Endogenous viral genes: association with reduced egg production rate and egg size in White Leghorns

Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses

The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4-7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry.

Avian Leukosis: Will We Be Able to Get Rid of It?

Avian leukosis viruses (ALVs) have been virtually eradicated from commercial poultry. However, some niches remain as pockets from which this group of viruses may reemerge and induce economic losses. Such is the case of fancy, hobby, backyard chickens and indigenous or native breeds, which are not as strictly inspected as commercial poultry and which have been found to harbor ALVs. In addition, the genome of both poultry and of several gamebird species contain endogenous retroviral sequences. Circumstances that support keeping up surveillance include the detection of several ALV natural recombinants between exogenous and endogenous ALV-related sequences which, combined with the well-known ability of retroviruses to mutate, facilitate the emergence of escape mutants. The subgroup most prevalent nowadays, ALV-J, has emerged as a multi-recombinant which uses a different receptor from the previously known subgroups, greatly increasing its cell tropism and pathogenicity and making it more transmissible. In this review we describe the ALVs, their different subgroups and which receptor they use to infect the cell, their routes of transmission and their presence in different bird collectivities, and the immune response against them. We analyze the different systems to control them, from vaccination to the progress made editing the bird genome to generate mutated ALV receptors or selecting certain haplotypes.

Short communication: diversity of endogenous avian leukosis virus subgroup E elements in 11 chicken breeds

Avian leukosis virus subgroup E (ALVE) as a kind of endogenous retroviruses extensively exists in chicken genome. The insertion of ALVE has some effects on chicken production traits and appearance. Most of the work on ALVEs has been done with commercial breeds. We present here an investigation of ALVE elements in seven Chinese domestic breeds and four standard breeds. Firstly, we established an ALVE insertion site dataset by using the obsERVer pipeline to identify ALVEs from whole-genome sequence data of eleven chicken breeds, seven Chinese domestic breeds, including Beijing You (BY), Dongxiang (DX), Luxi Game (LX), Shouguang (SG), Silkie (SK), Tibetan (TB) and Wenchang (WC), four standard breeds, including White Leghorn (WL), White Plymouth Rock (WR), Cornish (CS), and Rhode Island Red (RIR). A total of 37 ALVE insertion sites were identified and 23 of them were novel. Most of these insertion sites were distributed in intergenic regions and introns. We then used locus-specific PCR to validate the insertion sites in an expanded population with 18~60 individuals in each breed. The results showed that all predicted integration sites in 11 breeds were verified by PCR. Some ALVE insertion sites were breeds specific, and 16 out of 23 novel ALVEs were found in only one Chinese domestic chicken breed. We randomly selected three ALVE insertions including ALVE_CAU005, ALVE_ros127, and ALVE_ros276, and obtained their insertion sequences by long-range PCR and Sanger sequencing. The insertion sequences were all 7525 bp, which were full-length ALVE insertion and all of them were highly homologous to ALVE1 with similarity of 99%. Our study identified the distribution of ALVE in 11 chicken breeds, which expands the current research on ALVE in Chinese domestic breeds.

Advances on genetic and genomic studies of ALV resistance

Avian leukosis (AL) is a general term for a variety of neoplastic diseases in avian caused by avian leukosis virus (ALV). No vaccine or drug is currently available for the disease. Therefore, the disease can result in severe economic losses in poultry flocks. Increasing the resistance of poultry to ALV may be one effective strategy. In this review, we provide an overview of the roles of genes associated with ALV infection in the poultry genome, including endogenous retroviruses, virus receptors, interferon-stimulated genes, and other immune-related genes. Furthermore, some methods and techniques that can improve ALV resistance in poultry are discussed. The objectives are willing to provide some valuable references for disease resistance breeding in poultry.

Activation of lnc-ALVE1-AS1 inhibited ALV-J replication through triggering the TLR3 pathway in chicken macrophage like cell line

Endogenous retroviruses (ERVs) are remnants of the historical retroviral infections, and their derived transcripts with viral signatures are important sources of long noncoding RNAs (lncRNAs). We have previously shown that the chicken ERV-derived lncRNA lnc-ALVE1-AS1 exerts antiviral innate immunity in chicken embryo fibroblasts. However, it is not clear whether this endogenous retroviral RNA has a similar function in immune cells. Here, we found that lnc-ALVE1-AS1 was persistently inhibited in chicken macrophages after avian leukosis virus subgroup J (ALV-J) infection. Furthermore, overexpression of lnc-ALVE1-AS1 significantly inhibited the replication of exogenous ALV-J, whereas knockdown of lnc-ALVE1-AS1 promoted the replication of ALV-J in chicken macrophages. This phenomenon is attributed to the induction of antiviral innate immunity by lnc-ALVE1-AS1 in macrophages, whereas knockdown of lnc-ALVE1-AS1 had the opposite effect. Mechanistically, lnc-ALVE1-AS1 can be sensed by the cytosolic pattern recognition receptor TLR3 and trigger the type I interferons response. The present study provides novel insights into the antiviral defense of ERV-derived lncRNAs in macrophages and offers new strategies for future antiviral solutions.

