Detection of QTL for innate: non-specific antibody levels binding LPS and LTA in two independent populations of laying hens

Genetic Variation in Natural and Induced Antibody Responses in Layer Chickens

Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10-6 was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens.

Levels of Circulating IgM and IgY Natural Antibodies in Broiler Chicks: Association with Genotype and Farming Systems

Naturally occurring antibodies (NAbs), which are major components of innate immunity, exist in circulation under healthy conditions without prior antigenic stimulation and are able to recognize both self- and non-self-constituents. The present study aimed at identifying potential immunological differences between commercial fast- and slow-growth broilers (n = 555) raised in conventional and free-range systems, respectively, through the use of the specificity, isotypes and levels of circulating NAbs. The possible beneficial effect of oregano-based dietary supplementation was also evaluated. To this end, serum IgM and IgY NAbs against self- (actin and DNA) and non-self- antigens (trinitrophenol and lipopolysaccharide) were measured by ELISA and further correlated with genotype, season and performance. Significantly higher levels of IgM NAbs against all antigens were found in slow-growth compared to fast-growth broilers. IgM NAb levels were also significantly increased in dietarily supplemented slow-growth broilers versus those consuming standard feed. Moreover, significantly elevated levels of anti-DNA IgY NAbs were found in fast-growth compared to slow-growth broilers, whereas the opposite was observed for anti-LPS IgY NAbs. Multivariate linear regression analysis confirmed multiple interactions between NAb levels, genotype, season and performance. Overall, serum NAbs have proven to be valuable innovative immunotools in the poultry industry, efficiently differentiating fast-growing versus slow-growing broilers, and dietary supplementation of plant extracts can enhance natural immunity.

Relation between redox potential and natural antibody levels in goat kid serum

The redox potential and the natural antibody (NAb) levels are parameters commonly tested to verify the physiological response to stressful situations determined by farming conditions or research needs. In this paper, the redox potential, assessed by different spectrophotometric methods, was related to NAb levels together with total immunoglobulin (tot-Ig) levels in goat kid serum. Reactive oxygen metabolites (ROMs) and ceruloplasmin (CP) oxidase activity were significantly associated with NAb-IgG and NAb-IgM. Nitric oxide metabolites (NOx) and total thiol levels (TTLs) were significantly related to NAb-IgM and tot-IgM, and with NAb-IgG, respectively. A tendency was shown between ROMs and tot-IgM, and between CP and tot-IgM, where, however, the significance levels were above the cut-off values. Total oxidant status (TOS), total antioxidant activity (TAA), determined by the ABTS-based method, the ferric reducing ability of plasma (FRAP), and free radical scavenging activity (FRSA) were associated with neither NAb nor tot-Ig. The obtained results are discussed in light of the possible linkage between the (anti)oxidant status and the innate immune system in goats.

SNP prioritization in targeted sequencing data associated with humoral immune responses in chicken

Our study aimed to identify single nucleotide polymorphisms (SNPs) with a significant impact on the innate immunity represented by antibody response against lipopolysaccharide (LPS) and lipoteichoid acid (LTA) and the adaptive immune response represented toward keyhole limpet hemocyanin (KLH) using the SNP prioritization method. Data set consisted of 288 F2 experimental individuals, created by crossing Green-legged Partridgelike and White Leghorn. The analyzed SNPs were located within 24 short genomic regions of GGA1, GGA2, GGA3, GGA4, GGA9, GGA10, GGA14, GGA18, and GGZ, pre-targeted based on literature references and database information. For the specific antibody response toward KLH at d 0 the most highly prioritized SNP for additive and dominance effects were located on GGA2 in the 3’UTR of MYD88. For the response at d 7, the most highly prioritized SNP pointed at the 3’UTR of MYD88, but potential causal additive variants were located within ADIPOQ and one in PROCR. The highest priority for additive and dominance effects in the antibody response toward lipoteichoic acid at d 0 was attributed to the same SNP, located on GGA2 in the 3’UTR region of MYD88. Two SNPs among the top-10 for additive effect were located in the exon of NOCT. SNPs selected for their additive effect on antibody response toward lipopolysaccharide at d 0 marked 3 genes – NOCT, MYD88, and SNX8, while SNPs selected for their dominance effect marked – NOCT, ADIPOQ, and MYD88. The top-10 variants identified in our study were located in different functional parts of the genome. In the context of causality three groups can be distinguished: variants located in exons of protein coding genes (ADIPOQ, NOCT, PROCR, SNX8), variants within exons of non-coding transcripts, and variants located in genes’ UTR regions. Variants from the first group influence protein structure and variants from both latter groups’ exhibit regulatory roles on DNA (UTR) or RNA (lncRNA).

