Major histocompatibility complex class IV restriction fragment length polymorphism markers in replicated meat-type chicken lines divergently selected for high or low early immune response

Immunoglobulin-like receptors in chickens: identification, functional characterization, and renaming to cluster homolog of immunoglobulin-like receptors

The cluster homolog of immunoglobulin-like receptors (CHIRs), previously known as the "chicken homolog of immunogloublin-like receptors," represents is a large group of transmembrane glycoproteins that direct the immune response. However, the full repertoire of putatively activating, inhibitory, or dual function CHIRA, CHIRB, and CHIRAB on chickens' immune responses is poorly understood. Herein, the study objective was to determine the genes encoding CHIR proteins and predict their function by searching canonical protein structure. A bioinformatics pipeline based on previous work was employed to search for the CHIRs from the newly updated broiler and layer genomes. The categorization into CHIRA, CHIRB, and CHIRAB types was assigned through motif searches, multiple sequence alignment, and phylogeny. In total, 150 protein-encoding genes on Chromosome 31 were identified as CHIRs. Gene members of each functional group (CHIRA, CHIRB, CHIRAB) were classified in accordance with previously recognized proteins. The genes were renamed to "cluster homolog of immunoglobulin-like receptors" (CHIRs) to allow for the naming of orthologous genes in other avian species. Additionally, expression analysis of the classified CHIRs across various reinforces their importance as immune regulators and activation in inflammatory tissues. Furthermore, over 1,000 diverse and rare CHIRs variants associated with differential Marek's disease response (P < 0.05) emphasize the impact of CHIRs on shaping avian immune responses in diverse contexts. The practical applications of these findings encompass advancing immunology, improving poultry health management, optimizing breeding programs for disease resistance, and enhancing overall animal health through a deeper understanding of the roles and functions of CHIRA, CHIRB, and CHIRAB types in avian immune responses.

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.

Advances in methodologies for detecting MHC-B variability in chickens

The chicken major histocompatibility B complex (MHC-B) region is of great interest owing to its very strong association with resistance to many diseases. Variation in the MHC-B was initially identified by hemagglutination of red blood cells with specific alloantisera. New technologies, developed to identify variation in biological materials, have been applied to the chicken MHC. Protein variation encoded by the MHC genes was examined by immunoprecipitation and 2-dimensional gel electrophoresis. Increased availability of DNA probes, PCR, and sequencing resulted in the application of DNA-based methods for MHC detection. The chicken reference genome, completed in 2004, allowed further refinements in DNA methods that enabled more rapid examination of MHC variation and extended such analyses to include very diverse chicken populations. This review progresses from the inception of MHC-B identification to the present, describing multiple methods, plus their advantages and disadvantages.

Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance

Nearly all genes presently mapped to chicken chromosome 16 (GGA 16) have either a demonstrated role in immune responses or are considered to serve in immunity by reason of sequence homology with immune system genes defined in other species. The genes are best described in regional units. Among these, the best known is the polymorphic major histocompatibility complex-B (MHC-B) region containing genes for classical peptide antigen presentation. Nearby MHC-B is a small region containing two CD1 genes, which encode molecules known to bind lipid antigens and which will likely be found in chickens to present lipids to specialized T cells, as occurs with CD1 molecules in other species. Another region is the MHC-Y region, separated from MHC-B by an intervening region of tandem repeats. Like MHC-B, MHC-Y is polymorphic. It contains specialized class I and class II genes and c-type lectin-like genes. Yet another region, separated from MHC-Y by the single nucleolar organizing region (NOR) in the chicken genome, contains olfactory receptor genes and scavenger receptor genes, which are also thought to contribute to immunity. The structure, distribution, linkages and patterns of polymorphism in these regions, suggest GGA 16 evolves as a microchromosome devoted to immune defense. Many GGA 16 genes are polymorphic and polygenic. At the moment most disease associations are at the haplotype level. Roles of individual MHC genes in disease resistance are documented in only a very few instances. Provided suitable experimental stocks persist, the availability of increasingly detailed maps of GGA 16 genes combined with new means for detecting genetic variability will lead to investigations defining the contributions of individual loci and more applications for immunogenetics in breeding healthy poultry.

