Comparative Analysis of Different Inbred Chicken Lines Highlights How a Hereditary Inflammatory State Affects Susceptibility to Avian Influenza Virus

Evidence suggests that susceptibility to avian influenza A virus in chickens is influenced by host genetics, but the mechanisms are poorly understood. A previous study demonstrated that inbred line 0 chickens are more resistant to low-pathogenicity avian influenza (LPAI) infection than line CB.12 birds based on viral shedding, but the resistance was not associated with higher AIV-specific IFNγ responses or antibody titres. In this study, we investigated the proportions and cytotoxic capacity of T-cell subpopulations in the spleen and the early immune responses in the respiratory tract, analysing the innate immune transcriptome of lung-derived macrophages following in vitro stimulation with LPAI H7N1 or the TLR7 agonist R848. The more susceptible C.B12 line had a higher proportion of CD8αβ+ γδ and CD4+CD8αα+ αVβ1 T cells, and a significantly higher proportion of the CD8αβ+ γδ and CD8αβ+ αVβ1 T cells expressed CD107a, a surrogate marker of degranulation. Lung macrophages isolated from line C.B12 birds expressed higher levels of the negative regulator genes TRIM29 and IL17REL, whereas macrophages from line 0 birds expressed higher levels of antiviral genes including IRF10 and IRG1. After stimulation with R848, the macrophages from line 0 birds mounted a higher response compared to line C.B12 cells. Together, the higher proportion of unconventional T cells, the higher level of cytotoxic cell degranulation ex vivo and post-stimulation and the lower levels of antiviral gene expression suggest a potential role of immunopathology in mediating susceptibility in C.B12 birds.

Genetic and phenotypic correlations among feed efficiency, immune and production traits in indigenous chicken of Kenya

This study aimed at estimating genetic and phenotypic relationships among feed efficiency, immune and production traits measured pre- (9-20 weeks of age) and post- (12 weeks from on-set of lay) maturity. Production traits were average daily gain (ADG) and average daily feed-intake (ADFI₁) in the pre-maturity period and age at first egg (AFE), average daily feed-intake (ADFI₂) and average daily egg mass (EM) in the post-maturity period. Feed efficiency comprised of residual feed intake (RFI) estimated in both periods. Natural antibodies binding to keyhole limpet hemocyanin (KLH-IgM) and specific antibodies binding to Newcastle disease virus (NDV-IgG) measured at 16 and 28 weeks of age represented immune traits pre- and post-maturity, respectively. In the growing period, 1,820 records on ADG, KLH-IgM and NDV-IgG, and 1,559 records on ADFI₁ and RFI were available for analyses. In the laying period, 1,340 records on AFE, EM, KLH-IgM and NDV-IgG, and 1,288 records on ADFI₂ and RFI were used in the analyses. Bi-variate animal mixed model was fitted to estimate (co)variance components, heritability and correlations among the traits. The model constituted sex, population, generation, line and genotype as fixed effects, and animal and residual effects as random variables. During the growing period, moderate to high heritability (0.36-0.68) was estimated for the production traits and RFI while the antibody traits had low (0.10-0.22) heritability estimates. Post-maturity, the production traits and RFI were moderately (0.30-0.37) heritable while moderate to high (0.25-0.41) heritability was estimated for the antibody traits. Genetic correlations between feed efficiency and production traits in both periods showed that RFI had negative genetic correlations with ADG (-0.47) and EM (-0.56) but was positively correlated with ADFI₁ (0.60), ADFI₂ (0.74) and AFE (0.35). Among immune and production traits, KLH-IgM and NDV-IgG had negative genetic correlations with ADG (-0.22; -0.56), AFE (-0.39; -0.42) and EM (-0.35; -0.16) but were positively correlated with ADFI₁ (0.41; 0.34) and ADFI₂ (0.47; 0.52). Genetic correlations between RFI with KLH-IgM (0.62; 0.33) and NDV-IgG (0.58; 0.50) were positive in both production periods. Feed intake, RFI and antibody traits measured in both production periods were positively correlated with estimates ranging from 0.48 to 0.82. Results from this study indicate selection possibilities to improve production, feed efficiency and immune-competence in indigenous chicken. The genetic correlations suggest that improved feed efficiency would be associated with high growth rates, early maturing chicken, high egg mass and reduced feed intake. In contrast, improved general (KLH-IgM) and specific (NDV-IgG) immunity would result in lower growth rates and egg mass but associated with early sexual maturation and high feed intake. Unfavorable genetic correlations between feed efficiency and immune traits imply that chicken of higher productivity and antibody levels will consume more feed to support both functions. These associations indicate that selective breeding for feed efficiency and immune-competence may have genetic consequences on production traits and should therefore be accounted for in indigenous chicken improvement programs.