Sensitivity analysis based on the random forest machine learning algorithm identifies candidate genes for regulation of innate and adaptive immune response of chicken

Two categories of immune responses—innate and adaptive immunity—have both polygenic backgrounds and a significant environmental component. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chickens using machine learning–based sensitivity analysis for single-nucleotide polymorphisms (SNPs) located in candidate genes defined in quantitative trait loci regions. Here the adaptive immunity is represented by the specific antibody response toward keyhole limpet hemocyanin (KLH), whereas the innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). The analysis consisted of 3 basic steps: an identification of candidate SNPs via feature selection, an optimisation of the feature set using recursive feature elimination, and finally a gene-level sensitivity analysis for final selection of models. The predictive model based on 5 genes (MAPK8IP3 CRLF3, UNC13D, ILR9, and PRCKB) explains 14.9% of variance for KLH adaptive response. The models obtained for LTA and LPS use more genes and have lower predictive power, explaining respectively 7.8 and 4.5% of total variance. In comparison, the linear models built on genes identified by a standard statistical analysis explain 1.5, 0.5, and 0.3% of variance for KLH, LTA, and LPS response, respectively. The present study shows that machine learning methods applied to systems with a complex interaction network can discover phenotype-genotype associations with much higher sensitivity than traditional statistical models. It adds contribution to evidence suggesting a role of MAPK8IP3 in the adaptive immune response. It also indicates that CRLF3 is involved in this process as well. Both findings need additional verification.

The genetic basis of natural antibody titers of young healthy pigs and relationships with disease resilience

Background

Disease resilience is the ability to maintain performance under pathogen exposure but is difficult to select for because breeding populations are raised under high health. Selection for resilience requires a trait that is heritable, easy to measure on healthy animals, and genetically correlated with resilience. Natural antibodies (NAb) are important parts of the innate immune system and are found to be heritable and associated with disease susceptibility in dairy cattle and poultry. Our objective was to investigate NAb and total IgG in blood of healthy, young pigs as potential indicator traits for disease resilience.

Results

Data were from Yorkshire x Landrace pigs, with IgG and IgM NAb (four antigens) and total IgG measured by ELISA in blood plasma collected ~ 1 week after weaning, prior to their exposure to a natural polymicrobial challenge. Heritability estimates were lower for IgG NAb (0.12 to 0.24, + 0.05) and for total IgG (0.19 + 0.05) than for IgM NAb (0.33 to 0.53, + 0.07) but maternal effects were larger for IgG NAb (0.41 to 0.52, + 0.03) and for total IgG (0.19 + 0.05) than for IgM NAb (0.00 to 0.10, + 0.04). Phenotypically, IgM NAb titers were moderately correlated with each other (average 0.60), as were IgG NAb titers (average 0.42), but correlations between IgM and IgG NAb titers were weak (average 0.09). Phenotypic correlations of total IgG were moderate with NAb IgG (average 0.46) but weak with NAb IgM (average 0.01). Estimates of genetic correlations among NAb showed similar patterns but with small SE, with estimates averaging 0.76 among IgG NAb, 0.63 among IgM NAb, 0.17 between IgG and IgM NAb, 0.64 between total IgG and IgG NAb, and 0.13 between total IgG and IgM NAb. Phenotypically, pigs that survived had slightly higher levels of NAb and total IgG than pigs that died. Genetically, higher levels of NAb tended to be associated with greater disease resilience based on lower mortality and fewer parenteral antibiotic treatments. Genome-wide association analyses for NAb titers identified several genomic regions, with several candidate genes for immune response.

Conclusions

Levels of NAb in blood of healthy young piglets are heritable and potential genetic indicators of resilience to polymicrobial disease.