Falling fowl of the chicken reference genome: pitfalls of studying polymorphic endogenous retroviruses

High quality reference genomes have facilitated the study of endogenous retroviruses (ERVs). However, there are an increasing number of published works which assume the ERVs in reference genomes are universal; even those of evolutionarily recent integrations. Consequently, these studies fail to properly characterise polymorphic ERVs, and even propose biological functions for ERVs that may not actually be present in the genomes of interest. Here, I outline the pitfalls of three studies of chicken endogenous Avian Leukosis Viruses (ALVEs or "ev genes": the "original" ERVs), all confounded by the assumption that the reference genome provides a representative ALVE baseline.

The impact of endogenous Avian Leukosis Viruses (ALVE) on production traits in elite layer lines

Avian Leukosis Virus subgroup E (ALVE) integrations are endogenous retroviral elements found in the chicken genome. The presence of ALVE has been reported to have negative impacts on multiple traits, including egg production and body weight. The recent development of rapid, inexpensive and specific ALVE detection methods has facilitated their characterization in elite commercial egg production lines across multiple generations. The presence of 20 ALVE was examined in 8 elite lines, from 3 different breeds. Seventeen of these ALVE (85%) were informative and found to be segregating in at least one of the lines. To test for an association between specific ALVE inserts and traits, a large genotype by phenotype study was undertaken. Genotypes were obtained for 500 to 1500 males per line, and the phenotypes used were sire-daughter averages. Phenotype data were analyzed by line with a linear model that included the effects of generation, ALVE genotype and their interaction. If genotype effect was significant, the number of ALVE copies was fitted as a regression to estimate additive ALVE gene substitution effect. Significant associations between the presence of specific ALVE inserts and 18 commercially relevant performance and egg quality traits, including egg production, egg weight and albumen height, were observed. When an ALVE was segregating in more than one line, these associations did not always have the same impact (negative, positive or none) in each line. It is hypothesized that the presence of ALVE in the chicken genome may influence production traits by 3 mechanisms: viral protein production may modulate the immune system and impact overall production performance (virus effect); insertional mutagenesis caused by viral integration may cause direct gene alterations or affect gene regulation (gene effect); or the integration site may be within or adjacent to a quantitative trait region which impacts a performance trait (linkage disequilibrium, marker effect).

Avian Viruses that Impact Table Egg Production

Eggs are a common source of protein and other nutrient components for people worldwide. Commercial egg-laying birds encounter several challenges during the long production cycle. An efficient egg production process requires a healthy bird with a competent reproductive system. Several viral pathogens that can impact the bird's health or induce reversible or irreversible lesions in the female reproductive organs adversely interfere with the egg industry. The negative effects exerted by viral diseases create a temporary or permanent decrease in egg production, in addition to the production of low-quality eggs. Several factors including, but not limited to, the age of the bird, and the infecting viral strain and part of reproductive system involved contribute to the form of reproductive disease encountered. Advanced methodologies have successfully elucidated some of the virus-host interactions relevant to the hen's reproductive performance, however, this branch needs further research. This review discusses the major avian viral infections that have been reported to adversely affect egg productivity and quality and aims to summarize the current understanding of the mechanisms that underlie the observed negative effects.

Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Background

Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants.

Results

We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes.

Conclusions

obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.

Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens

Background

Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated.

Results

In total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines.

Conclusions

Identification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.

Endogenous avian leukosis virus subgroup E elements of the chicken reference genome

The chicken reference genome contains 2 endogenous avian leukosis virus subgroup E (ALVE) insertions, but gaps and unresolved repetitive sequences in previous assemblies have hindered their precise characterization. Detailed analysis of the most recent reference genome (GRCg6a) now shows both ALVEs within contiguous chromosome assemblies for the first time. ALVE6 (ALVE-JFevA) and ALVE-JFevB are both located on chromosome 1, with ALVE6 close to the p-arm telomere. ALVE-JFevB is a structurally intact element containing the ALVE gag, pol, and env genes and is capable of forming replication competent viruses. In contrast, ALVE6 contains a 3,352 bp 5′ truncation and lacks the entire 5′ long terminal repeat and gag gene. Despite this, ALVE6 remains able to produce intact envelope protein, likely due to a mutation in the recognition site for a known inhibitory miRNA (miR-155). Whole genome resequencing data sets from layers, broilers, and 3 independent sources of wild-caught red junglefowl were surveyed for the presence of each of these reference genome ALVEs. ALVE-JFevB was found in no other chicken or red junglefowl genomes, whereas ALVE6 was identified in some layers, broilers, and native breeds but not within any other red junglefowl genome. Improved assembly contiguity has facilitated better characterization of the 2 ALVEs of the chicken reference genome. However, both the limited ALVE content and unique presence of ALVE-JFevB suggests that the reference individual is unrepresentative of ancestral Gallus gallus ALVE diversity.

Human-Aided Movement of Viral Disease and the Archaeology of Avian Osteopetrosis

The term avian osteopetrosis is used to describe alterations to the skeletal elements of several species of domestic bird, most typically the chicken, Gallus gallus domesticus (L. 1758). Such lesions are routinely identified in animal bones from archaeological sites due to their distinctive appearance, which is characterised by proliferative diaphyseal thickening. These lesions are relatively uncomplicated for specialists to differentially diagnose and are caused by a range of avian leucosis viruses in a series of subgroups. Only some avian leucosis viruses cause the development of such characteristic lesions in osteological tissue. Viraemia is necessary for the formation of skeletal pathology, and avian osteopetrosis lesions affect skeletal elements at different rates. Lesion expression differs by the age and sex of the infected individual, and environmental conditions have an impact on the prevalence of avian leucosis viruses in poultry flocks. These factors have implications for the ways in which diagnosed instances of avian osteopetrosis in archaeological assemblages are interpreted. By integrating veterinary research with archaeological evidence for the presence of avian leucosis viruses across Western Europe, this paper discusses the nature of these pathogens, outlines criteria for differential diagnosis, and offers a fresh perspective on the human-aided movement of animal disease in the past through investigation of the incidence and geographic distribution of avian osteopetrosis lesions from the first century BC to the post-medieval period.

Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected]

Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.

Anorexia is Associated with Stress-Dependent Orexigenic Responses to Exogenous Neuropeptide Y

Chicken lines that have been divergently selected for either low (LWS) or high (HWS) body weight at 56 days of age for more than 57 generations have different feeding behaviours in response to a range of i.c.v. injected neurotransmitters. The LWS have different severities of anorexia, whereas the HWS become obese. Previously, we demonstrated that LWS chicks did not respond, whereas HWS chicks increased food intake, after central injection of neuropeptide Y (NPY). The present study aimed to determine the molecular mechanisms underlying the loss of orexigenic function of NPY in LWS. Chicks were divided into four groups: stressed LWS and HWS on day of hatch, and control LWS and HWS. The stressor was a combination of food deprivation and cold exposure. On day 5 post-hatch, each chick received an i.c.v. injection of vehicle or 0.2 nmol of NPY. Only the LWS stressed group did not increase food intake in response to i.c.v. NPY. Hypothalamic mRNA abundance of appetite-associated factors was measured at 1 h post-injection. Interactions of genetic line, stress and NPY treatment were observed for the mRNA abundance of agouti-related peptide (AgRP) and synaptotagmin 1 (SYT1). Intracerebroventricular injection of NPY decreased and increased AgRP and SYT1 mRNA, respectively, in the stressed LWS and increased AgRP mRNA in stressed HWS chicks. Stress was associated with increased NPY, orexin receptor 2, corticotrophin-releasing factor receptor 1, melanocortin receptor 3 (MC3R) and growth hormone secretagogue receptor expression. In conclusion, the loss of responsiveness to exogenous NPY in stressed LWS chicks may be a result of the decreased and increased hypothalamic expression of AgRP and MC3R, respectively. This may induce an intensification of anorexigenic melanocortin signalling pathways in LWS chicks that block the orexigenic effect of exogenous NPY. These results provide insights onto the anorexic condition across species, and especially for forms of inducible anorexia such as human anorexia nervosa.

A rapid profiling assay for avian leukosis virus subgroup E proviruses in chickens

Endogenous retroviral elements (ERVs) are prolific components of the genomes of complex species, typically occupying more sequence space than do essential, protein-encoding genes. Much of what we know today about the structure and function, as well as the evolution and pathogenic potential, of ERVs was fleshed out over several decades during the last century using the avian leukosis virus subgroup E-related (ALVE) family of endogenous retroviruses of chickens as a model system. A critical enabling factor in the elucidation of ALVE structure and function is the ability to detect and unambiguously identify specific ALVE proviral elements and to develop accurate element profiles for individual chickens under study. Currently, the most common approach for ALVE locus detection involves element-specific PCR assays carried out using primers that target host DNA near the insertion site of the provirus (i.e., the upstream and downstream flanks of the unoccupied site). Here we describe a new approach for proviral detection that exploits restriction enzyme sites in flanking DNA to develop ALVE element profiles more rapidly than with assays currently in use. Moreover, unlike element-specific PCR tests, the "profiling" assay detects novel ALVEs for which insertion sites have not yet been identified as well as previously characterized elements.

Characterization of insertion sites and development of locus-specific assays for three broiler-derived subgroup E avian leukosis virus proviruses

This report deals with the identification of novel elements belonging to a family of endogenous retroviruses, designated endogenous avian leukosis virus-type proviral elements (ALVE), that reside in the genome of the chicken and are closely related to exogenous avian leukosis viruses. The study of ALVE elements in the chicken genome serves as a model system for understanding the interplay between endogenous viruses and their vertebrate hosts in general, including humans. In this report, we characterize the insertion sites and describe locus-specific, diagnostic polymerase chain reaction-based assays for three previously discovered, but as yet not localized, ALVE elements. In addition, we assess the proviral integrity, provide the complete element sequence and examine the genomic environs of the three broiler-derived elements.

Methods for evaluating and developing commercial chicken strains free of endogenous subgroup E avian leukosis virus

The genome of nearly all chickens contains various DNA proviral insertions of retroviruses of subgroup E avian leukosis virus (ALVE). However, the elimination or control of ALVE gene expression is desirable to improve productivity, to improve resistance to avian leukosis virus (ALV)-induced tumours, and to develop safer live virus vaccines in chick embryos and cultured chick cells. Restriction fragment length polymorphism and polymerase chain reaction methods are used to define the presence of ALVE genes; and the expression of ALVE in chicken plasma or on cells, and the susceptibility of cells to ALVE is determined by flow cytometry using a specific (R2) antibody. ADOL line 0 chickens have been selected to be free of ALVE genes, while being resistant (i.e. lack receptors to ALVE), but susceptible to exogenous ALV (i.e. ALVA, ALVB, ALVC and ALVJ). To develop improved line 0-type chickens, ADOL line 0 was outcrossed to a commercial line that had one ALVE gene and evidence for ALVE resistance. Rous sarcoma virus (RSV) challenge was used to confirm resistance of F1 chickens to ALVE, and susceptibility of F2 breeders to ALVA and ALVB using test chicks produced by matings to line 7(2). Selected F2 breeders were resistant to ALVE, but susceptible to exogenous ALVA, ALVB, ALVC and ALVJ, based on challenge tests of progeny chick cells using an enzyme-linked immunosorbent assay. The new line, 0(1), has evidence for improved egg size, productivity, fertility and hatchability. Similar procedures may be used for development of productive ALVE free chicken lines with preferred ALV susceptibility traits.

