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. CRISPR/Cas9 targeted genome editing recently facilitated the generation of genetically modified chickens with a mutation of the chicken ALV-J receptor Na+/H+ exchanger type 1 (chNHE1). In this study, we provide evidence that this mutation protects a commercial chicken line (NHE1ΔW38) against the virulent ALV-J prototype strain HPRS-103. We demonstrate that replication of HPRS-103 is severely impaired in NHE1ΔW38 birds and that ALV-J-specific antigen is not detected in cloacal swabs at later time points. Consistently, infected NHE1ΔW38 chickens gained more weight compared to their non-transgenic counterparts (NHE1W38). Histopathology revealed that NHE1W38 chickens developed ALV-J typical pathology in various organs, while no pathological lesions were detected in NHE1ΔW38 chickens. Taken together, our data revealed that this mutation can render a commercial chicken line resistant to highly pathogenic ALV-J infection, which could aid in fighting this pathogen and improve animal health in the field.

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. 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.

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. 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.

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. Severe economic losses caused by ALV-J remain an unsolved problem in many parts of the world due to inefficient eradication strategies and lack of effective vaccines. ALV-J attachment and entry are mediated through the specific receptor, chicken Na+/H+ exchanger type 1 (chNHE1). The non-conserved amino acid tryptophan 38 (W38) in chNHE1 is crucial for virus entry, making it a favorable target for the introduction of disease resistance. In this study, we obtained ALV-J-resistance in a commercial chicken line by precise deletion of chNHE1 W38, utilizing the CRISPR/Cas9-system in combination with homology directed repair. The genetic modification completely protected cells from infection with a subgroup J retrovirus. W38 deletion did neither have a negative effect on the development nor on the general health condition of the gene edited chickens. Overall, the generation of ALV-J-resistant birds by precise gene editing demonstrates the immense potential of this approach as an alternative disease control strategy in poultry.

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). 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.

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. 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.

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. 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.

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. 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.

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. 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.

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. 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.

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. 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<0.001) and induced lower laying intensity and daily egg mass production in the laying period (p<0.05). Parameters fitted to Gompertz function suggested higher adult body weight in L-arginine supplemented birds compared to insufficient supplied ones (p<0.01). Groups fed with insufficient L-arginine reached age of maximum daily weight gain later and showed lowest maximum daily weight gain (p<0.001). As a consequence of limitations in dietary L-arginine and crude protein, high performing genotypes decreased strongly in body weight, daily feed intake and performance compared to the low performing genotypes. In conclusion, L-arginine modified the amount of weight gain and feed intake, especially in growing chicks and pullets independent of genetic background. The high performing hens were more nutritionally stressed than the low performing ones, because concentrations of dietary crude protein were relatively low.

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 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<0.01) that induced growth depression in turn (p <0.05). During the entire trial chicken's heart, gizzard and liver decreased relatively to their body growth (p<0.001) and showed strong positive correlations among each other. On the contrary, proportions of pancreas and lymphoid organs increased until week 12 (p<0.001) and correlated positively among each other. Due to their opposite growth behaviour (p<0.001), internal organs were assigned to two separate groups. Furthermore, insufficient Arg induced larger proportions of bursa, gizzard and liver compared with a higher Arg supply (p<0.05). In contrast to less Arg containing diets, surplus Arg decreased relative spleen weights (p<0.01). The overall allometric evaluation of data indicated a precocious development of heart, liver, gizzard, pancreas and bursa independent of chicken's genetic and nutritional background. However, insufficient Arg retarded the maturation of spleen and thymus compared with an adequate Arg supply. In conclusion, the present results emphasised the essential function of Arg in layer performance, and indicated different sensitivities of internal organs rather to chicken's dietary Arg supply than to their genetic background.

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. It is well known that most LD measures depend on minor allele frequencies (MAF) of the considered loci and the magnitude of LD is influenced by the physical distances between loci. In the present study, a procedure to compare the LD structure between genomic regions comprising several markers each is suggested. The approach accounts for different scaling factors, namely the distribution of MAF, the distribution of pair-wise differences in MAF, and the physical extent of compared regions, reflected by the distribution of pair-wise physical distances. In the first step, genomic regions are matched based on similarity in these scaling factors. In the second step, chromosome- and genome-wide significance tests for differences in medians of LD measures in each pair are performed. The proposed framework was applied to test the hypothesis that the average LD is different in genic and non-genic regions. This was tested with a genome-wide approach with data sets for humans (Homo sapiens), a highly selected chicken line (Gallus gallus domesticus) and the model plant Arabidopsis thaliana. In all three data sets we found a significantly higher level of LD in genic regions compared to non-genic regions. About 31% more LD was detected genome-wide in genic compared to non-genic regions in Arabidopsis thaliana, followed by 13.6% in human and 6% chicken. Chromosome-wide comparison discovered significant differences on all 5 chromosomes in Arabidopsis thaliana and on one third of the human and of the chicken chromosomes.

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. METHODS: First, we compared the sets of variants detected with different variant callers, namely GATK, freebayes and SAMtools, and checked the quality of genotypes of the called variants in a set of 50 fully sequenced white and brown layers. Second, we assessed the imputation accuracy (measured as the correlation between imputed and true genotype per SNP and per individual, and genotype conflict between father-progeny pairs) when imputing from high density SNP array data to whole-genome sequence using data from around 1000 individuals from six different generations. Three different imputation programs (Minimac, FImpute and IMPUTE2) were checked in different validation scenarios. RESULTS: There were 1,741,573 SNPs detected by all three callers on the studied chromosomes 3, 6, and 28, which was 71.6 % (81.6 %, 88.0 %) of SNPs detected by GATK (SAMtools, freebayes) in total. Genotype concordance (GC) defined as the proportion of individuals whose array-derived genotypes are the same as the sequence-derived genotypes over all non-missing SNPs on the array were 0.98 (GATK), 0.97 (freebayes) and 0.98 (SAMtools). Furthermore, the percentage of variants that had high values (>0.9) for another three measures (non-reference sensitivity, non-reference genotype concordance and precision) were 90 (88, 75) for GATK (SAMtools, freebayes). With all imputation programs, correlation between original and imputed genotypes was >0.95 on average with randomly masked 1000 SNPs from the SNP array and >0.85 for a leave-one-out cross-validation within sequenced individuals. CONCLUSIONS: Performance of all variant callers studied was very good in general, particularly for GATK and SAMtools. FImpute performed slightly worse than Minimac and IMPUTE2 in terms of genotype correlation, especially for SNPs with low minor allele frequency, while it had lowest numbers in Mendelian conflicts in available father-progeny pairs. Correlations of real and imputed genotypes remained constantly high even if individuals to be imputed were several generations away from the sequenced individuals.

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. 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.

Response and inbreeding from a genomic selection experiment in layer chickens.

BACKGROUND: 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. METHODS: In 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. RESULTS: Birds 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. CONCLUSIONS: The results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens.

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. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

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. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.

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. 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.