Genetic Analysis of a Commercial Egg Laying Line Challenged With Newcastle Disease Virus

In low income countries, chickens play a vital role in daily life. They provide a critical source of protein through egg production and meat. Newcastle disease, caused by avian paramyxovirus type 1, has been ranked as the most devastating disease for scavenging chickens in Africa and Asia. High mortality among flocks infected with velogenic strains leads to a devastating loss of dietary protein and buying power for rural households. Improving the genetic resistance of chickens to Newcastle Disease virus (NDV), in addition to vaccination, is a practical target for improvement of poultry production in low income countries. Because response to NDV has a component of genetic control, it can be influenced through selective breeding. Adding genomic information to a breeding program can increase the amount of genetic progress per generation. In this study, we challenged a commercial egg-laying line with a lentogenic strain of NDV, measured phenotypic responses, collected genotypes, and associated genotypes with phenotypes. Collected phenotypes included viral load at 2 and 6 days post-infection (dpi), antibody levels pre-challenge and 10 dpi, and growth rates pre- and post-challenge. Six suggestive QTL associated with response to NDV and/or growth were identified, including novel and known QTL confirming previously reported associations with related traits. Additionally, previous RNA-seq analysis provided support for several of the genes located in or near the identified QTL. Considering the trend of negative genetic correlation between antibody and Newcastle Disease tolerance (growth under disease) and estimates of moderate to high heritability, we provide evidence that these NDV response traits can be influenced through selective breeding. Producing chickens that perform favorably in challenging environments will ultimately increase the supply of quality protein for human consumption.

Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

Background

Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells.

Results

We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented.

Conclusions

The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3414-7) contains supplementary material, which is available to authorized users.

Evaluation of the effects of dexamethasone-induced stress on levels of natural antibodies in immunized laying hens

Natural antibodies (NAb) are an important humoral component of innate immunity, playing a pivotal role as first line of defence against pathogens even without prior antigen-specific activation or antigen-driven selection. The levels of NAb in plasma of young laying hens were explored in more detail and identified 2,4,6-trinitrophenyl bovine serum albumin (TNP-BSA), as the non-self antigen showing the highest levels of IgΥ- and IgM-NAb. Subsequently, the relation between specific antibody (SpAb) levels and NAb levels, and the effect of dexamethasone (DEX)-induced stress on the acquired Ab response and on NAb levels were examined. According to obtained results, the affinity of NAb and SpAb, measured using the thiocyanate elution method, resulted higher in SpAb than in NAb. After stress induction, IgM-NAb and SpAb levels showed a transient decrease, whereas the levels of IgΥ-NAb were not changed. Moreover, statistical analysis showed positive correlations between IgΥ- and IgM-NAb levels and between IgM-NAb and SpAb levels that are lost as stress has been induced, whereas no correlation was observed between IgΥ-NAb and SpAb levels, neither before nor after the DEX-administration. This indicates that IgM-NAb assessment could be a valid tool to estimate the potential of the acquired Ab response and that the dexamethasone-induced stress condition causes depression of IgM-NAb levels and the acquired Ab response, but it has no evaluable effects on IgΥ-NAb levels.

The identification of loci for immune traits in chickens using a genome-wide association study

The genetic improvement of disease resistance in poultry continues to be a challenge. To identify candidate genes and loci responsible for these traits, genome-wide association studies using the chicken 60k high density single nucleotide polymorphism (SNP) array for six immune traits, total serum immunoglobulin Y (IgY) level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against Avian Influenza Virus (AIV) and Sheep Red Blood Cell (SRBC), were performed. RT-qPCR was used to quantify the relative expression of the identified candidate genes. Nine significantly associated SNPs (P < 2.81E-06) and 30 SNPs reaching the suggestively significant level (P < 5.62E-05) were identified. Five of the 10 SNPs that were suggestively associated with the antibody response to SRBC were located within or close to previously reported QTL regions. Fifteen SNPs reached a suggestive significance level for AIV antibody titer and seven were found on the sex chromosome Z. Seven suggestive markers involving five different SNPs were identified for the numbers of heterophils and lymphocytes, and the heterophil/lymphocyte ratio. Nine significant SNPs, all on chromosome 16, were significantly associated with serum total IgY concentration, and the five most significant were located within a narrow region spanning 6.4kb to 253.4kb (P = 1.20E-14 to 5.33E-08). After testing expression of five candidate genes (IL4I1, CD1b, GNB2L1, TRIM27 and ZNF692) located in this region, changes in IL4I1, CD1b transcripts were consistent with the concentrations of IgY, while abundances of TRIM27 and ZNF692 showed reciprocal changes to those of IgY concentrations. This study has revealed 39 SNPs associated with six immune traits (total serum IgY level, numbers of, and the ratio of heterophils and lymphocytes, and antibody responses against AIV and SRBC) in Beijing-You chickens. The narrow region spanning 247kb on chromosome 16 is an important QTL for serum total IgY concentration. Five candidate genes related to IgY level validated here are novel and may play critical roles in the modulation of immune responses. Potentially useful candidate SNPs for marker-assisted selection for disease resistance are identified. It is highly likely that these candidate genes play roles in various aspects of the immune response in chickens.