Endogenous expression of ASLV viral proteins in specific pathogen free chicken embryos: relevance for the developmental biology research field

Background

The use of Specific Pathogen Free (SPF) eggs in combination with RCAS retrovirus, a member of the Avian Sarcoma-Leukosis Virus (ASLV) family, is of standard practice to study gene function and development. SPF eggs are certified free of infection by specific pathogen viruses of either exogenous or endogenous origin, including those belonging to the ASLV family. Based on this, SPF embryos are considered to be free of ASLV viral protein expression, and consequently in developmental research studies RCAS infected cells are routinely identified by immunohistochemistry against the ASLV viral proteins p19 and p27. Contrary to this generally accepted notion, observations in our laboratory suggested that certified SPF chicken embryos may endogenously express ASLV viral proteins p19 and p27. Since these observations may have significant implications for the developmental research field we further investigated this possibility.

Results

We demonstrate that certified SPF chicken embryos have transcriptionally active endogenous ASLV loci (ev loci) capable of expressing ASLV viral proteins, such as p19 and p27, even when those loci are not capable of producing viral particles. We also show that the extent of viral protein expression in embryonic tissues varies not only among flocks but also between embryos of the same flock. In addition, our genetic screening revealed significant heterogeneity in ev loci composition even among embryos of the same flock.

Conclusions

These observations have critical implications for the developmental biology research field, since they strongly suggest that the current standard methodology used in experimental studies using the chick embryo and RCAS vectors may lead to inaccurate interpretation of results. Retrospectively, our observations suggest that studies in which infected cells have been identified simply by pan-ASLV viral protein expression may need to be considered with caution. For future studies, they point to a need for careful selection and screening of the chick SPF lines to be used in combination with RCAS constructs, as well as the methodology utilized for qualitative analysis of experimental results. A series of practical guidelines to ensure research quality animals and accuracy of the interpretation of results is recommended and discussed.

Novel avian leukosis virus-related endogenous proviruses from layer chickens: characterization and development of locus-specific assays

During the course of evolution, vertebrate genomes have been invaded and colonized by retroviruses. In humans, for example, endogenous retroviruses (long terminal repeat elements) occupy roughly twice as much sequence space as essential genes. There are numerous reports in the literature implicating endogenous proviruses in the modulation of host physiology. The fact that many of these host-virus interactions take place in a proviral locus-specific manner speaks to the need for rapid assays for element profiling. This report deals with the identification of novel elements belonging to a family of endogenous retroviruses, designated ALVE, that reside in the genome of the chicken and that are closely related to exogenous avian leukosis viruses. The study of ALVE elements in the chicken genome serves as a model system for understanding the interplay between endogenous viruses and their vertebrate hosts in general, including humans. In this report, we present locus-specific, diagnostic PCR-based assays for 2 novel ALVE elements. In addition, we characterize the proviral structures and examine the genomic environments of both novel elements along with a previously described element known as ALVE-NSAC-3.

Proviral integrations and expression of endogenous avian leucosis virus during long term selection for high and low body weight in two chicken lines

Background

Long-term selection (> 45 generations) for low or high juvenile body weight from a common founder population of White Plymouth Rock chickens has generated two extremely divergent lines, the LWS and HWS lines. In addition to a > 9-fold difference between lines for the selected trait, large behavioural and metabolic differences between the two lines evolved during the course of the selection. We recently compared gene expression in brain tissue from birds representing these lines using a global cDNA array analysis and the results showed multiple but small expression differences in protein coding genes. The main differentially expressed transcripts were endogenous retroviral sequences identified as avian leucosis virus subgroup-E (ALVE).

Results

In this work we confirm the differential ALVE expression and analysed expression and number of proviral integrations in the two parental lines as well as in F₉ individuals from an advanced intercross of the lines. Correlation analysis between expression, proviral integrations and body weight showed that high ALVE levels in the LWS line were inherited and that more ALVE integrations were detected in LWS than HWS birds.

Conclusion

We conclude that only a few of the integrations contribute to the high expression levels seen in the LWS line and that high ALVE expression was significantly correlated with lower body weights for the females but not males. The conserved correlation between high expression and low body weight in females after 9 generations of intercrosses, indicated that ALVE loci conferring high expression directly affects growth or are very closely linked to loci regulating growth.