Genetic variation at the MHC in a population of introduced wild turkeys

Genetic variation in the major histocompatibility complex (MHC) is known to affect disease resistance in many species. Investigations of MHC diversity in populations of wild species have focused on the antigen presenting class IIβ molecules due to the known polymorphic nature of these genes and the role these molecules play in pathogen recognition. Studies of MHC haplotype variation in the turkey ( Meleagris gallopavo ) are limited. This study was designed to examine MHC diversity in a group of Eastern wild turkeys ( Meleagris gallopavo silvestris ) collected during population expansion following reintroduction of the species in southern Wisconsin, USA. Southern blotting with BG and class IIβ probes and single nucleotide polymorphism (SNP) genotyping was used to measure MHC variation. SNP analysis focused on single copy MHC genes flanking the highly polymorphic class IIβ genes. Southern blotting identified 27 class IIβ phenotypes, whereas SNP analysis identified 13 SNP haplotypes occurring in 28 combined genotypes. Results show that genetic diversity estimates based on RFLP (Southern blot) analysis underestimate the level of variation detected by SNP analysis. Sequence analysis of the mitochondrial D-loop identified 7 mitochondrial haplotypes (mitotypes) in the sampled birds. Results show that wild turkeys located in southern Wisconsin have a genetically diverse MHC and originate from several maternal lineages.

Genotypic variability at the major histocompatibility complex (B and Rfp-Y) in Camperos broiler chickens

Evidence for the importance of major histocompatibility complex (MHC) genotype in immunological fitness of chickens continues to accumulate. The MHC B haplotypes contribute resistance to Marek's and other diseases of economic importance. The Rfp-Y, a second cluster of MHC genes in the chicken, may also contribute to disease resistance. Nevertheless, the MHC B and Rfp-Y haplotypes segregating in broiler chickens are poorly documented. The Camperos, free-range broiler chickens developed in Argentina, provide an opportunity to evaluate MHC diversity in a genetically diverse broiler stock. Camperos are derived by cross-breeding parental stocks maintained essentially without selection since their founding. We analysed 51 DNA samples from the Camperos and their parental lines for MHC B and Rfp-Y variability by restriction fragment pattern (rfp) and SSCP typing methods for B-G, B-F (class Ia), B-Lbeta (class II) and Y-F (class Ib) diversity. We found evidence for 38 B-G genotypes. The Camperos B-G patterns were not shared with White Leghorn controls, nor were any of a limited number of Camperos B-G gene sequences identical to published B-G sequences. The SSCP assays provided evidence for the presence of at least 28 B-F and 29 B-Lbeta genotypes. When considered together B-F, B-L, and B-G patterns provide evidence for 40 Camperos B genotypes. We found even greater Rfp-Y diversity. The Rfp-Y class I-specific probe, 163/164f, revealed 44 different rfps among the 51 samples. We conclude that substantial MHC B and Rfp-Y diversity exists within broiler chickens that might be drawn upon in selecting for desirable immunological traits.

Single-strand conformation polymorphism (SSCP) assays for major histocompatibility complex B genotyping in chickens

We have developed a DNA-based method for defining MHC B system genotypes in chickens. Genotyping by this method requires neither prior determination of allele-specific differences in nucleotide sequence nor the preparation of haplotype-specific alloantisera. Allelic differences at chicken B-F (class I) and B-L (class II) loci are detected in PCR single-strand conformation polymorphism (SSCP) assays. PCR primer pairs were designed to hybridize specifically with conserved sequences surrounding hypervariable regions within the two class I and two class I loci of the B-complex and used to generate DNA fragments that are heat- and formamide-denatured and then analyzed on nondenaturing polyacrylamide gels. PCR primer pairs were tested for the capacity to produce SSCP patterns allowing the seven B haplotypes in the MHC B congenic lines, and seven B haplotypes known to be segregating in two commercial broiler breeder lines to be distinguished. Primer pairs were further evaluated for their capacity to reveal the segregation of B haplotypes in a fully pedigreed family and in a closed population. Concordance was found between SSCP patterns and previously assigned MHC types. B-F and B-L SSCP patterns segregated in linkage as expected for these closely linked loci. We conclude that this method is valuable for defining MHC B haplotypes and for detecting potential recombinant haplotypes especially when used in combination with B-G (class IV) typing by restriction fragment pattern.