Identification of candidate genes and mutations in QTL regions for immune responses in chicken

There are two categories of immune responses – innate and adaptive immunity – both having polygenic backgrounds and a significant environmental component. In our study, adaptive immunity was represented by the specific antibody response toward keyhole limpet hemocyanin (KLH); innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). Defining genetic bases of immune responses leads from defining quantitative trait loci (QTL) toward a single mutation responsible for variation in the phenotypic trait. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chicken by performing an association study of SNPs located in candidate genes defined in QTL regions. Candidate genes and SNPs in QTL regions were selected in silico. SNP association was based on a custom SNP panel, GoldenGate genotyping assay (Illumina) and two statistical models: random mixed model and CAR score. The most significant SNP for immune response toward KLH was located in the JMJD6 gene located on GGA18. Four SNPs in candidate genes FOXJ1 (GGA18), EPHB1 (GGA9), PTGER4 (GGAZ) and PRKCB (GGA14) showed association with natural antibodies for LPS. A single SNP in ITGB4 (GGA18) was associated with natural antibodies for LTA. All associated SNPs mentioned above showed additive effects.

Meta - and combined - QTL analysis of different experiments on immune traits in chickens

Meta and/or combined QTL analysis from multiple studies can improve quantitative trait loci (QTL) position estimates compared to the individual experiments. Hereby we present results of a meta-analysis of QTL on chicken chromosome 9, 14 and 18 using data from three separate experiments and joint QTL analysis for chromosome 14 and 18. Meta QTL analysis uses information from multiple QTLs studies. Joint QTL analysis is based on combining raw data from different QTL experimental populations. QTLs under the study were related to specific antibody response to keyhole lymphet hemocyanin (KLH), and natural antibodies to environmental antigens, lipopolisaccharide (LPS) and lipoteichoic acid (LTA). Meta QTL analysis resulted in narrowing down the confidence interval for two QTLs on GGA14. The first one for natural antibodies against LTA and the second one for specific antibody response toward KLH. Also, a confidence interval of a QTL for natural antibodies against LPS located on GGA18 was narrowed down. Combined QTL analysis was successful for two QTLs: for specific antibody response toward KLH on GGA14, and for natural antibodies against LPS on GGA18. The greatest statistical power for QTL detection in joint analysis was achieved when raw data from segregating half–sib families from different populations under the study was used.

Genome-wide association study for Marek's disease mortality in layer chickens

A genome-wide association study (GWAS) using Bayesian variable selection was performed to determine genomic regions associated with mortality due to Marek's disease virus (MDV) infection in layers. Mortality (%) under experimental disease challenge (500 plaque-forming units of a very virulent plus MDV strain) was recorded for progeny groups (average 15.5 birds; range 3 to 30) of 253 genotyped sires from four generations of a brown-egg layer line. An additional generation of 43 sires with progeny data was used to validate results. Sires were genotyped with a 42K Illumina single-nucleotide polymorphism (SNP) chip. Methods BayesB (pi = 0.995) and BayesCpi, with or without weighting residuals by the size of progeny groups were applied. The proportion of genetic variance contributed by SNPs within each 1-megabase (Mb) genomic region was quantified. Average mortality was 33% but differed significantly between generations. Genetic markers explained about 11% of phenotypic variation in mortality. Correlations between genomic estimated breeding values and percentage of progeny mortality for the validation generation (sons of individuals in training) were 0.12, 0.17, 0.02, and 0.16 for BayesB, weighted BayesB, BayesCpi, and weighted BayesCpi, respectively, when using the whole genome, and 0.03, 0.20, -0.06, and 0.14, when using only SNP from the 10, 1-Mb regions, explaining the largest proportion of genetic variance according to each method. Results suggest that regions on chromosomes 2, 3, 4, 9, 15, 18, and 21 are associated with Marek's disease resistance and can be used for selection and that accounting for the size of progeny groups has a large impact on correct localization of such genomic regions.