Development of an alloantiserum (R2) that detects susceptibility of chickens to subgroup E endogenous avian leukosis virus

An alloantiserum, termed R2, specifically agglutinates red blood cells (RBC) from line 100B chickens that are susceptible to avian leukosis viruses (ALV) belonging to subgroups B and E, but does not agglutinate RBC from congenic inbred line 7(2) chickens that are resistant to ALV B and E. The R2 antigen was also detected on lymphocytes and thrombocytes. Using chickens from a special cross, it was found that R2 reactivity requires that the chickens must: (1) be susceptible to infection by ALV-E; and (2) express a viral envelope gene with subgroup E specificity. With R2 antiserum, a nearly perfect association was observed between agglutination and susceptibility to ALV-B in F2 chickens containing endogenous viral genes ev2 and/or ev3. These results support earlier evidence that ALV-B and ALV-E share receptors. Moreover, the R2 antiserum was shown to neutralize ALV-E. The R2 antigen showed Mendelian segregation in chickens of a commercial White Leghorn strain-cross containing ev3, ev6 and ev9. However, commercial chickens with or without the R2 antigen did not differ in susceptibility to lymphoid leukosis induction or immune response on infection with ALV of subgroup A for complex reasons we discuss.

Molecular characterization of three recombinant isolates of avian leukosis virus obtained from contaminated Marek's disease vaccines

Three natural recombinant avian leukosis viruses (ALV; PDRC-1039, PDRC-3246, and PDRC-3249) expressing a subgroup A gp85 envelope protein and containing long terminal repeats (LTR) of endogenous ALV-E viruses were isolated from contaminated commercial Marek's disease vaccines, cloned, and completely sequenced. Their full genomes were analyzed and compared with representative strains of ALV. The proviral DNA of all three isolates displayed 99.3% identity to each other, suggesting a possible common ancestor, even though the contaminating viruses were obtained from three separate vaccine serials produced by two different vaccine manufacturing companies. The contaminating viruses have a genetic organization typical of replication-competent alpharetroviruses. The proviral genomes of PDRC-1039 and PDRC-3246 are 7497 bp long, and the PDRC-3249 is three base pairs shorter because of a deletion of a threonine residue within the gp85 coding region. The LTR, gag, pol, and the transmembrane (TM) region (gp37) of the env gene of all three viruses displayed high identity to endogenous counterpart sequences (>98%). Only the surface (SU) region (gp85) of the env gene displayed high identity with exogenous ALV-A (98.7%). Locus-specific polymerase chain reaction (PCR) analysis for ALV endogenous sequences (ev loci) in the chicken embryo fibroblasts used to produce the original vaccine vials identified the presence of ev-1, ev-2, ev-3, ev-4, and ev-6 in all three vaccines. Homologous recombination most likely took place to involve the SU region of the env gene because the recombinant viruses only differ in this particular region from the consensus ALV-E. These results suggest that the contaminating ALV isolates probably emerged by recombination of ALV-A with endogenous virus sequences before vaccine preparation.

Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay

The tumour virus B (TVB) locus encodes cellular receptors mediating infection by three subgroups of avian leukosis virus (B, D, and E). Three major alleles, TVB*S1, TVB*S3, and TVB*R, have been described. TVB*S1 encodes a cellular receptor mediating infection of subgroups B, D, and E. TVB*S3 encodes the receptor for two subgroups, B and D, and TVB*R encodes a dysfunctional receptor that does not permit infection by any of the subgroups, B, D, or E. Genetic diversity at the TVB locus of chickens was investigated in both layer and broiler commercial pure lines and laboratory lines. Genotyping assays were developed for both medium-throughput and high-throughput analysis. Of the 36 broiler lines sampled, 14 were fixed for the susceptible allele TVB*S1. Across all broiler lines, 83% of chickens were typed as TVB*S1/*S1, 3% as TVB*R/*R, and 14% as TVB*S1/*R. In the egg-layer lines, five of the 16 tested were fixed for TVB*S1/*S1. About 44% of egg-layers were typed as TVB*S1/*S1, 15% as TVB*R/*R, with the rest segregating for two or three of the alleles. In the laboratory chickens, 60% were fixed for TVB*S1/*S1, 6% for TVB*S3/*S3, 14% for TVB*R/*R, and the rest were heterozygotes (TVB*S1/*S3 or TVB*S1/*R). All commercial pure lines examined in this study carry the TVB*S1 allele that sustains the susceptibility to avian leukosis viruses B, D, and E. More importantly, the TVB*R allele was identified in multiple populations, thus upholding the opportunities for genetic improvement through selection.

A review of the development of chicken lines to resolve genes determining resistance to diseases

The resolution of genes that determine resistance to disease is described using chicken lines maintained at the Avian Disease and Oncology Laboratory (ADOL). This description includes a summary 1) of existing selected and inbred lines differing for resistance to viral-induced tumors, i.e., Marek's disease (MD) and lymphoid leukosis (LL), and of the use of inbred and line crosses to define relevant disease-resistant genes, e.g., TV, ALVE, B, R, LY4, TH1, BU1, and IGG1; 2) of the development of TVB*/ALVE congenic lines to establish the affects of endogenous virus (EV) expression on resistance to avian leukosis virus (ALV), and methods to detect ALVE expression; 3) of the development of B congenic lines to define the influence of the MHC on MD resistance and vaccinal immunity, for producing B antisera, and for evaluating DNA sequences of Class I and II genes; and 4) of the current development of 6C.7 recombinant congenic strains (RCS) to define the role of non-MHC genes influencing susceptibility to MD and LL tumors, immune competence, and epistatic effects of genes. The procedures of pedigree mating, to avoid or maintain inbreeding, and of blood-typing, to ensure genetic purity of the lines, are also described.

