10-.25, can contribute to reducing the risk of severe cannibalism. 4. For better skeletal integrity, the assessment of bone quality in pedigree birds housed in enriched cages is done by keel bone palpation or ultrasound measurement of the humerus. Both traits show similar heritabilities in the range of .15-.30 and can be included in a balanced selection approach for performance, quality and welfare traits. 5. The combination of performance testing and genome-wide DNA marker analysis is a promising tool to generate more progress for a balanced performance and behaviour profile.

Enterococcus faecalis is the major pathogen found in field cases of amyloid arthropathy in chickens. Given the need for a better understanding of the virulence mechanisms of the causative strains, the embryo lethality assay (ELA) is proposed in the present study as a model to evaluate the virulence of E. faecalis strains, specifically the pathogenic avian strain K923/96, which was previously related with amyloid arthropathy. Hence, 0.2 ml of five doses of the cited strain (from 2.5 to 2500 colony-forming units (CFU) per ml) were inoculated into the allantoic cavity of 10-day-old embryos. The embryo mortality rate (EMR) was determined by daily candling of the eggs over a period of seven days and based on this information the median lethal dose (LD50) was calculated. The ELA was repeated four times on a sample of 3443 eggs. The infectious dose showed a significant effect on the EMR. The EMR with the doses of 2.5, 5, 25, 250 and 2500 CFU/ml was 43%, 45%, 63%, 90% and 93%, respectively. The estimated dose at LD50 was 6.6 CFU/ml. As expected, the higher the infectious dose, the greater the EMR and the lower the embryo survival time. The highest EMR was recorded after three and four days post-inoculation in all doses. In conclusion, these results can be used as a basis for further researches on the E. faecalis virulence. In order to corroborate its model capacity to predict the virulence of this bacterium, more ELAs with different E. faecalis strains are required.

Summary The cuticle is a proteinaceous layer covering the avian egg and is believed to form a defence to microorganism ingress. In birds that lay eggs in challenging environments, the cuticle is thicker, suggesting evolutionary pressure; however, in poultry, selection pressure for this trait has been removed because of artificial incubation. This study aimed to quantify cuticle deposition and to estimate its genetic parameters and its role on trans-shell penetration of bacteria. Additionally, cuticle proteins were characterised to establish whether alleles for these genes explained variation in deposition. A novel and reliable quantification was achieved using the difference in reflectance of the egg at 650 nm before and after staining with a specific dye. The heritability of this novel measurement was moderate (0.27), and bacteria penetration was dependent on the natural variation in cuticle deposition. Eggs with the best cuticle were never penetrated by bacteria (P

Random regression models allow for analysis of longitudinal data, which together with the use of genomic information are expected to increase accuracy of selection, when compared with analyzing average or total production with pedigree information. The objective of this study was to estimate variance components for egg production over time in a commercial brown egg layer population using genomic relationship information. A random regression reduced animal model with a marker-based relationship matrix was used to estimate genomic breeding values of 3,908 genotyped animals from 6 generations. The first 5 generations were used for training, and predictions were validated in generation 6. Daily egg production up to 46 wk in lay was accumulated into 85,462 biweekly (every 2 wk) records for training, of which 17,570 were recorded on genotyped hens and the remaining on their nongenotyped progeny. The effect of adding additional egg production data of 2,167 nongenotyped sibs of selection candidates [16,037 biweekly (every 2 wk) records] to the training data was also investigated. The model included a 5th order Legendre polynomial nested within hatch-week as fixed effects and random terms for coefficients of quadratic polynomials for genetic and permanent environmental components. Residual variance was assumed heterogeneous among 2-wk periods. Models using pedigree and genomic relationships were compared. Estimates of residual variance were very similar under both models, but the model with genomic relationships resulted in a larger estimate of genetic variance. Heritability estimates increased with age up to mid production and decreased afterward, resulting in an average heritability of 0.20 and 0.33 for pedigree and genomic models. Prediction of total egg number was more accurate with the genomic than with the pedigree-based random regression model (correlation in validation 0.26 vs. 0.16). The genomic model outperformed the pedigree model in most of the 2-wk periods. Thus, results of this study show that random regression reduced animal models can be used in breeding programs using genomic information and can result in substantial improvements in the accuracy of selection for trajectory traits.

