A Genetically Engineered Commercial Chicken Line Is Resistant to Highly Pathogenic Avian Leukosis Virus Subgroup J.

Viral diseases remain a major concern for animal health and global food production in modern agriculture. In chickens, avian leukosis virus subgroup J (ALV-J) represents an important pathogen that causes severe economic loss. Until now, no vaccine or antiviral drugs are available against ALV-J and strategies to combat this pathogen in commercial flocks are desperately needed.

Corticosterone in feathers: Inter- and intraindividual variation in pullets and the importance of the feather type.

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.

Acquiring Resistance Against a Retroviral Infection via CRISPR/Cas9 Targeted Genome Editing in a Commercial Chicken Line.

Genome editing technology provides new possibilities for animal breeding and aid in understanding host-pathogen interactions. In poultry, retroviruses display one of the most difficult pathogens to control by conventional strategies such as vaccinations. Avian leukosis virus subgroup J (ALV-J) is an oncogenic, immunosuppressive retrovirus that causes myeloid leukosis and other tumors in chickens.

An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens.

Background: Skeletal damage is a challenge for laying hens because the physiological adaptations required for egg laying make them susceptible to osteoporosis. Previously, we showed that genetic factors explain 40% of the variation in end of lay bone quality and we detected a quantitative trait locus (QTL) of large effect on chicken chromosome 1. The aim of this study was to combine data from the commercial founder White Leghorn population and the F2 mapping population to fine-map this QTL and understand its function in terms of gene expression and physiology.

Immune responses upon in ovo HVT-IBD vaccination vary between different chicken lines.

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).

Innovative layer genetics to handle global challenges in egg production.

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.

Characterization of Enterococcus faecalis isolates by chicken embryo lethality assay and ERIC-PCR.

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.

Chicken embryo lethality assay for determining the lethal dose and virulence of Enterococcus faecalis.

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.

Subgroup detection in genotype data using invariant coordinate selection.

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.

Immunological Competence of Different Domestic Chicken Breeds Against Avian Influenza Infection.

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.

Effects of Graded Dietary L-arginine Supply on Organ Growth in Four Genetically Diverse Layer Lines during Rearing Period.

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 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.

Effects of Long-term Graded L-arginine Supply on Growth Development, Egg Laying and Egg Quality in Four Genetically Diverse Purebred Layer Lines.

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.

A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions.

The understanding of non-random association between loci, termed linkage disequilibrium (LD), plays a central role in genomic research. Since causal mutations are generally not included in genomic marker data, LD between those and available markers is essential for capturing the effects of causal loci on localizing genes responsible for traits. Thus, the interpretation of association studies requires a detailed knowledge of LD patterns.

Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken.

Background: The technical progress in the last decade has made it possible to sequence millions of DNA reads in a relatively short time frame. Several variant callers based on different algorithms have emerged and have made it possible to extract single nucleotide polymorphisms (SNPs) out of the whole-genome sequence. Often, only a few individuals of a population are sequenced completely and imputation is used to obtain genotypes for all sequence-based SNP loci for other individuals, which have been genotyped for a subset of SNPs using a genotyping array.

Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.

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.

Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations.

Population genomic analyses based on 1 million SNPs in commercial egg layers.

Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations.

QTL mapping of egg albumen quality in egg layers.

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.

Efficiency of genomic selection in an established commercial layer breeding program.

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+.

Development of a high density 600K SNP genotyping array for chicken.

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.

A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens.

In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data.

Mapping of QTL affecting incidence of blood and meat inclusions in egg layers.

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.