Retrovirus-induced disease in poultry

Three species of avian retrovirus cause disease in poultry: the avian leukosis/sarcoma virus (ALSV), reticuloendotheliosis virus (REV), and lymphoproliferative disease virus (LPDV) of turkeys. The ALSV can be classified as slowly transforming viruses, which lack a viral oncogene, and acutely transforming viruses, which possess a viral oncogene. Slowly transforming viruses induce late onset leukoses of the B cell lymphoid, erythroid, and myeloid cell lineages, and other tumors, by viral promoter insertion into the genome of a host cell and activation of a cellular protooncogene. The various acutely transforming leukemia and sarcoma viruses induce leukotic or other tumors rapidly and carry one or anther (sometimes two) viral oncogenes, of which some 15 have been identified. The ALSV fall into six envelope subgroups, A through E, and the recently recognized J subgroup, which induces myeloid leukosis. With the exception of Subgroup E viruses, these viruses spread vertically and horizontally as infectious virions, and are termed exogenous viruses. Subgroup E viruses are usually spread genetically as DNA proviruses (often defective) in host germ cell genome, and are termed endogenous viruses. Several other families of endogenous viruses also exist, one of which, endogenous avian retrovirus (EAV), is related to Subgroup J ALV. Exogenous viruses, and sometimes endogenous viruses, can have detrimental effects on commercially important production traits. Exogenous viruses are currently controlled by virus eradication schemes. Reticuloendotheliosis virus, which lacks a viral oncogene, causes chronic B cell and T-cell lymphomas in chickens, and also chronic lymphomas in turkeys and other species of birds. An acutely transforming variant of REV, Strain T, carries a viral oncogene, and induces reticuloendotheliosis within a few days. In chickens and turkeys, REV spreads vertically and horizontally. No commercial control schemes are operated. In turkeys, LPDV infection has occurred in several countries, where it caused a lymphoproliferative disease of uncertain nature.

Locus-specific diagnostic tests for endogenous avian leukosis-type viral loci in chickens

The genome of the chicken, Gallus gallus, contains endogenous proviral elements (ALVE elements or ev genes) that display a high degree of similarity to the Avian Leukosis class of retroviruses. The ALVE proviruses are known to modulate physiological processes of the host birds. Different ALVE elements retain variable portions of the complete, prototype viral genome, and each provirus resides in its own specific location within the host genome. Thus, each ALVE element has its own particular potential to modulate host physiology depending on the nature of its integration site, the completeness of the proviral genome, and the level of expression of the locus. It is important, therefore, to be able to establish the ALVE element profiles of chickens quickly and accurately, both in the laboratory and in a commercial setting. The current method of choice for simple, quick, and accurate typing is the polymerase chain reaction (PCR). This paper reviews the present status of PCR typing of ALVE proviruses and lists the assay protocols for 19 different elements. In addition, it compares the insertion sites of these elements in an effort to identify common motifs at ALVE integration sites.

Molecular characterization of endogenous viral genes of the avian leukosis virus family in an experimental population of brown-egg layers

Retroviral DNA sequences similar to the exogenous avian leukosis virus can be found in the genome of many chicken breeds and have been identified as the ALVE family of endogenous viral (ev) genes. Most of them have been described by a restriction fragment length polymorphism (RFLP) procedure with two restriction enzymes and a full length viral probe. In order to facilitate the comparison of ALVE genes between strains, the nomenclature workshop held at the XXIV International Society for Animal Genetics Congress recommended that four enzymes and several viral subprobes be used to characterize each locus. This approach has been followed in the present study of a Rhode Island Red experimental population. A previous study had identified ev genes with the SacI and BamHI enzymes and the Rous-associated virus-2 probe (RAV-2). Chickens carrying only one ALVE locus at a time have been produced to facilitate the analysis. Additional enzymes (EcoRI, HindIII, and KpnI), the full probe RAV-2 and three viral subprobes for the gag, pol, and LTR regions have been used. In addition, a PCR diagnostic test has been used to search for homologies with the ALVE1 (= ev1), ALVE6 (= ev6) and evA loci. Currently, 12 loci have been identified precisely: three were identical to ALVE loci described previously, either in White Leghorns, ALVE6 and ALVE18 (= ev18) or in broilers (evB8). In addition, the evB8 locus was found to be identical to the evA locus previously described in brown-egg layers. Nine loci appeared specific to this Rhode Island Red population. Four of these specific loci were complete and one of them could be considered of characteristic of this population, because of its very high frequency. The remaining five specific loci showed small deletions, either in the pol region for one of them or in the env region for three of them or at the 3' long terminal repeat for one of them. Altogether, 5 out of 12 loci were structurally complete, which could suggest that deleted proviruses may have been preferentially retained.

Association of endogenous viral genes with quantitative traits in chickens selected for high egg production and susceptibility or resistance to Marek's disease

1. The association of endogenous viral (ev) genes with quantitative traits in 2 genetically distinct sets of White Leghorn strains were investigated. Strain S had been selected for susceptibility to Marek's disease (MD) whereas strain K had been selected for resistance to MD and high egg production and egg weight. 2. In all, 8 ev genes were typed. Ev10, ev19 and 'newB' occurred exclusively in strain S, 'newA' occurred only in strain K, and ev1, ev3, ev6 and ev8 occurred in both strains. 3. Whereas ev6 and ev8 were associated with reduction in egg production rate in strain S, in strain K, the presence of ev3 was associated with increased group specific antigen. 4. The genetic background of the chicken strain may play a role in the way certain ev genes affect traits. 5. It was thought that the position of ev genes on the chromosome may be important and their association with traits of economic importance make them potential genetic markers for uncovering quantitative trait loci.