SummaryThe pioneering work by Professor Soller et al., among others, on the use of genetic markers to analyze quantitative traits has provided opportunities to discover their genetic architecture in livestock by identifying quantitative trait loci (QTL). The recent availability of high-density singl

The size and orientation of calcium carbonate crystals influence the structure and strength of the eggshells of chickens. In this study, estimates of heritability were found to be high (0.6) for crystal size and moderate (0.3) for crystal orientation. There was a strong positive correlation (0.65) for crystal size and orientation with the thickness of the shell and, in particular, with the thickness of the mammillary layer. Correlations with shell breaking strength were positive but with a high standard error. This was contrary to expectations, as in man-made materials smaller crystals would be stronger. We believe the results of this study support the hypothesis that the structural organization of shell, and in particular the mammillary layer, is influenced by crystal size and orientation, especially during the initial phase of calcification. Genetic associations for crystal measurements were observed between haplotype blocks or individual markers for a number of eggshell matrix proteins. Ovalbumin and ovotransferrin (LTF) markers for example were associated with crystal size, while ovocleidin-116 and ovocalyxin-32 (RARRES1) markers were associated with crystal orientation. The location of these proteins in the eggshell is consistent with different phases of the shell-formation process. In conclusion, the variability of crystal size, and to a lesser extent orientation, appears to have a large genetic component, and the formation of calcite crystals are intimately related to the ultrastructure of the eggshell. Moreover, this study also provides evidence that proteins in the shell influence the variability of crystal traits and, in turn, the shell's thickness profile. The crystal measurements and/or the associated genetic markers may therefore prove to be useful in selection programs to improve eggshell quality.

Good eggshell quality is important for both table egg quality and chicken reproductive performance. Weak eggshells cause economic losses in all production steps. Poor eggshell quality also poses increased risk for Salmonella infections. Eggshell quality has been a difficult trait to improve by traditional breeding, as it can be measured only for females and it is difficult and expensive to measure. Breeding for improved shell quality may therefore benefit from the use of marker-assisted selection. In an effort to find markers linked to eggshell quality, we have used an F(2) population of 668 females to map quantitative trait loci (QTL) affecting eggshell traits (eggshell deformation, breaking force, weight). By using 160 microsatellite markers on 27 chromosomes, we found 11 genome-wide and 15 suggestive QTL for shell traits measured at different times during production. Loci affecting the deformation were found on chromosomes 1, 2, 6, 10, 14 and Z. Loci affecting the breaking force were detected on chromosomes 2, 3, 10, 12 and Z. Loci affecting the shell weight were detected on chromosomes 6, 12, 24 and Z. Each QTL explains between 1.5% and 4.6% of the phenotypic variance, adding up to 10-15% of total phenotypic variance explained for the different traits. No epistatic effects were observed between loci affecting eggshell traits. Because the effects for quality are mainly additive, these results provide a basis for further characterization of the loci to identify closely linked markers to be used in marker-assisted selection.

SABRE-hankkeessa tutkimuspopulaatio koostuu Lohmann Tierzucht jalostusyhtiön kahden eri ruskean linjan risteytyksestä. Noin 2000 kanasta koostuva tutkimussukupolvi oli koko tuotantokauden (elinviikot 18 - 60) tuotannontarkkailussa. Munan laatua tutkittiin Canadian Egg Shell Tester laitteella, jolla saadaan selville munankuoren jousto ja kesto. Kuorenpaino mitattiin kerran 42 viikon iässä. Vuoden 2007 loppuun mennessä tehtiin alustava ominaisuuksiin vaikuttavien kromosomialueiden kartoitus tutkimuspopulaation 668 eläimestä. Kaikista tutkimusukupolven eläimistä ja niiden vanhemmista ja isovanhemmista otettiin verinäyte, josta eristettiin DNA. DNA- merkkeinä käytettiin selkeästi tunnistettavia DNA-jaksoja, joiden paikka kromosomissa on tarkalleen jo määritetty. Näillä merkeillä ei itse ole vaikutusta tutkittavaan ominaisuuteen. Mitä lähempänä tiettyä geenimerkkiä ominaisuuteen vaikuttava geeni sijaitsee, sitä useammin geenimerkki ja geeni periytyvät yhdessä. Tätä tietoa käytetään hyväksi kun tilastotieteen menetelmillä analysoidaan minkä geenimerkin läheisyydessä tutkittavaan ominaisuuteen vaikuttava geeni sijaitsee. Tutkimus käsitti 160 DNA-merkkiä 26 kromosomissa. Tutkimuksessa testattiin erilaisia tilastollisia analyysimalleja sekä geenien yhdysvaikutuksia kuoren laatuominaisuuksiin yhteistyössä Roslin Instituutin kanssa. Kanan genomista löytyi useita kuoren laatuun vaikuttavia kromosomialueita, joista lupaavimmat valittiin jatkotutkimuksiin. Kuoren kestävyyteen ja joustoon sekä alku- että loppumunintakaudella vaikuttavia alueita löytyi kromosomeista 2, 3, 6, 14, ja Z. Jatkokartoituksessa keskitytään näiden alueiden tarkempaan analysointiin koko 2000 eläimen populaatiossa käyttäen lähekkäin sijaitsevia DNA-merkkejä. MTT:ssä keskitytään kromosomeissa 14 ja Z oleviin alueisiin.