Comparative Analysis of the Liver Transcriptome of Beijing You Chickens and Guang Ming Broilers under Salmonella enterica Serovar Typhimurium Infection

Salmonella enterica serovar Typhimurium (ST) is a food-borne pathogen that can infect animals and humans. It is currently the most common bacterial pathogen that negatively affects the poultry industry. Although different chicken breeds have been observed to exhibit diverse resistance to ST infection, the underlying genetic mechanisms remain unclear and the genes involved in this differential disease resistance need to be identified. To overcome this knowledge gap, we used a liver transcriptome analysis to screen differentially expressed genes (DEGs) in two different chicken breeds (local Beijing You (BY) and commercial Guang Ming No. 2 broiler line B (GM)) before and after ST infection. We also performed weighted gene co-expression network analysis (WGCNA) to detect hub genes, and employed selection signal analysis of candidate genes. Three promising genes (EGR1, JUN and FOS) were eventually identified, and were significantly and differentially expressed in the same breed under different conditions, and in the two breeds after ST infection. Hub genes, such as PPFIA4 and ZNF395, were identified using WGCNA, and were associated with the ratio of heterophils to lymphocytes (H/L), an indicator of disease resistance. the present study identified several genes and pathways associated with resistance to ST infection, and found that BY had greater resistance to ST infection than GM. The results obtained provide valuable resources for investigating the mechanisms of resistance to ST infection in different chicken breeds.

Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry

Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avβ-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.

Omics technologies in poultry health and productivity - part 1: current use in poultry research

In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.

Genetic resistance to avian pathogenic Escherichia coli (APEC): current status and opportunities

Infections with avian pathogenic Escherichia coli (APEC) can be extremely detrimental to poultry health and production. Investigating host genetic variation could identify the biological mechanisms that control resistance to this pathogen and allow selection for improved resistance in experimental and commercial poultry populations. In this review, the current knowledge of how host genetics contributes to APEC resistance and future opportunities that would benefit the understanding or application of genetic resistance are discussed. Phenotypes, such as antibody responses, lesion scores, and mortality, revealed that genetic background impacts APEC resistance and interacts with other factors including the environment and challenge conditions. Experiments have used divergent selection for APEC-specific antibody levels to facilitate genetic studies, estimated heritabilities in relevant traits, detected quantitative trait loci using microsatellites, and made associations with sequence variation in the major histocompatibility complex, which collectively suggest that improving APEC resistance through selection is feasible, although genetic control is partial, complex, and highly polygenic. Additionally, functional genomics techniques have identified antimicrobial responses, toll-like receptor and cytokine signalling, and the cell cycle as central pathways in the host response to APEC challenge. Opportunities for future research are discussed, including the expansion of existing lines of research and the application of new technologies that are relevant to the study of host genetics and APEC. This review closes with prospective strategies for improvement of host genetic resistance to APEC.

Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken

Disease control and prevention have been critical factors in the dramatic growth of the poultry industry. Disease resistance in chickens can be improved through genetic selection for immunocompetence. The heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. Our objective was to conduct a genome-wide association study (GWAS) and pathway analysis to identify possible biological mechanisms involved in H/L traits. In this study, GWAS for H/L was performed in 1317 Cobb broilers to identify significant single-nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (p < 1/8068) reached a significant level of association. The significant SNP on GGA 19 (chicken chromosome 19) was in the gene for complement C1q binding protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five identified SNPs (p < 0.05). According to the results of pathway analysis, nine associated pathways (p < 0.05) were identified. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L, and 52 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

The Genetic Architecture of Early Body Temperature and Its Correlation With Salmonella Pullorum Resistance in Three Chicken Breeds

New-born chicks are vulnerable to bacterial infections and not good at regulating body temperature. There is a close relationship between thermal regulation and immunity, however, the underlying mechanism is not well understood. Salmonella Pullorum (SP) is a major concern in developing countries and causes significant economic losses in poultry industry. Early body temperature (EBT) has previously shown to be correlated with host immunity and resistance to pullorum disease. In this study, we challenged three independent chick populations (Beijing You, Dwarf and Rhode Island Red) with SP at 4 days of age, and rectal temperature was measured before and after the SP attack from 2 to 7 days of age. Host defense to SP was evaluated by survival and spleen SP carrier status. The results showed that chicks with higher EBT before SP infection tend to have higher resistance to later SP attack in two populations (Dwarf and Beijing You). The association between EBT before SP attack and SP resistance was non-significant in Rohde Island Red population (P = 0.06), but the trend was consistent with the other two populations. We also found low to moderate heritability in all three populations for EBT before and after the SP attack ranging from 0.14 to 0.20. Genome-wide association studies identified several genomic regions and biological pathways determining EBT before SP attack, which provides candidate functional genes of this trait. Our results reveal the genetic determination of EBT, and the relationship between EBT and SP resistance, providing an alternative strategy for improving SP resistant activities in chicken.