Quantitative trait loci associated with the humoral innate immune response in chickens were confirmed in a cross between Green-Legged Partridgelike and White Leghorn

Natural antibodies (NA) create a crucial barrier at the initial steps of the innate humoral immune response. The main role of NA in the defense system is to bind the pathogens at early stages of infection. Different pathogens are recognized by the presence of highly conserved antigen determinant [e.g., lipopolysaccharide (LPS) in gram-negative bacteria or lipoteichoic acid (LTA) in gram-positive bacteria]. In chickens, a different genetic background of NA binds LPS and LTA antigens, encoded by different QTL. The main objective of this work was to confirm known QTL associated with LPS and LTA NA. For this purpose a chicken reference population was created by crossing 2 breeds: a commercial layer, White Leghorn, and a Polish indigenous chicken, Green-Legged Partridgelike. The chromosomal regions analyzed harbored to GGA3, GGA5, GGA6, GGA8, GGA9, GGA10, GGA14, GGA15, GGA18, and GGAZ. The data collected consisted of the NA titers binding LPS and LTA (determined by ELISA at 12 wk of age) as well as the genotypes (30 short tandem repeat markers; average of 3 markers/chromosome, collected for generations F(0), F(1), and F(2)). The analyses were performed with 3 statistical models (paternal and maternal half-sib, line cross, and linkage analysis and linkage disequilibrium) implemented in GridQTL software (http://www.gridqtl.org.uk/). The QTL study of humoral innate immune response traits resulted in the confirmation of 3 QTL associated with NA titers binding LPS (located on GGA9, GGA18, and GGAZ) and 2 QTL associated with NA titers binding LTA (located on GGA5 and GGA14). A set of candidate genes within the regions of the validated QTL has been proposed.

In silico analysis of candidate genes associated with humoral innate immune response in chicken

Background

Production and function of natural antibodies (NAbs) constitutes an important mechanism of the humoral innate immunity in vertebrates. The level of NAbs in chicken is heritable and the genetic background has been partly investigated. However, to date the genetic determination of humoral innate immune response in avian species has not been fully described. The goal of this study was to propose a new set of candidate genes with a potential effect on the NAb phenotype for further SNP association study.

Methods

In silico analysis of positional and functional candidate genes covered 14 QTL regions associated with LPS, LTA & KLH NAbs and located on six chromosomes: GGA5, GGA6, GGA9, GGA14, GGA18 and GGAZ. The function of the genes was subsequently determined based on the NCBI, KEGG, Gene Ontology and InnateDB databases.

Results

As a result, the core panel of 38 genes participating in metabolic pathways of innate immune response was proposed. Most of them were assigned to chromosomes: GGA14, GGA5, GGA6 and GGAZ (13, 9, 8 and 5 genes, respectively). These candidate genes encode proteins predicted to play a role in (i) proliferation, differentiation and function of B lymphocytes; (ii) TLR signalling pathway, and (iii) MAP signalling cascade.

Conclusions

Proposed set of candidate genes is recommended to be included in the follow-up studies to model genetic networks of innate humoral immune response in chicken.

Genetic parameters for levels of natural antibodies in chicken lines divergently selected for specific antibody response

The present study estimated the heritability of natural antibody (NAb) levels binding rabbit red blood cells at the day of immunization with SRBC (NAb0) and 5 d postimmunization (NAb5) in 2 chicken lines divergently selected for specific antibody levels (SpAb) against SRBC and a randombred control line. In addition, genetic correlations between the levels of NAb binding rabbit red blood cells and levels of SpAb binding SRBC were estimated. The heritability of the SpAb level against SRBC was estimated based on data from 23 generations of selection and in total 21,842 chickens. The heritability of NAb levels against rabbit red blood cells was estimated on 1,764 chickens in generations 22 and 23 using a bivariate analysis including the trait under selection (i.e., SpAb responses to SRBC). Maternal environmental effects were accounted for in the analyses. The heritability for SpAb was 0.17, the heritability for NAb0 levels was 0.23, and the heritability for NAb5 was 0.09. The genetic correlation between SpAb and NAb0 was 0.15 and the genetic correlation between SpAb and NAb5 was 0.50. The weak, though positive, genetic correlation between SpAb responses and the NAb0 levels in nonimmunized chickens, as well as the moderate genetic correlation between SpAb responses and the NAb levels 5 d postimmunization with SRBC, suggest that selection for enhanced adaptive immune system results in a positive correlated response of the innate immunity of chickens.