Genetic diversity at the major histocompatibility complex (B) and microsatellite loci in three commercial broiler pure lines

Genetic diversity at the MHC and non-MHC loci was investigated in three commercial broiler chicken pure lines. The MHC class II and IV loci were evaluated in Southern hybridizations and molecular genotypes based on RFLP were interpreted from pedigreed families. Four MHC class II and eight class IV genotypes were identified in the broiler lines, and their frequencies differed among the lines. Line-specific MHC genotypes were identified. The observed heterozygosities (59 to 67%) suggest that the MHC loci are highly polymorphic in the broiler lines. At least 9% of the genetic variation at the MHC was due to line differences; the remainder reflected individual variations. To characterize non-MHC genes, 41 microsatellite loci located throughout the chicken genome were evaluated in the broiler lines. Genetic variation was also observed at the microsatellite loci for the broiler lines; the number of alleles at a single locus ranged from one to eight, and the average number of alleles per locus was 3.5, 2.8, and 3.1 for each of the lines, respectively. The observed heterozygosities for microsatellite loci ranged between 0 and 89% in the lines. Based on the fixation index (Fst), about 19% of the genetic variation at microsatellite loci was attributed to broiler line differences. Deviations from Hardy-Weinberg equilibrium were detected at both MHC and non-MHC loci. Possible explanations for these deviations include genetic selection by the primary broiler breeder or the presence of null alleles that were not identified by the typing procedures described in this report. This study contributes to our knowledge on the molecular characteristics and genetic structure of a commercial broiler chicken population. Analysis of MHC and non-MHC loci suggests that there is still sufficient genetic diversity in the broiler lines to continue the progress toward improved broiler chicken production.

Phenotypic variation among three broiler pure lines for Marek's disease, coccidiosis, and antibody response to sheep red blood cells

To identify candidate genes, chicken lines with the most divergent phenotypes are usually crossed to generate resource mapping populations, for example, either backcrossed or F2 populations. Linkage between the genetic marker and the phenotypic trait locus is then tested in the mapping population. As an initial step in the development of a mapping population from commercial broilers, the goal of the current research was to evaluate the phenotypic variation among three pure lines for antibody response to SRBC and in resistance to two economically important poultry diseases, Marek's disease (MD) and coccidiosis (Eimeria acervulina). Chicks from each line were received and separated into three experimental studies to evaluate each of their responses. In summary, broiler Line 3 had significantly lower antibody responses to SRBC immunizations compared to the other two lines, and nonvaccinated birds from Line 3 were also more susceptible to MD. With coccidiosis, the response was complex, and ranking of the lines was dependent on the age of infection, and whether it was a first or second challenge. With the first challenge, Line 1 was most susceptible at the younger age (Day 30), whereas Line 3 was susceptible at the older age (Day 58). Upon the second challenge, broiler Line 1 remained susceptible at the younger age, but Line 2 was more susceptible at the older age. Line 3 was completely resistant to the second challenge at the older age. Thus, although the broiler lines have been intensively selected for productivity and general livability, this study also demonstrates that the lines differ for immune response and disease resistance. Based on the phenotypic differences between Lines 1 and 3, they were chosen to establish a mapping population for identifying candidate genes that affect MD and coccidiosis in commercial broiler chickens.

Resistance to Marek's disease virus in White Leghorn chickens: effects of avian leukosis virus infection genotype, reciprocal mating, and major histocompatibility complex