A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens

Background

Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which causes high mortality. Furthermore, an outbreak of SP infection can result in a considerable number of carriers that become potential transmitters, thus, threatening fellow chickens and offspring. In this study, we conducted a genome-wide association study (GWAS) to detect potential genomic loci and candidate genes associated with two disease-related traits: death and carrier state.

Methods

In total, 818 birds were phenotyped for death and carrier state traits through a SP challenge experiment, and genotyped by using a 600 K high-density single nucleotide polymorphism (SNP) array. A GWAS using a single-marker linear mixed model was performed with the GEMMA software. RNA-sequencing on spleen samples was carried out for further identification of candidate genes.

Results

We detected a region that was located between 33.48 and 34.03 Mb on chicken chromosome 4 and was significantly associated with death, with the most significant SNP (rs314483802) accounting for 11.73% of the phenotypic variation. Two candidate genes, FBXW7 and LRBA, were identified as the most promising genes involved in resistance to SP. The expression levels of FBXW7 and LRBA were significantly downregulated after SP infection, which suggests that they may have a role in controlling SP infections. Two other significant loci and related genes (TRAF3 and gga-mir-489) were associated with carrier state, which indicates a different polygenic determinism compared with that of death. In addition, genomic inbreeding coefficients showed no correlation with resistance to SP within each breed in our study.

Conclusions

The results of this GWAS with a carefully organized Salmonella challenge experiment represent an important milestone in understanding the genetics of infectious disease resistance, offer a theoretical basis for breeding SP-resistant chicken lines using marker-assisted selection, and provide new information for salmonellosis research in humans and other animals.

Selective breeding for high natural antibody level increases resistance to avian pathogenic Escherichia coli (APEC) in chickens

Keyhole limpet hemocyanin (KLH)-binding natural antibody (NAb) titers in chickens are heritable, and higher levels have previously been associated with a higher survival. This suggests that selective breeding for higher NAb levels might increase survival by means of improved general disease resistance. Chickens were divergently selected and bred for total NAb levels binding KLH at 16 weeks of age for six generations, resulting in a High NAb selection line and a Low NAb selection line. To for test differences in disease resistance, chickens were challenged with avian pathogenic Escherichia coli (APEC) in two separate experiments. Chickens at 8 days of age received one of four intratracheal inoculations of 0.2 mL phosphate buffered saline (PBS): 1) mock inoculate, 2) with 0.2 mL PBS containing 10^8.20 colony-forming units (CFU)/mL APEC, 3) with 0.2 mL PBS containing 10^6.64 CFU/mL APEC, and 4) with 0.2 mL PBS containing 10^7.55 CFU/mL APEC. Mortality was recorded during 7 days post inoculation. Overall, 50-60% reduced mortality was observed in the High line compared to the Low line for all APEC doses. In addition, morbidity was determined of the surviving chickens at 15 days of age. The High line had lower morbidity scores compared to the Low line. We conclude that selective breeding for high KLH-binding NAb levels at 16 weeks of age increase APEC resistance in early life. This study and previous studies support the hypothesis that KLH-binding NAb might be used as an indicator trait for to selective breed for general disease resistance in an antigen non-specific fashion.

Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek's disease

Background

Marek’s disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. However, the mechanisms of genetic resistance for MD are complex and not fully understood. MD-resistant line 6₃ and MD-susceptible line 7₂ are two highly inbred progenitor lines of White Leghorn. Recombinant Congenic Strains (RCS) were developed from these two lines, which show varied susceptibility to MD.

Results

We investigated genetic structure and genomic signatures across the genome, including the line 6₃ and line 7₂, six RCSs, and two reciprocally crossed flocks between the lines 6₃ and 7₂ (F1 6₃ × 7₂ and F1 7₂ × 6₃) using Affymetrix® Axiom® HD 600 K genotyping array. We observed 18 chickens from RCS lines were specifically clustered into resistance sub-groups distributed around line 6₃. Additionally, homozygosity analysis was employed to explore potential genetic components related to MD resistance, while runs of homozygosity (ROH) are regions of the genome where the identical haplotypes are inherited from each parent. We found several genes including SIK, SOX1, LIG4, SIK1 and TNFSF13B were contained in ROH region identified in resistant group (line 6₃ and RCS), and these genes have been reported that are contribute to immunology and survival. Based on F_ST based population differential analysis, we also identified important genes related to cell death and anti-apoptosis, including AKT1, API5, CDH13, CFDP and USP15, which could be involved in divergent selection during inbreeding process.