Trait association of genetic markers in the growth hormone and the growth hormone receptor gene in a White Leghorn strain

Alleles of the growth hormone (GH) gene and GH receptor (GHR) gene were analyzed for association with juvenile body weight (HBWT), age at first egg (AFE), the hen-day rate of egg production (HDR), egg specific gravity (SPG), and egg weight (EWT) in a strain of White Leghorns. The particular strain segregated at near equal frequencies for two GH alleles defined by differences at three restriction fragment length polymorphisms (RFLP) and for two GHR alleles defined by a single RFLP. The GH genotype was significantly associated with AFE (P < or = 0.04) as well as HDR from 274 to 385 d (P < or = 0.04) and 386 to 497 d (P < or = 0.0003). The GHR genotype (haploid in female chickens) had trends for association with HBW (P < or = 0.06) and HDR from AFE to 273 d (P < or = 0.07). The effects on the egg quality traits SPG and EWT were not significant. Regression analysis revealed that HDR was associated negatively with AFE and positively with HBWT. The slope of the regression line of HDR on AFE varied with the GH genotype, with the effect that the differences in HDR between GH genotypes was relatively small in chickens with early AFE and large in chickens with late AFE. Similarly, the slope of the regression of HDR on HBWT varied between GHR genotypes, with the result that the effect of the GHR genotype on HDR in chickens with low HBWT was opposite to its effect in chickens with high HBWT. The complex relationship between genotypes and traits may reflect gene interaction and indicates that simple models based on additive gene effects may not be adequate for the dissection of the genetic architecture of quantitative traits.

Long range-inverse PCR (LR-IPCR): extending the useful range of inverse PCR

The inverse PCR technique (IPCR) has proven to be very useful for the amplification of uncharacterized stretches of DNA upstream or downstream of regions that have already been cloned and sequenced. In practice, however, chromosome walking using standard IPCR is often a slow, repetitive process because only small DNA fragments are effectively amplified. The development of long and accurate PCR methodology has greatly expanded the range of DNA fragment sizes that is amenable to amplification by conventional PCR. We reasoned that combining long range PCR with IPCR would also extend the useful range of the IPCR technique. In this paper we demonstrate the utility of the hybrid, long range-inverse PCR (LR-IPCR) technique by generating clones containing long stretches of DNA flanking endogenous chicken proviral elements.

Characterization of eight endogenous viral (ev) genes of meat chickens in semi-congenic lines

Restriction fragment length polymorphism analysis was conducted for a set of eight different meat chicken-derived endogenous viral genes (ev genes) of the avian leukosis viral (ALV) family. Each viral element was first isolated into a separate single-element line by selective breeding. Genomic DNA from the founder male for each semi-congenic, single-element line was digested with each of four restriction enzymes, and the resulting Southern blots were each hybridized with up to four probes representing different portions of the ALV retroviral genome. Among the eight elements, there was one that represents the broiler equivalent of locus ev3 of White Leghorn chickens. A second broiler element showed a SacI-specific junction fragment similar to that of ev8. The remainder appeared to be different from any of the 21 ev genes previously described for White Leghorn chickens. Four of the eight elements examined were essentially complete, but the rest have sustained internal deletions.

Association of endogenous avian viral and endogenous viral genes with feed conversion and six-week body weight in broilers

The consistency of the effect of selection on the frequencies of endogenous avian viral (eav) and endogenous viral (ev) specific restriction fragment length polymorphism (RFLP) bands was studied in two broiler lines selected from a single base population and in an F2 population derived from a reciprocal cross of both lines. One broiler line (FC line) was selected for low feed conversion ratio and the other line (GL line) was selected for high 6-wk body weight. In the F2 population, the band frequencies were determined in groups representing separate tails of the distribution of two production traits, namely, low feed conversion ratio between 29 and 42 d of age and body weight at 42 d of age. The F2 population consisted of 288 females belonging to 24 full-sib families. To rule out family effects, the tails for these production traits were composed by either the best or by the worst female performer for each trait in each full-sib family. In total, 29 HindIII-eav, 34 MspI-eav, and 21 BamHI-ev bands could be distinguished by RFLP analysis. This report describes the influence of selection on 11 potentially interesting bands. Two bands, the 9.5-kb HindIII-eav and the 15-kb MspI-eav band, which were found both in higher frequencies in the parental FC line, were also found in higher (P < or = .05) frequencies in the F2 tail with a favorable feed conversion ratio. A third band, the 6.5-kb HindIII-eav band, present in lower frequencies in the parental GL line, was also present in lower (P < or = .05) frequencies in the F2 tail of birds with heavy body weight.