Across-line SNP association study of innate and adaptive immune response in laying hens

The aim of the present study was to detect quantitative trait loci (QTL) for innate and adaptive immunity in laying hens. For this purpose, the associations between 1022 single nucleotide polymorphism (SNP) markers and immune traits were studied in 583 hens from nine different layer lines. Immune traits were natural antibodies for keyhole limpet haemocyanin (KLH) and lipopolysaccharide (LPS) at 20, 40 and 65 weeks, acquired antibodies to the vaccinal virus of Newcastle disease at 20 weeks, and complement activity measured on sheep and bovine red blood cells at 20, 40 and 65 weeks. We adopted a novel approach based on across-line analysis and testing of the SNP-by-line interaction. Among lines, linkage disequilibrium is conserved at shorter distances than in individual lines; therefore, SNPs significantly associated with immune traits across lines are expected to be near the functional mutations. In the analysis, the SNPs that had a significant across-line effect but did not show significant SNP-by-line interaction were identified to test whether the association was consistent in the individual lines. Ultimately, 59 significant associations between SNPs and immune traits were detected. Our results confirmed some previously identified QTL and identified new QTL potentially involved in the immune function. We found evidence for a role of IL17A (chromosome 3) in natural and acquired antibody titres and in the classical and alternative pathways of complement activation. The major histocompatibility genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The IL12B gene on chromosome 13 was associated with natural antibody titres.

Modeling variability in immunocompetence and immunoresponsiveness

The purposes of this paper were to 1) develop a stochastic model that would reflect observed variation between animals and across ages in immunocompetence and responsiveness; and 2) illustrate consequences of this variability for the statistical power of genotype comparisons and selection. A stochastic model of immunocompetence development and responsiveness kinetics was developed. This model enabled variability in immunological variables to be taken into account in the evaluation of challenge and measurement strategies for selection. The characteristics of the variation in model output reflect those observed in the literature, to the extent that variation in the literature shows a consistent pattern; knowledge of true variation and patterns of variation in immunological variables is limited. The model created correlations between immunocompetence and immunoresponsiveness components, as well as correlations within each component across time. These correlations were generally in agreement with literature estimates, where available. The model enabled predictions of the effectiveness of selection for improved health through immunocompetence or immunoresponsiveness. It was predicted that effective selection for increased general immunocompetence to improve health should be done only when baseline immunity has matured. Further, the model implied that selection is unlikely to be successful if it is based only on a single measurement. Problems with low statistical power to detect differences between genotypes can be reduced by increasing challenge age in the experimental design, and one should ensure that the effects of maternal immunity are minimal when the challenge is done. The ability to detect differences between different groups of animals differs substantially with measurement timing because of low repeatabilities of immunocompetence and responsiveness across time. In general, the probability of detecting differences becomes higher when the challenge age is increased. Consequently, both the age at selection and the age at which information is gathered for selection must be considered carefully when designing genetic evaluations.

Identification of quantitative trait loci affecting shank length, body weight and carcass weight from the Japanese cockfighting chicken breed, Oh-Shamo (Japanese Large Game)

We performed a quantitative trait locus (QTL) analysis to map QTLs controlling shank length, body weight, and carcass weight in a resource family of 245 F(2) birds developed from a cross of the large-sized, native, Japanese cockfighting breed, Oh-Shamo (Japanese Large Game), and the White Leghorn breed of chickens. Interval mapping revealed three significant QTLs for shank length on chromosomes 1, 4 and 24 at the experiment-wise 5% level, and a suggestive shank length QTL on chromosome 27 at the experiment-wise 10% level. For body weight two QTLs, one significant and the other suggestive, were identified on chromosomes 4 and 24, respectively. As expected, QTLs for carcass weight, which was highly correlated with body weight (r = 0.95), were detected at the same chromosomal locations as the detected body weight QTLs. Interestingly, the chromosomal locations containing these body weight and carcass weight QTLs coincided with those of two of the four shank length QTLs detected. No QTL with an epistatic interaction effect was discovered for any trait. The total contribution of all detected QTLs to genetic variance was 98.4%, 27.0% and 25.9% for shank length, body weight and carcass weight, respectively, indicating that most shank length QTLs have been identified but many body weight and carcass weight QTLs have been overlooked by the present analysis because of a low coverage rate of the 88 microsatellite markers used here (approximately 46% of the whole genome).