The aim of the present study was to evaluate the relationship between Flavincontaining monooxygenase 3 (FMO3) genotype and dietary FMO3 inhibitors on trimethylamine (TMA)-N content in egg yolks of laying hens. Fishy taint is characteristic for the tertiary amine TMA. Rhode Island Red pure breed hens and Lohmann Brown commercial layers were genotyped for non-synonymous A to T polymorphism at position nt1034 of the cDNA of the FMO3 gene. This polymorphism is associated with variation in TMA-N levels in egg yolks. Hens of the FMO3 genotype AA, AT and TT were used for the experiments. Genotypes were equally distributed among the varying experimental diets. As dietary FMO3 inhibitors natural or hydrothermally treated field beans (100 g/kg diet) or rapeseed cake (0, 100 and 300 g/kg diet) were incorporated in the diets. Field beans contain tannins, vicine and convicine as antinutritive substances. Rapeseed cake contains the TMA-precursors glucosinolates and sinapine. TMA was extracted from egg yolks with trichloroacetic acid and analysed as TMA-N by a photometric method. The performance parameters number of laid eggs, egg weight, laying intensity, egg mass, daily feed intake and feed-to-egg-mass ratio were recorded. High amount of TMA-N was found in egg yolk of TT-hens when fed with the experimental diets. In contrast, hens of the AA-genotype and heterozygous AT-hens only exhibited low levels of TMA-N. 300 g rapeseed cake/kg diet reduced performance of hens. No negative effect on performance could be found in the experimental groups fed on natural and hydrothermally treated field beans, respectively. It can be concluded both field beans and rape seed cake at concentrations of antinutritive substances used in this experiment can be fed to brown egg layer hens of the FMO3 genotypes AA and AT without leading to fishy tainted eggs.

E. coli infections in avian species have become an economic threat to the poultry industry worldwide. Several factors have been associated with the virulence of E. coli in avian hosts, but no specific virulence gene has been identified as being entirely responsible for the pathogenicity of avian pathogenic E. coli (APEC). Needless to say, the chicken would serve as the best model organism for unravelling the pathogenic mechanisms of APEC, an extraintestinal pathogen. Five-week-old white leghorn SPF chickens were infected intra-tracheally with a well characterized APEC field strain IMT5155 (O2:K1:H5) using different doses corresponding to the respective models of infection established, that is, the lung colonization model allowing re-isolation of bacteria only from the lung but not from other internal organs, and the systemic infection model. These two models represent the crucial steps in the pathogenesis of APEC infections, including the colonization of the lung epithelium and the spread of bacteria throughout the bloodstream. The read-out system includes a clinical score, pathomorphological changes and bacterial load determination. The lung colonization model has been established and described for the first time in this study, in addition to a comprehensive account of a systemic infection model which enables the study of severe extraintestinal pathogenic E. coli (ExPEC) infections. These in vivo models enable the application of various molecular approaches to study host-pathogen interactions more closely. The most important application of such genetic manipulation techniques is the identification of genes required for extraintestinal virulence, as well as host genes involved in immunity in vivo. The knowledge obtained from these studies serves the dual purpose of shedding light on the nature of virulence itself, as well as providing a route for rational attenuation of the pathogen for vaccine construction, a measure by which extraintestinal infections, including those caused by APEC, could eventually be controlled and prevented in the field.