Conclusions

Our findings offer valuable insights for understanding the genetic mechanism of resistance to MD and the identified genes could be considered as candidate biomarkers in further evaluation.

Electronic supplementary material

The online version of this article (10.1186/s40104-018-0281-x) contains supplementary material, which is available to authorized users.

Application of omics technologies for a deeper insight into quali-quantitative production traits in broiler chickens: A review

The poultry industry is continuously facing substantial and different challenges such as the increasing cost of feed ingredients, the European Union's ban of antibiotic as growth promoters, the antimicrobial resistance and the high incidence of muscle myopathies and breast meat abnormalities. In the last decade, there has been an extraordinary development of many genomic techniques able to describe global variation of genes, proteins and metabolites expression level. Proper application of these cutting-edge omics technologies (mainly transcriptomics, proteomics and metabolomics) paves the possibility to understand much useful information about the biological processes and pathways behind different complex traits of chickens. The current review aimed to highlight some important knowledge achieved through the application of omics technologies and proteo-genomics data in the field of feed efficiency, nutrition, meat quality and disease resistance in broiler chickens.

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.

Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken

Background

The domestic chicken (Gallus gallus) is widely used as a model in developmental biology and is also an important livestock species. We describe a novel approach to data integration to generate an mRNA expression atlas for the chicken spanning major tissue types and developmental stages, using a diverse range of publicly-archived RNA-seq datasets and new data derived from immune cells and tissues.

Results

Randomly down-sampling RNA-seq datasets to a common depth and quantifying expression against a reference transcriptome using the mRNA quantitation tool Kallisto ensured that disparate datasets explored comparable transcriptomic space. The network analysis tool Graphia was used to extract clusters of co-expressed genes from the resulting expression atlas, many of which were tissue or cell-type restricted, contained transcription factors that have previously been implicated in their regulation, or were otherwise associated with biological processes, such as the cell cycle. The atlas provides a resource for the functional annotation of genes that currently have only a locus ID. We cross-referenced the RNA-seq atlas to a publicly available embryonic Cap Analysis of Gene Expression (CAGE) dataset to infer the developmental time course of organ systems, and to identify a signature of the expansion of tissue macrophage populations during development.

Conclusion

Expression profiles obtained from public RNA-seq datasets – despite being generated by different laboratories using different methodologies – can be made comparable to each other. This meta-analytic approach to RNA-seq can be extended with new datasets from novel tissues, and is applicable to any species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4972-7) contains supplementary material, which is available to authorized users.

Genomic Region Containing Toll-Like Receptor Genes Has a Major Impact on Total IgM Antibodies Including KLH-Binding IgM Natural Antibodies in Chickens

Natural antibodies (NAb) are antigen binding antibodies present in individuals without a previous exposure to this antigen. Keyhole limpet hemocyanin (KLH)-binding NAb levels were previously associated with survival in chickens. This suggests that selective breeding for KLH-binding NAb may increase survival by means of improved general disease resistance. Genome-wide association studies (GWAS) were performed to identify genes underlying genetic variation in NAb levels. The studied population consisted of 1,628 adolescent layer chickens with observations for titers of KLH-binding NAb of the isotypes IgM, IgA, IgG, the total KLH-binding (IgT) NAb titers, total antibody concentrations of the isotypes IgM, IgA, IgG, and the total antibodies concentration in plasma. GWAS were performed using 57,636 single-nucleotide polymorphisms (SNP). One chromosomal region on chromosome 4 was associated with KLH-binding IgT NAb, and total IgM concentration, and especially with KLH-binding IgM NAb. The region of interest was fine mapped by imputing the region of the study population to whole genome sequence, and subsequently performing an association study using the imputed sequence variants. 16 candidate genes were identified, of which FAM114A1, Toll-like receptor 1 family member B (TLR1B), TLR1A, Krüppel-like factor 3 (KLF3) showed the strongest associations. SNP located in coding regions of the candidate genes were checked for predicted changes in protein functioning. One SNP (at 69,965,939 base pairs) received the maximum impact score from two independent prediction tools, which makes this SNP the most likely causal variant. This SNP is located in TLR1A, which suggests a fundamental role of TLR1A on regulation of IgM levels (i.e., KLH-binding IgM NAb, and total IgM concentration), or B cells biology, or both. This study contributes to increased understanding of (genetic) regulation of KLH-binding NAb levels, and total antibody concentrations.