Antibody Responses to Keyhole Limpet Hemocyanin, Lipopolysaccharide, and Newcastle Disease Virus Vaccine in F2 and Backcrosses of White Leghorn Lines Selected for Two Different Immune Response Traits

Planned crosses were designed to produce an F(2) and 2 backcross populations from 2 lines of White Leghorn chickens previously selected over 10 generations for 2 different in vivo immune responses. The selection criteria applied on the 2 grandparental lines were as follows: high antibody response to Newcastle disease virus vaccine 3 wk after vaccination (ND3) and high cell-mediated immune response [response to phytohemagglutinin]. Furthermore a control line was kept by random breeding. The objective of the study was to estimate if the 2 selection criteria applied on the pure lines had changed the level of and type of immune (humoral) response to a new antigen, keyhole limpet hemocyanin (KLH), in the various second-generation progeny groups. In addition, correlations between parameters of acquired and innate immunity were tested. Primary total (IgT) and isotype-specific (IgG and IgM) antibody response to KLH 1 wk after immunization and levels of natural antibodies (NAB) binding to Salmonella enteriditis-derived lipopolysaccharide (LPS) were measured. Although no differences were present between IgM and IgG antibodies to KLH and the phytohemagglutinin skin-swelling response, significant differences were present between all the progeny groups for IgT to KLH and ND3 and NAB binding to LPS. The mean values for IgT to ND3 and KLH were significantly different between the crosses using the selected lines compared with the control line, indicating a contribution of the previous selection. In addition, a sex effect was found for IgM to KLH and NAB to LPS, for which females had a higher response than males in both cases. No interaction between progeny type and sex was found. Furthermore, significant positive correlations were found between NAB to LPS and specific antibody titers to KLH. Finally, the results of the present study demonstrated an interaction between innate and acquired immunity under this strategy of selection and crossbreeding and confirmed the effect of selection on general immune response to a new antigen in second-generation crosses.

Review of Quantitative Trait Loci Identified in the Chicken

Methods for mapping QTL are actively used in the chicken to identify chromosomal regions contributing to variation in traits related to growth, disease resistance, egg production, behavior, and metabolic parameters. However, higher-resolution mapping and better knowledge of the genetic architecture underlying QTL are needed for successful application of this information into breeding programs. Therefore, this paper summarizes and integrates original, primary QTL studies in the chicken to identify basic information on the genetic architecture of quantitative traits in chickens. The results of this review show several instances of consensus of QTL locations for similar traits from independent studies. Furthermore, the consensus of QTL location for different traits and evidence for QTL with parent-of-origin effect, transgressive alleles, epistatic QTL, and QTL x sex interaction in chicken are presented and discussed. This information can be helpful in identifying genes or mutations underlying the QTL and in the application of genomic information in marker-assisted breeding programs.

Probiotics stimulate production of natural antibodies in chickens

Commensal bacteria in the intestine play an important role in the development of immune response. These bacteria interact with cells of the gut-associated lymphoid tissues (GALT). Among cells of the GALT, B-1 cells are of note. These cells are involved in the production of natural antibodies. In the present study, we determined whether manipulation of the intestinal microbiota by administration of probiotics, which we had previously shown to enhance specific systemic antibody response, could affect the development of natural antibodies in the intestines and sera of chickens. Our findings demonstrate that when 1-day-old chicks were treated with probiotics, serum and intestinal antibodies reactive to tetanus toxoid (TT) and Clostridium perfringens alpha-toxin in addition to intestinal immunoglobulin A (IgA) reactive to bovine serum albumin (BSA) were increased in unimmunized chickens. Moreover, IgG antibodies reactive to TT were increased in the intestines of probiotic-treated chickens compared to those of untreated controls. In serum, IgG and IgM reactive to TT and alpha-toxin were increased in probiotic-treated, unimmunized chickens compared to levels in untreated controls. However, no significant difference in serum levels of IgM or IgG response to BSA was observed. These results are suggestive of the induction of natural antibodies in probiotic-treated, unimmunized chickens. Elucidating the role of these antibodies in maintenance of the chicken immune system homeostasis and immune response to pathogens requires further investigation.