Dataset Information

Genome-wide association study for bone strength in laying hens.

ABSTRACT: Bone fracture in egg laying hens is a growing welfare and economic concern in the industry. Although environmental conditions and management (especially nutrition) can exacerbate it, the primary cause of bone weakness and the resulting fractures is believed to have a genetic basis. To test this hypothesis, we performed a genome-wide association study to identify the loci associated with bone strength in laying hens. Genotype and phenotype data were obtained from 752 laying hens belonging to the same pure line population. These hens were genotyped for 580,961 SNPs, with 232,021 SNPs remaining after quality control. Each of the SNPs were tested for association with tibial breaking strength using the family-based score test for association. A total of 52 SNPs across chromosomes 1, 3, 8, and 16 were significantly associated with tibial breaking strength with the genome-wide significance threshold set as a corrected P value of 10e-5. Based on the local linkage disequilibrium around the significant SNPs, 5 distinct and novel QTLs were identified on chromosomes 1 (2 QTLs), 3 (1 QTL), 8 (1 QTL) and 16 (1 QTL). The strongest association was detected within the QTL region on chromosome 8, with the most significant SNP having a corrected P value of 4e-7. A number of candidate genes were identified within the QTL regions, including the BRD2 gene that is required for normal bone physiology. Bone-related pathways involving some of the genes were also identified including chloride channel activity, which regulates bone reabsorption, and intermediate filament organization, which plays a role in the regulation of bone mass. Our result supports previous studies that suggest that bone strength is highly regulated by genetics. It is therefore possible to reduce bone fractures in laying hens through genetic selection and ultimately improve hen welfare.

SUBMITTER: Raymond B

PROVIDER: S-EPMC6159512 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Genome-wide association study for bone strength in laying hens.

Raymond Biaty B Johansson Anna Maria AM McCormack Heather Anne HA Fleming Robert Hall RH Schmutz Matthias M Dunn Ian Chisholm IC De Koning Dirk Jan DJ

Journal of animal science 20180601 7

Bone fracture in egg laying hens is a growing welfare and economic concern in the industry. Although environmental conditions and management (especially nutrition) can exacerbate it, the primary cause of bone weakness and the resulting fractures is believed to have a genetic basis. To test this hypothesis, we performed a genome-wide association study to identify the loci associated with bone strength in laying hens. Genotype and phenotype data were obtained from 752 laying hens belonging to the ...[more]

PMID: 29701819

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Project description:BACKGROUND: An association study between single nucleotide polymorphism markers (SNP) and (innate and adaptive) immune parameters but also feather condition score on the back, rump and belly of laying hens was performed. The immune parameters measured in blood samples were natural and acquired antibody titers and complement activity. Feather condition score as a measure of feather damage was determined, this parameter is closely related to feather pecking behavior in hens housed in groups.The aim of the study was to detect associations between genetic markers and immune parameters and feather condition score across nine lines of laying hens, focusing on the feather peckers as well as on the victims of feather pecking. METHODS: A novel approach based on across-line analysis and testing of the SNP-by-line interaction was performed. RESULTS: In total 59 significant associations between SNP and immune traits were detected. Previously identified QTL were confirmed and new associations of genes regulating immune function identified. The IL17A gene (chromosome 3) influences natural and acquired antibody titers and activation of classical and alternative complement pathways. The major histocompatibility complex on chromosome 16 showed significant association with natural and acquired antibody titers and classical complement activity. The IL12B and IRF1 genes on chromosome 13 were associated with natural antibody titers.The direct effect of the genotype of an individual on its feather condition and the associative effect of the genotype of the cage mates on the individual's feather condition were analyzed. The direct genetic effect can be described as the susceptibility to be pecked at, and the associative genetic effect as the propensity to perform feather pecking. Eleven significant associations were detected for the direct effect, and 81 for the associative effect. The serotonin receptor 2C (HTR2C) on chromosome 4 was highlighted in both analyses. CONCLUSIONS: Our results confirmed previously identified QTL and identified new associations of genes regulating immune function. The results for feather condition score supports existing evidence of involvement of the serotonergic system in feather pecking in laying hens. Immune regulatory genes were found to be associated to feather condition score, revealing relationships between the immune system and behavior.

Project description:Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines. Here, we performed a genome-wide association analysis (GWAS) for feather pecking and aggressive pecking behavior, then combined the results with those from the recent selection signature experiment, and linked them to those obtained from a differential gene expression study.A large F2 cross of 960 F2 hens was generated using the divergent lines as founders. Hens were phenotyped for feather pecks delivered (FPD), aggressive pecks delivered (APD), and aggressive pecks received (APR). Individuals were genotyped with the Illumina 60K chicken Infinium iSelect chip. After data filtering, 29,376 SNPs remained for analyses. Single-marker GWAS was performed using a Poisson model. The results were combined with those from the selection signature experiment using Fisher's combined probability test.Numerous significant SNPs were identified for all traits but with low false discovery rates. Nearly all significant SNPs were located in clusters that spanned a maximum of 3 Mb and included at least two significant SNPs. For FPD, four clusters were identified, which increased to 13 based on the meta-analysis (FPDmeta). Seven clusters were identified for APD and three for APR. Eight genes (of the 750 investigated genes located in the FPDmeta clusters) were significantly differentially-expressed in the brain of hens from both lines. One gene, SLC12A9, and the positional candidate gene for APD, GNG2, may be linked to the monomanine signaling pathway, which is involved in feather pecking and aggressive behavior.Combining the results from the GWAS with those of the selection signature experiment substantially increased the statistical power. The behavioral traits were controlled by many genes with small effects and no single SNP had effects large enough to justify its use in marker-assisted selection.