Genetics and genomics of susceptibility and immune response to necrotic enteritis in chicken: a review

Global poultry production is facing many challenges and is currently under pressure due to the presence of several diseases like Necrotic Enteritis (NE). It is estimated that NE-caused global economic losses has increased from 2 billion to 6 billion US$ in 2015 because it is not easy to diagnose and control disease at the earlier stage of occurrence. Additionally, ban on the in-feed antibiotics and some other genetic and non-genetic predisposing factors affect the occurrence of the disease. Though the incidence of the disease can be reduced by minimizing the predisposing factors and through immunization of birds but there is no single remedy to control the disease. Therefore, we suggest that there is need to find out the genetic variants that could help to select the birds resistant to NE. The current review details the pertinent features about the genetic and genomics of susceptibility and immune response of birds to Necrotic Enteritis. We report here the list of candidate gene reported for their involvement with the susceptibility and/or resistance to the disease. However, most of these genes are involved in immune-related functions. For better understanding of the role of Clostridium perfringens and its toxins in the pathogenesis of disease there is need to unveil the association between any specific genetic variation and clinical status of NE. However, the presence of substantial genetic variations among different breeds/strains of chicken shows that it is possible to develop broiler strain with genetic resistant against NE. It would help in the cost-effective and sustainable production of safe broiler meat.

A premature stop codon within the tvb receptor gene results in decreased susceptibility to infection by avian leukosis virus subgroups B, D, and E

Avian leukosis virus (ALV) is an oncogenic virus causing a variety of neoplasms in chickens. The group of avian leukosis virus in chickens contains six closely related subgroups, A to E and J. The prevalence of ALVs in hosts may have imposed strong selective pressure toward resistance to ALVs infection. The tvb gene encodes Tvb receptor and determines susceptibility or resistance to the subgroups B, D, and E ALV. In this study, we characterized a novel resistant allele of the tvb receptor gene, tvbr3, which carries a single-nucleotide substitution (c.298C>T) that constitutes a premature termination codon within the fourth exon and leads to the production of a truncated TvbR3 receptor protein. As a result, we observed decreased susceptibility to infection by ALV-B, ALV-D and ALV-E both in vitro and in vivo, and decreased the binding affinity of the TvbR3 receptor for the subgroups B, D, and E ALV envelope glycoproteins. Additionally, we found that the tvbr3 allele was prevalent in Chinese broiler lines. This study demonstrated that premature termination codon in the tvb receptor gene can confer genetic resistance to subgroups B, D, and E ALV in the host, and indicates that tvbr3 could potentially serve as a resistant target against ALV-B, ALV-D and ALV-E infection.

Characterization of Copy Number Variation's Potential Role in Marek's Disease

Marek’s Disease (MD) is a highly contagious pathogenic and oncogenic disease primarily affecting chickens. Chicken Lines 63 and 72, as well as their recombinant congenic strains (RCS) with varied susceptibility to MD, are ideal models to study the complex mechanisms of genetic resistance to MD. In this study, we investigated copy number variation (CNV) in these inbred chicken lines using the Affymetrix Axiom HD 600 K SNP genotyping array. We detected 393 CNV segments across all ten chicken lines, of which 12 CNVs were specifically identified in Line 72. We then assessed genetic structure based on CNV and observed markedly different patterns. Finally, we validated two deletion events in Line 72 and correlated them with genes expression using qPCR and RNA-seq, respectively. Our combined results indicated that these two CNV deletions were likely to contribute to MD susceptibility.

Emergence and Evolution of Secondary Lymphoid Organs

For effective adaptive immunity to foreign antigens (Ag), secondary lymphoid organs (SLO) provide the confined environment in which Ag-restricted lymphocytes, with very low precursor frequencies, interact with Ag on Ag-presenting cells (APC). The spleen is the primordial SLO, arising in conjunction with adaptive immunity in early jawed vertebrates. The spleen, especially the spleen's lymphoid compartment, the white pulp (WP), has undergone numerous modifications over evolutionary time. We describe the progressive advancement of splenic WP complexity, which evolved in parallel with the increasing functionality of adaptive immunity. The Ag-presenting function of follicular dendritic cells (FDC) also likely emerged at the inception of adaptive immunity, and we propose that a single type of hematopoietically derived APC displayed Ag to both T and B cells. A dedicated FDC, derived from a vascular precursor, is a recent evolutionary innovation that likely permitted the robust affinity maturation found in mammals.