Osteoporosis, resulting from progressive loss of structural bone during the period of egg-laying in hens, is associated with an increased susceptibility to bone breakage. To study the genetic basis of bone strength, an F(2) cross was produced from lines of hens that had been divergently selected for bone index from a commercial pedigreed White Leghorn population. Quantitative trait loci (QTL) affecting the bone index and component traits of the index (tibiotarsal and humeral strength and keel radiographic density) were mapped using phenotypic data from 372 F(2) individuals in 32 F(1) families. Genotypes for 136 microsatellite markers in 27 linkage groups covering approximately 80% of the genome were analysed for association with phenotypes using within-family regression analyses. There was one significant QTL on chromosome 1 for bone index and the component traits of tibiotarsal and humeral breaking strength. Additive effects for tibiotarsal breaking strength represented 34% of the trait standard deviation and 7.6% of the phenotypic variance of the trait. These QTL for bone quality in poultry are directly relevant to commercial populations.

International audience; Genomic selection (GS) using estimated breeding values (GS-EBV) based on dense marker data is a promising approach for genetic improvement. A simulation study was undertaken to illustrate the opportunities offered by GS for designing breeding programs. It consisted of a selection program for a sex-limited trait in layer chickens, which was developed by deterministic predictions under different scenarios. Later, one of the possible schemes was implemented in a real population of layer chicken.MethodsIn the simulation, the aim was to double the response to selection per year by reducing the generation interval by 50 %, while maintaining the same rate of inbreeding per year. We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year. A multi-trait GS scenario was subsequently implemented in a real population of brown egg laying hens. The population was split into two sub-lines, one was submitted to conventional phenotypic selection, and one was selected based on genomic prediction. At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.ResultsBirds that were selected based on genomic prediction outperformed those that were submitted to conventional selection for most of the 16 traits that were included in the index used for selection. However, although the two programs were designed to achieve the same rate of inbreeding per year, the realized inbreeding per year assessed from pedigree was higher in the genomic selected line than in the conventionally selected line.ConclusionsThe results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

Fishy odor of urine and other secretions is a characteristic of trimethylaminuria in humans, resulting from loss-of-function mutations in the flavin-containing mono-oxygenase isoform FMO3. A similar phenotype exists in cattle, in which a nonsense mutation in the bovine orthologue causes fishy off-flavor in cow's milk. The fishy odor is caused by an elevated level of excreted odorous trimethylamine (TMA), due to deficient oxidation of TMA. We report the mapping of a similar disorder (fishy taint of eggs) and the chicken FMO3 gene to chicken chromosome 8. The only nonsynonymous mutation identified in the chicken FMO3 gene (T329S) changes an evolutionarily highly conserved amino acid and is associated with elevated levels of TMA and fishy taint in the egg yolk in several chicken lines. No differences in the expression of FMO3 were found among individuals with different associated genotypes, indicating that the trait is not caused by a linked polymorphism causing altered expression of the gene. The results support the importance and function of the evolutionarily conserved motif FATGY, which has been speculated to be a substrate recognition pocket of N-hydroxylating siderophore enzymes and flavin-containing mono-oxygenases.

(1) The study was conducted to estimate the heritability, genetic correlations and breeding values of laying hens based on individual records and group mean records. (2) Records of two pure lines from a commercial breeding programme of White Leghorns from three generations housed in single cages and in group cages were used. A total of 8483 and 8817 individual records of lines A and D, respectively, and a total of 1358 (line A) and 1161 (line D) group mean records were analysed. (3) An animal model using Restricted Maximum Likelihood (REML) was used to estimate variance components of individual records. Group mean records were analysed using the sire model, taking heterogeneity of error variance and correlated residual effects into account. Breeding values of sires were estimated based on the BLUP method using a multivariate sire model. Spearman Rank correlations were used to compare sire breeding values estimated from individual records and from group mean records. The traits studied were monthly egg production, cumulative production and egg weight. (4) Heritability estimates based on individual records were higher than from group mean records. Heritabilities for cumulative production records were higher than for monthly production, based on individual as well as group mean records. The estimates of genetic correlations between monthly egg production and cumulative production were moderate to high. Egg production and egg weight recorded individually were highly genetically correlated with those recorded on group means. Sire breeding values estimated from individual records showed high correlations with those from group mean records. (5) Differences in the ranking of sire breeding values estimated from individual vs group mean records were negligible, indicating that no genotype x environment interaction exists. Selection based on individual performance records of laying hens housed in single cages could give a good response on performance of laying hens housed in group cages. Cumulative egg production over periods 1 to 6 is the best trait for the selection programme.