Influence of the alv6 recombinant avian leukosis virus transgene on production traits and infection with avian tumor viruses in chickens

The biological costs of the alv6 recombinant transgene that in chickens induces dominant resistance to the subgroup A avian leukosis virus (ALV), in terms of effects on production traits, were studied. Four generations of White Leghorn chickens of Line TR, segregating for alv6 but free of endogenous viral genes, as well as two generations of crosses between TR and Ottawa Line WG (WGTR) were tested under a specific-pathogen-free environment. In the birds studied, the transgene appeared unchanged compared to the original alv6: No major changes in alv6 DNA were detected by restriction analysis, the transgene did not express the group-specific antigen of ALV, and its presence was associated with absence of immune response to ALV. In most test years, and both TR and WGTR genomic backgrounds, alv6 was associated with delayed sexual maturity by 4 to 6 d, reduced egg production to 497 d of age by 20 to 46 eggs, and a 3.6 to 15% decline in egg production rate. No consistent effects on other traits, including mortality, were detected. When inoculated with the AC-1 isolate of Marek's disease virus in a separate experiment, TR birds with alv6 had a significantly lower body weight gain to 10 d of age than their sibs without the transgene. Thus, transgenesis has biological costs that have to be assessed against desirable effects of transgenes.

Effect of tumor virus susceptibility alleles on the late-feathering gene K on early growth of White Leghorns

The influence of tumor virus susceptibility (tvb) alleles and the sex-linked, late-feathering-endogenous virus 21 complex (K-ev21) on early growth was observed in progeny from late-feathering (LF) and early-feathering (EF) dams. At 2, 4, 6 and 10 wk of age, homozygous (K/K) males that carried a dominant tvbs1 allele were significantly (P < .05) lighter in total body weight than K/K homozygous endogenous virus (EV) EV21-resistant (tvbr/tvbr) hatchmates. Among heterozygous (K/k+) males, tvbs1 did not significantly influence growth when compared with tvbr/tvbr hatchmates. At 10 wk of age, tvbs1-positive K/w female progeny from LF dams were also significantly lighter than tvbr/tvbr K/w hatchmates. However, among progeny from EF dams no significant within sex differences in body weight were found regardless of their feather or EV susceptibility phenotype. Results indicate that susceptibility to EV21 infection is particularly detrimental to early growth of ev21-K homozygous male and hemizygous female progeny of LF dams.

Synergism between the endogenous viral loci ev6 and ev9 in inducing immunological tolerance to avian leukosis virus

1. The course of infection by exogenous avian leukosis virus was followed in a commercial strain of White Leghorn domestic fowls by measuring viral antigen in feather pulp and egg albumin. Ten days after hatching, 2 out of 360 birds tested positive and at 286 days of age about 60% of the birds had been antigen positive at least once. 2. Among the antigen positive birds, two groups could be distinguished: those which permanently and those which transiently expressed viral antigen. Permanent antigen expression was associated with low antibody titres, while transient antigen expression was associated with high antibody titres. 3. The strain segregated for the two endogenous viral genes ev6 and ev9, both of which express endogenous viral envelope protein, and have been implicated in affecting immune-responsiveness. The antibody titre in individuals positive for both ev6 and ev9, was significantly lower than in those which had none or only one of the two ev-genes. In addition, individuals positive for both ev-genes occurred more frequently in the group permanently positive for viral antigen than in the group transiently antigen positive. 4. The results indicate that there was a strong synergism between ev6 and ev9 in reducing the antibody response to exogenous avian leukosis virus infection, perhaps by inducing immune tolerance or interfering with antibody formation.

A new diagnostic method for the detection of endogenous Rous-associated virus-type provirus in chickens

A quick and simple method has been developed to detect the presence or absence of the endogenous Rous-associated virus (RAV) element ev1 in chickens. The procedure consists of a one-tube multiplex polymerase chain reaction (PCR) involving three oligonucleotide primers that are specific for the upstream flanking region, the long terminal repeat (LTR), and the downstream flanking region of the proviral insert, respectively. The multiplex reaction allows for the unambiguous discrimination between ev1+/ev1+ homozygote, ev1-/ev1- homozygote, and ev1+/ev1- heterozygote birds. The method works best with purified genomic DNA as substrate, but can also be used with rapidly prepared, "crude" DNA samples. The combination of speed with the safety of a nonradioactive procedure, and the ability to perform large numbers of assays by a semi-automated procedure, make this method attractive for large-scale screening projects. The ev1 locus has been used as a model system to demonstrate the feasibility of the PCR diagnostic approach. However the same principle should be applicable to the analysis of other RAV-type ev loci, as well as endogenous elements belonging to other families of viruses as sequence information for the flanking regions of these inserts becomes available.

Endogenous viral gene distribution in populations of meat-type chickens

The present study was designed to document the complexity of endogenous viral (ev) genes and seek evidence for their association with production traits in selected and control strains of meat-type chickens. Three populations were studied, each consisting of a control strain and one to three strains selected for various production traits. The ev genes were revealed by digesting genomic DNA with restriction enzymes and detecting DNA fragments on Southern blots using radioactive probes from nucleotide sequences of the avian leukosis virus genome. A total of 31 polymorphic ev loci were identified in these populations from a SacI digest, with an average of 7.3 ev genes per bird. There were no significant differences in ev genes per bird between strains within populations or between selected and control strains overall. Thirty of 62 comparisons in the three populations indicated ev gene frequency differences (P less than .05). Within populations, 13 of 93 comparisons of ev gene frequencies between control and selected strains and 8 of 62 between three selected strains of a sire population showed such differences (P less than .05). Selection for body weight and feed efficiency had been observed to reduce gene frequencies of the slow-feathering gene, which usually contains the ev21 locus; however, these effects were not detected (.05 less than P less than .06) between strains of the dam population in the current study. Such differences suggested possible associations between ev genes and production traits in meat-type chickens.