Differential ex vivo responses of primary leukocytes from turkey pedigree lines to Salmonella Heidelberg

Escalating product recalls as a consequence of Salmonella-contaminated poultry products have resulted in detrimental economic impacts in the poultry industry. One potential long-term alternative method to Salmonella prevention is genetic selection to improve innate resistance. This study evaluated the ex vivo effects of Salmonella Heidelberg (SH) on phagocytic and bactericidal leukocyte function in turkeys from six pedigree lines (A-F). Day-of-hatch poults (n = 48) were placed and raised in cages (2 birds/gender/genetic line/cage) to 35 d when heterophils and peripheral blood mononuclear cells (PBMCs) were extracted from males and females of each line. Cells were used in phagocytic and bactericidal assays to determine the ex vivo effects of SH on turkey leukocyte activity. Data were analyzed using the Fit Model platform in JMP Pro 10.0 (SAS Institute Inc.) with differences considered significant at P ≤ 0.05 and data reported as LS Means with SEM. Although genetic line had no significant effect on phagocytosis of SH by heterophils and PBMCs, cumulatively, female cells exhibited higher phagocytosis potential than those from males. The main effect of gender was significant on bactericidal activity of PBMCs when incubated at a 1:10 and 1:100 PBMC to SH ratio. Genetic line also had a significant effect on bactericidal activity of PBMCs with cells from line F exhibiting the best activity. These results suggest that gender had a marked cumulative effect on phagocytosis of SH by heterophils and PBMCs while both genetic line and gender had a prominent effect on bacterial killing of SH by turkey PBMCs. Once able to determine genetic markers associated with these immune responses to Salmonella, genetic selection for increased resistance may become feasible in turkeys.

Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek's disease

Background

Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Lines 6₃ and 7₂ are two highly inbred experimental chicken lines that differ greatly in susceptibility to Marek’s disease (MD), and have been used extensively in efforts to identify the genetic and molecular basis for genetic resistance to MD. Using next generation sequencing, we present a genome-wide assessment of CNVs that are potentially associated with genetic resistance to MD.

Methods

Three chickens randomly selected from each line were sequenced to an average depth of 20×. Two popular software, CNVnator and Pindel, were used to call genomic CNVs separately. The results were combined to obtain a union set of genomic CNVs in the two chicken lines.

Results

A total of 5,680 CNV regions (CNVRs) were identified after merging the two datasets, of which 1,546 and 1,866 were specific to the MD resistant or susceptible line, respectively. Over half of the line-specific CNVRs were shared by 2 or more chickens, reflecting the reduced diversity in both inbred lines. The CNVRs fixed in the susceptible lines were significantly enriched in genes involved in MAPK signaling pathway. We also found 67 CNVRs overlapping with 62 genes previously shown to be strong candidates of the underlying genes responsible for the susceptibility to MD.

Conclusions

Our findings provide new insights into the genetic architecture of the two chicken lines and additional evidence that MAPK signaling pathway may play an important role in host response to MD virus infection. The rich source of line-specific CNVs is valuable for future disease-related association studies in the two chicken lines.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2080-5) contains supplementary material, which is available to authorized users.

Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek's disease is predominantly determined by transcriptional regulation

Background

Marek’s disease (MD) is a lymphoproliferative disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout the chicken genome.

Methods

Hypothesizing that variants located in transcriptional regulatory regions are the main mechanism underlying this complex trait, a genome-wide association study was conducted by genotyping a ~1,000 bird MD resource population derived from experimental inbred layers with SNPs containing 1,824 previously identified allele-specific expression (ASE) SNPs in response to MDV infection as well as 3,097 random SNPs equally spaced throughout the chicken genome. Based on the calculated associations, genomic predictions were determined for 200 roosters and selected sires had their progeny tested for Marek’s disease incidence.

Results

Our analyses indicate that these ASE SNPs account for more than 83 % of the genetic variance and exhibit nearly all the highest associations. To validate these findings, 200 roosters had their genetic merit predicted from the ASE SNPs only, and the top 30 and bottom 30 ranked roosters were reciprocally mated to random hens. The resulting progeny showed that after only one generation of bidirectional selection, there was a 22 % difference in MD incidence and this approach gave a 125 % increase in accuracy compared to current pedigree-based estimates.

Conclusions

We conclude that variation in transcriptional regulation is the major driving cause for genetic resistance to MD, and ASE SNPs identify the underlying genes and are sufficiently linked to the causative polymorphisms that they can be used for accurate genomic prediction as well as help define the underlying molecular basis. Furthermore, this approach should be applicable to other complex traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2016-0) contains supplementary material, which is available to authorized users.