Title of the paper: Genetic evaluation of egg production traits based on additive and dominance models in laying hens The study was conducted to estimate additive and dominance variances for egg production traits of two commercial purebred lines (A & D) of laying hens using an animal model analysis. Breeding values estimated from a dominance model were compared to those from an additive model. In total, 8625 records of line A and 8968 records of line D from three generations were used in the analysis. Every record contained information on the number of eggs laid between 20 and 28 (EN1-2), 28 and 48 (EN3-7) and between 20 and 48 (EN1-7) weeks of age. Further average egg weight (EW), egg weight at 28 (EW1), 33 (EW2) and 40 (EW3) weeks of age were available. An additive animal model and one- and three-trait dominance models including the inbreeding coefficients as covariates were fitted to the data. Simultaneous estimates of the additive and dominance variance components were obtained using the REML method. The estimates of h2 from the dominance models for EN1-2, EN3-7, EN1-7 and EW were 0.40, 0.15, 0.28 and 0.62 for line A and 0.38, 0.16, 0.26 and 0.53 for line D. The ratios d2 of the dominance variance to total variance were moderate for EN (0.12–0.13) and low for EW (0.04–0.07) within line A but relatively low for EN (0.03–0.12) and high for EW (0.12–0.21) within line D. Between the breeding values of the best 100 hens of each generation estimated with the additive and the dominance models for EN1-2, EN3-7, EN1-7 and EW high rank correlations (0.946, 0.896, 0.945 and 0.991 in line A and 0.996, 0.899, 0.971 and 0.951 in line D were found

Background Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds. Results To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93 % validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43–87 % of the InDels were found to be fixed within each line. The majority of detected InDels (86 %) were 1–5 bases and about 63 % were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33 % of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5 % of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction. Conclusions The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1711-1) contains supplementary material, which is available to authorized users.

1. The responses to genetic selection on yolk proportion as a technique for increasing egg dry matter content, an important criterion for the egg-product industry, was investigated in a pedigree flock of White Leghorn hens. 2. Parents were preselected on high and low yolk proportion from a base population. The absolute estimated breeding value for yolk proportion of both groups differed by 3%. The realised selection difference in dry matter content of eggs between groups was more than 1% in the analysed offspring population. 3. Heritability estimates were moderate and dry matter had a lower heritability (h(2) = 0.39) than yolk proportion (h(2) = 0.44). 4. The genetic correlation between yolk proportion and dry matter content was highly positive (rg = 0.91). Genetic correlations with egg weight were negative and would have to be compensated for in a breeding programme (rg = -0.76 with yolk proportion and rg = -0.64 with dry matter content). The genetic correlation between the laying performance and yolk proportion was rg = 0.28 and close to zero (rg = -0.05) for dry matter content. 5. Easy recording and lower undesirable correlations make yolk proportion more suitable for commercial selection compared with egg dry matter content in layer breeding.

Feed efficiency data from multiple generations of a brown egg layer line were analyzed with pedigree- and marker-based methods. Marker information improved accuracy of estimated breeding values (EBV), especially for long-term prediction. Several regions in the genome were found to be associated with feed consumption and efficiency.