Project description:Keel bone fractures (KBF) in commercial poultry production systems are a major welfare problem with possible economic consequences for the poultry industry. Recent investigations suggest that the overall situation may be worsening. Depending on the housing system, fracture prevalences exceeding 80% have been reported from different countries. No specific causes have yet been identified and this has consequently hampered risk factor identification. The objective of the current study was to investigate the prevalence of KBF in Danish layer hens and to identify risk factors in relation to KBF in all major productions systems, including parent stock production. For risk factor identification, production data from the included flocks was used. In total, 4794 birds from 40 flocks were investigated at end-of-lay. All birds were euthanized on farm and underwent inspection and palpation followed by necropsy. All observations were recorded and subsequently analysed using the SAS statistical software package. In flocks from non-caged systems, fracture prevalence in the range 53%-100%, was observed whereas the prevalence in flocks from enriched cages ranged between 50-98%. Furthermore, often multiple fractures (≥4) were observed in individual birds (range 5-81% of the birds with fractures) depending on the flock. The localization of the fractures at the distal end of the keel bone is highly consistent in all flocks (>96%). Macroscopically the fractures varied morphologically from an appearance with an almost total absence of callus, most frequently observed in caged birds, to large callus formations in and around the fracture lines, which was a typical finding in non-caged birds. Despite being housed under cage-free conditions, parent birds had significantly fewer fractures (all flocks were 60 weeks old) per bird, than other birds from cage-free systems. The body weight at end-of-lay had an effect on the risk of having fractures, heavy hens have significantly fewer fractures at end-of-lay. The older the hens were at onset of lay, the lower was the flock prevalence at end-of-lay. Additionally, the daily egg size at onset of lay was of importance for the risk of developing fractures, the production of heavier eggs initially, resulted in higher fracture prevalence at depopulation. The odds ratio of body weight, (+100 g) was 0.97, age at onset of lay (+1 week) was 0.87 and daily egg weight at onset (+1 gram) was 1.03. In conclusion, the study demonstrated a very high prevalence of KBF in hens from all production systems and identified hen size, age at onset of lay and daily egg weight at onset of lay to be major risk factors for development of KBF in the modern laying hen. Further research regarding this is warranted to strengthen the longevity and enhance the welfare of laying hens.

Project description:Members of Salmonella enterica are frequently involved in egg and egg product related human food poisoning outbreaks worldwide. In Australia, Salmonella Typhimurium is frequently involved in egg and egg product related foodborne illness and Salmonella Mbandaka has also been found to be a contaminant of the layer farm environment. The ability possessed by Salmonella Enteritidis to colonize reproductive organs and contaminate developing eggs has been well-described. However, there are few studies investigating this ability for Salmonella Typhimurium. The hypothesis of this study was that the Salmonella Typhimurium can colonize the gut for a prolonged period of time and that horizontal infection through feces is the main route of egg contamination. At 14 weeks of age hens were orally infected with either S. Typhimurium PT 9 or S. Typhimurium PT 9 and Salmonella Mbandaka. Salmonella shedding in feces and eggs was monitored for 15 weeks post-infection. Egg shell surface and internal contents of eggs laid by infected hens were cultured independently for detection of Salmonella spp. The mean Salmonella load in feces ranged from 1.54 to 63.35 and 0.31 to 98.38 most probable number/g (MPN/g) in the S. Typhimurium and S. Typhimurium + S. Mbandaka group, respectively. No correlation was found between mean fecal Salmonella load and frequency of egg shell contamination. Egg shell contamination was higher in S. Typhimurium + S. Mbandaka infected group (7.2% S. Typhimurium, 14.1% S. Mbandaka) compared to birds infected with S. Typhimurium (5.66%) however, co-infection had no significant impact on egg contamination by S. Typhimurium. Throughout the study Salmonella was not recovered from internal contents of eggs laid by hens. Salmonella was isolated from different segments of oviduct of hens from both the groups, however pathology was not observed on microscopic examination. This study investigated Salmonella shedding for up to 15 weeks p.i which is a longer period of time compared to previously published studies. The findings of current study demonstrated intermittent but persistent fecal shedding of Salmonella after oral infection for up to 15 weeks p.i. Further, egg shell contamination, with lack of internal egg content contamination and the low frequency of reproductive organ infection suggested that horizontal infection through contaminated feces is the main route of egg contamination with S. Typhimurium in laying hens.

Dataset Information

Genome-wide association study for bone strength in laying hens.

Publications

Genome-wide association study for bone strength in laying hens.

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