Single nucleotide polymorphism variants within tva and tvb receptor genes in Chinese chickens

Avian leukosis is an immunosuppressive neoplastic disease caused by avian leukosis viruses (ALV), which causes tremendous economic losses in the worldwide poultry industry. The susceptibility or resistance of chicken cells to subgroup A ALV and subgroup B, D, and E ALV are determined by the receptor genes tumor virus locus A (tva) and tumor virus locus B (tvb), respectively. Four genetic resistant loci (tva(r1), tva(r2), tva(r3), and tva(r4)) in tva receptor gene and a genetic resistant locus tvb(r) in the tvb receptor gene have been identified in inbred lines of White Leghorn. To evaluate the genetic resistance to subgroup A, B, D, and E ALV, genetic variations within resistant loci in tva and tvb genes were screened in Chinese local chicken breeds and commercial broiler lines. Here, the heterozygote tva(s1/r1) and the resistant genotype tva(r2/r2), tva(r3/r3), and tva(r4/r4) were detected in Chinese chickens by direct sequencing. The heterozygote tva(s1/r1) was detected in Huiyang Bearded chicken (HYBC), Rizhaoma chicken, and commercial broiler line 13 to 15 (CB13 to CB15), with the frequencies at 0.08, 0.18, 0.17, 0.25, and 0.15, respectively. The resistant genotype tva(r2/r2) was detected in Jiningbairi chicken (JNBRC), HYBC, and CB15, with the frequencies at 0.03, 0.08, and 0.06, respectively, whereas tva(r3/r3) and tva(r4/r4) were detected in 19 and 17 of the 25 Chinese chickens tested, with the average frequencies at 0.13 and 0.20, respectively. Furthermore, the resistant genotype tvb(r/r) was detected in JNBRC, CB07, CB12, CB14, and CB15 by pyrosequencing assay, with the frequencies at 0.03, 0.03, 0.11, 0.09, and 0.15, respectively. These results demonstrated that the potential for genetic improvement of resistance to subgroup A, B, D, and E ALV were great both in Chinese local chickens and commercial broilers. This study provides valuable insight into the selective breeding for chickens genetically resistant to ALV.

RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens

Avian influenza virus (AIV) is a type A virus of the family Orthomyxoviridae. Avian influenza virus infection can cause significant economic losses to the poultry industry, and raises a great public health threat due to potential host jump from animals to humans. To develop more effective intervention strategies to prevent and control AIV infection in poultry, it is essential to elucidate molecular mechanisms of host response to AIV infection in chickens. The objective of this study was to identify genes and signal pathways associated with resistance to AIV infection in 2 genetically distinct highly inbred chicken lines (Fayoumi, relatively resistant to AIV infection, and Leghorn, susceptible to AIV infection). Three-week-old chickens were inoculated with 10(7) EID50 of low pathogenic H5N3 AIV, and lungs and trachea were harvested 4 d postinoculation. Four cDNA libraries (1 library each for infected and noninfected Leghorn, and infected and noninfected Fayoumi) were prepared from the lung samples and sequenced by Illumina Genome Analyzer II, which yielded a total of 116 million, 75-bp single-end reads. Gene expression levels of all annotated chicken genes were analyzed using CLC Genomics Workbench. DESeq was used to identify differentially expressed transcripts between infected and noninfected birds and between genetic lines (false discovery rate < 0.05 and fold-change > 2). Of the expressed transcripts in a total of 17,108 annotated chicken genes in Ensembl database, 82.44 and 81.40% were identified in Leghorn and Fayoumi birds, respectively. The bioinformatics analysis suggests that the hemoglobin family genes, the functional involvements for oxygen transportation and circulation, and cell adhesion molecule signaling pathway play significant roles in disease resistance to AIV infection in chickens. Further investigation of the roles of these candidate genes and signaling pathways in the regulation of host-AIV interaction can lead new directions for the development of antiviral drugs or vaccines in poultry.

Differential expression of Toll-like receptor pathway genes in chicken embryo fibroblasts from chickens resistant and susceptible to Marek's disease

The Toll-like receptor (TLR) signaling pathway is one of the innate immune defense mechanisms against pathogens in vertebrates and invertebrates. However, the role of TLR in non-MHC genetic resistance or susceptibility to Marek's disease (MD) in the chicken is yet to be elucidated. Chicken embryo fibroblast (CEF) cells from MD susceptible and resistant lines were infected either with Marek's disease virus (MDV) or treated with polyionosinic-polycytidylic acid, a synthetic analog of dsRNA, and the expression of TLR and pro-inflammatory cytokines was studied at 8 and 36 h posttreatment by quantitative reverse transcriptase PCR. Findings of the present study reveal that MDV infection and polyionosinic-polycytidylic acid treatment significantly elevated the mRNA expression of TLR3, IL6, and IL8 in both susceptible and resistant lines. Furthermore, basal expression levels in uninfected CEF for TLR3, TLR7, and IL8 genes were significantly higher in resistant chickens compared with those of susceptible chickens. Our results suggest that TLR3 together with pro-inflammatory cytokines may play a significant role in genetic resistance to MD.