SummaryIn commercial egg type chicken breeding three and four way crosses are used to produce commercial layers. The primary breeders are using closed nucleus breeding programmes, with birds kept under maximum biosecurity. All grand parents and parents are produced from a closed nucleus for the world wide demand of commercial layers. The breeding goals have been focused for several decades on increasing number of eggs per hen housed. Additional traits have become more important during the last decade, i.e. feed efficiency, internal and external egg quality and general adaptability. Prior to each selection, weights for individual traits within the selection index are adjusted to meet market demands. Breeding stock and commercial layers have to be bred to perform adequately in a variety of systems ranging from large intensive cage units to free range management under different environmental conditions world-wide.Despite intensive selection for egg production the decrease in genetic variation observed in closed commercial lines is not yet critical. Peak production is approaching the biological limit of one egg a day. During this period genetic and phenotypic variation have been significantly reduced. But for early production (sexual maturity) and late production (persistency) genetic variation is still high. In a mating scheme avoiding full and half sib matings no serious inbreeding depression is observed. To achieve continued future genetic progress, selection pressure will shift to other traits like internal and external egg quality and perhaps behaviour traits which still respond to selection.Primary breeders are responding to this challenge by testing pedigreed cross-line hens in a wide range of environments and housing systems while the pure-line elite stock is kept under conditions of maximum biosecurity. Marker assisted selection is already part of commercial breeding programmes. In the past, blood typing has been used to improve Marek's resistance, whereas today anonymous microsatellites which are linked to traits of economic interest are used for selection. In particular, selection between full sib males can give a major improvement.The whole industry is getting more specialised. While the genetic potential of the birds is improved management and nutrition have also to be adapted to changing demands. The general goal for the future is to breed chickens with the ability to function well within a wider range of production conditions and do not respond to the slightest stress.

Discovery of genes with large effects on economically important traits has for many years been of interest to breeders. The development of SNP panels which cover the whole genome with high density and, more importantly, that can be genotyped on large numbers of individuals at relatively low cost, has opened new opportunities for genome-wide association studies (GWAS). The objective of this study was to find genomic regions associated with egg production and quality traits in layers using analysis methods developed for the purpose of whole genome prediction. Genotypes on over 4500 birds and phenotypes on over 13,000 hens from eight generations of a brown egg layer line were used. Birds were genotyped with a custom 42K Illumina SNP chip. Recorded traits included two egg production and 11 egg quality traits (puncture score, albumen height, yolk weight and shell colour) at early and late stages of production, as well as body weight and age at first egg. Egg weight was previously analysed by Wolc et al. (2012). The Bayesian whole genome prediction model--BayesB (Meuwissen et al. 2001) was used to locate 1 Mb regions that were most strongly associated with each trait. The posterior probability of a 1 Mb window contributing to genetic variation was used as the criterion for suggesting the presence of a quantitative trait locus (QTL) in that window. Depending upon the trait, from 1 to 7 significant (posterior probability0.9) 1 Mb regions were found. The largest QTL, a region explaining 32% of genetic variance, was found on chr4 at 78 Mb for body weight but had pleiotropic effects on other traits. For the other traits, the largest effects were much smaller, explaining7% of genetic variance, with regions on chromosomes 2, 12 and 17 explaining above 5% of genetic variance for albumen height, shell colour and egg production, respectively. In total, 45 of 1043 1 Mb windows were estimated to have a non-zero effect with posterior probability0.9 for one or more traits.

Background A fresh, good quality egg has a firm and gelatinous albumen that anchors the yolk and restricts growth of microbiological pathogens. As the egg ages, the gel-like structure collapses, resulting in thin and runny albumen. Occasionally thin albumen is found in a fresh egg, giving the impression of a low quality product. A mapping population consisting of 1599 F2 hens from a cross between White Rock and Rhode Island Red lines was set up, to identify loci controlling albumen quality. The phenotype for albumen quality was evaluated by albumen height and in Haugh units (HU) measured on three consecutive eggs from each F2 hen at the age of 40 weeks. For the fine-mapping analysis, albumen height and HU were used simultaneously to eliminate contribution of the egg size to the phenotype. Results Linkage analysis in a small population of seven half-sib families (668 F2) with 162 microsatellite markers spread across 27 chromosomes revealed two genome-wide significant regions with additive effects for HU on chromosomes 7 and Z. In addition, two putative genome-wide quantitative trait loci (QTL) regions were identified on chromosomes 4 and 26. The QTL effects ranged from 2 to 4% of the phenotypic variance. The genome-wide significant QTL regions on chromosomes 7 and Z were selected for fine-mapping in the full set composed of 16 half-sib families. In addition, their existence was confirmed by an association analysis in an independent commercial Hy-Line pure line. Conclusions We identified four chicken genomic regions that affect albumen quality. Our results also suggest that genes that affect albumen quality act both directly and indirectly through several different mechanisms. For instance, the QTL regions on both fine-mapped chromosomes 7 and Z overlapped with a previously reported QTL for eggshell quality, indicating that eggshell membranes may play a role in albumen quality.