Host genetic resistance to Marek's disease sustains protective efficacy of herpesvirus of turkey in both experimental and commercial lines of chickens

Marek's disease (MD) remains a continual threat to the poultry industry worldwide as the MD virus continues evolving in virulence. MD has been controlled primarily by intensive use of vaccines since 1969. Based on the antigenic and pathogenic differences of the viruses that the vaccines were derived from, commercially available MD vaccines are classified into three categories, MDV-1, -2, and -3 vaccines. This study was designed to compare the protective efficacy of MDV-1 (CVI988/Rispens) and MDV-3 (HVT) vaccines against challenge of a very virulent plus strain of Marek's disease virus (vv+MDV) in experimental and commercial egg-layer lines of chickens under controlled experimental conditions. The two experimental lines (63 and 72) of chickens carry a uniform MHC B*2 haplotype and are known to differ in resistance to MD. One of the two commercial egg-layer lines (WL and BL) segregates for three MHC haplotypes (B*2, B*15, and B*21); the other is unclear. MD incidences of the unvaccinated groups of both experimental lines and both commercial lines were 100% or close to 100% induced by the vv+MDV, 648A. Survived day patterns of the unvaccinated groups significantly differed between the two experimental lines, but did not between the two commercial lines, which suggested the two experimental lines do differ in resistance to MD but not between the two commercial lines. At manufacturers' recommended vaccine dosage, two HVTs conveyed comparable protection for the MD resistant line 63 chickens as did both CVI988/Rispens used in this study. The two HVTs also conveyed comparable protection for both commercial lines of chickens as did one of two CVI988/Rispens (CVI988/Rispens-A). At a 2000PFU uniform dose, HVT and CVI988/Rispens again conveyed comparable protection for the MD resistant experimental line of chickens. The findings suggest vaccine protective efficacy is modulated by factors including the types and the sources of vaccines and the genetic backgrounds of chickens. The findings also suggest HVT delivers equal protection in MD resistant lines of chickens as does the industry-recognized golden standard of MD vaccine, CVI988/Rispens.

Applied animal genomics: results from the field

Genomic selection (GS) is the use of statistical methods to estimate the genetic merit of a genotyped animal based on prediction equations derived from large ancestral populations with both phenotypes and genotypes. It has revolutionized the dairy cattle breeding industry and has been implemented with varying degrees of success in other animal breeding programs, including swine, poultry, and beef cattle. The findings of empirical field studies applying GS to the breeding sectors of these main animal protein industries are reviewed. Several translational considerations must be addressed before implementing GS in genetic improvement programs. These include determining and obtaining economically relevant phenotypes and determining the optimal size of the training population, cost-effective genotyping strategies, the practicality of field implementation, and the relative costs versus the benefits of the realized rate of genetic gain. GS may additionally change the optimal breeding scheme design, and studies that address this consideration are also reviewed briefly.

Transcriptional profiling of mEq-dependent genes in Marek's disease resistant and susceptible inbred chicken lines

Marek’s disease (MD) is an economically significant disease in chickens caused by the highly oncogenic Marek’s disease virus (MDV). Understanding the genes and biological pathways that confer MD genetic resistance should lead towards the development of more disease resistant commercial poultry flocks or improved MD vaccines. MDV mEq, a bZIP transcription factor, is largely attributed to viral oncogenicity though only a few host target genes have been described, which has impeded our understanding of MDV-induced tumorigenesis. Given the importance of mEq in MDV-induced pathogenesis, we explored the role of mEq in genetic resistance to MDV. Using global transcriptome analysis and cells from MD resistant or susceptible birds, we compared the response to infection with either wild type MDV or a nononcogenic recombinant lacking mEq. As a result, we identified a number of specific genes and pathways associated with either MD resistance or susceptibility. Additionally, integrating prior information from ChIP-seq, microarray analysis, and SNPs exhibiting allele-specific expression (ASE) in response to MDV infection, we were able to provide evidence for 24 genes that are polymorphic within mEq binding sites are likely to account for gene expression in an allele-specific manner and potentially for the underlying genetic differences in MD incidence.