Background In breeding programs for layers, selection of hens and cocks is based on recording phenotypic data from hens in different housing systems. Genomic information can provide additional information for selection and/or allow for a strong reduction in the generation interval. In this study, a typical conventional layer breeding program using a four-line cross was modeled and the expected genetic progress was derived deterministically with the software ZPLAN+. This non-genomic reference scenario was compared to two genomic breeding programs to determine the best strategy for implementing genomic information in layer breeding programs. Results In scenario I, genomic information was used in addition to all other information available in the conventional breeding program, so the generation interval was the same as in the reference scenario, i.e. 14.5 months. Here, we assumed that either only young cocks or young cocks and hens were genotyped as selection candidates. In scenario II, we assumed that breeders of both sexes were used at the biologically earliest possible age, so that at the time of selection only performance data of the parent generation and genomic information of the selection candidates were available. In this case, the generation interval was reduced to eight months. In both scenarios, the number of genotyped male selection candidates was varied between 800 and 4800 males and two sizes of the calibration set (500 or 2000 animals) were considered. All genomic scenarios increased the expected genetic gain and the economic profit of the breeding program. In scenario II, the increase was much more pronounced and even in the most conservative implementation led to a 60% improvement in genetic gain and economic profit. This increase was in all cases associated with higher breeding costs. Conclusions While genomic selection is shown to have the potential to improve genetic gain in layer breeding programs, its implementation remains a business decision of the breeding company; the possible extra profit for the breeding company depends on whether the customers of breeding stock are willing to pay more for improved genetic quality.

Background Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. Results Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. Conclusions There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens.

Introduction Through the application of genomic or whole-genome selection (Meuwissen et al. 2001), marker information from high-density SNP genotyping can improve accuracy of selection at young ages, shorten generation intervals and provide better control of inbreeding, which should lead to higher genetic gain per time unit. Multiple simulation studies have been conducted showing that the benefits of the technology depend on heritability, number and effects of QTL, population structure, size of the training data set, and other factors (Goddard, 2009). There are however few studies on real data. The objective of this study was to evaluate the accuracy of breeding values estimated using high-density SNP genotypes in predicting the next generation in a commercial layer breeding line, and to compare the accuracy of different methods of breeding value estimation.

Background The availability of larger-scale SNP data sets in the chicken genome allows to achieve a higher resolution of the pattern of linkage disequilibrium (LD). In this study, 36 k and 57 k genotypes from two independent genotyping chips were used to systematically characterize genome-wide extent and structure of LD in the genome of four chicken populations. In total, we analyzed genotypes of 454 animals from two commercial and two experimental populations of white and brown layers which allows to some extent a generalization of the results. Results The number of usable SNPs in this study was 19 k to 37 k in brown layers and 8 k to 19 k in white layers. Our analyzes showed a large difference of LD between the lines of white and brown layers. A mean value of r2 = 0.73 ± 0.36 was observed in pair-wise distances of < 25 Kb for commercial white layers, and it dropped to 0.60 ± 0.38 with distances of 75 to 120 Kb, the interval which includes the average inter-marker space in this line. In contrast, an overall mean value of r2= 0.32 ± 0.33 was observed for SNPs less than 25 Kb apart from each other and dropped to 0.21 ± 0.26 at a distance of 100 kb in commercial brown layers. There was a remarkable similarity of the LD patterns among the two populations of white layers. The same was true for the two populations of brown layers, while the LD pattern between white and brown layers was clearly different. Inferring the population demographic history from LD data resulted in a larger effective population size in brown than white populations, reflecting less inbreeding among brown compared to white egg layers. Conclusions We report comprehensive LD map statistics for the genome of egg laying chickens with an up to 3 times higher resolution compared to the maps available so far. The results were found to be consistent between analyzes based on the parallel SNP chips and across different populations (commercial vs. experimental) within the brown and the white layers. It is concluded that the current density of usable markers in this study is sufficient for association mapping and the implementation of genomic selection in these populations to achieve a similar accuracy as in implementations of association mapping and genomic selection in mammalian farm animals.