Genetic improvement for resistance to Marek's Disease (MD) in chickens continues to be of interest to the poultry industry. The aims of this study were to identify effects of the MHC on the molecular level and of avian leukosis virus (ALV) resistance status on MD mortality in two noninbred White Leghorn chicken lines that differ in B blood group type. Previously, within each of the chicken lines, sublines had been selected for resistance or susceptibility to ALV infection with Subgroups A and B. In this study, F2 offspring, obtained by crossing the two ALV-resistant or the two ALV-susceptible sublines, were tested for MD mortality after contact exposure at 1 d of age. Reciprocal matings were made in the grandparental generation. The MD mortality percentages, in an observation period of 17 wk, of F2 offspring from two hatches were 82.63 and 92.35%, respectively. Survival analysis (Cox model) was applied to assess the risk of dying from MD. No differences in MD mortality risk profiles were found between ALV-resistant and ALV-susceptible F2 offspring. Within ALV-susceptible F2 offspring, however, a reciprocal mating effect was observed in both hatches. The MHC Class I, II, and IV restriction fragment length polymorphism (RFLP) analyses were carried out on birds of the first hatch. Although two of 11 MHC class IV RFLP bands displayed a significant effect, in general, a strong association of MHC and MD mortality was not detectable.

Immune response and resistance to infectious bursal disease virus of chicken lines selected for high or low antibody response to Escherichia coli

Two experimental broiler lines were developed by divergent selection for high (HH) and low (LL) antibody response to Escherichia coli. Antibody response of these lines to immunization with a commercial vaccine (whole inactivated virus, WIV) against infectious bursal disease virus (IBDV) or with proteins VP2 and VP3 of that virus, and their resistance to challenge with a virulent IBDV, were tested. The study was performed with 213 male and female chicks from the tenth generation of the HH and LL lines. At 15 d of age, after disappearance of maternal antibodies, chicks from each line were randomly divided into four groups and injected with WIV, VP2, VP3, or adjuvant alone as a negative control. Chicks were bled 18 d postinjection, and antibody titers were determined by ELISA. Ten days later, the chicks were challenged with a virulent strain of the virus and killed after 10 d; the ratio of bursa of Fabricius to 100 g BW was determined for each bird. Significant differences in antibody titers were found among immunized and control chicks. Chicks from the HH line exhibited significantly higher antibody titers than LL chicks in response to WIV and VP2 vaccines but not to VP3 vaccine. Following challenge, bursa weight (relative to BW) of HH and LL chicks vaccinated with WIV and VP2 was significantly higher (P < 0.01) than that of chicks vaccinated with VP3 or the challenged unvaccinated control. No difference was found in this parameter between the latter two groups. Possible explanations for the differences in the line response to VP2 and VP3 are discussed.

Major histocompatibility complex (MHC) related cDNA probes associated with antibody response in meat-type chickens

The major histocompatibility complex (MHC) region was examined as a set of candidate genes for association between DNA markers and antibody response. Intercross F2 families of chickens were generated from a cross between high (HC) and low (LC) Escherichia coli(i) antibody lines. Restriction fragment length polymorphism (RFLP) analysis was conducted by using three MHC-related cDNA probes: chicken MHC class IV (B-G), chicken MHC class I (B-F), and human MHC-linked Tap2. Association between RFLP bands and three antibody response traits (E. coli, sheep red blood cells and Newcastle disease virus) were determined by two methods: by statistically analyzing each band separately and also by analyzing all bands obtained from the three probes by using multiple regression analysis to account for the multiple comparisons. The MHC class IV probe was the highest in polymorphisms but had the lowest number of bands associated with antibody response. The MHC class I probe yielded 15 polymorphic bands of which four exhibited association with antibody response traits. The Tap2 probe yielded 20 different RFLP bands of which five were associated with antibody production. Some Tap2 bands were associated with multiple antibody response traits. The multiband analysis of the three probes' bands revealed more significant effects than the analysis of each band separately. This study illustrates the efficacy of using multiple MHC region probes as candidate markers for quantitative trait loci (QTLs) controlling antibody response in chickens.

Impact of genetics on disease resistance

The genetics of a bird or flock has a profound impact on its ability to resist disease, because genetics define the maximum achievable performance level. Careful attention should be paid to genetics as an important component of a comprehensive disease management program including high-level biosecurity, sanitation, and appropriate vaccination programs. Some specific genes (e.g., the MHC) are known to play a role in disease resistance, but resistance is generally a polygenic phenomenon. Future research directions will expand knowledge of the impact of genetics on disease resistance by identifying non-MHC genetic control of resistance and by further elucidating mechanisms regulating expression of genes related to immune response.

The influence of major histocompatibility complex genotypes on resistance to Pasteurella multocida and Newcastle disease virus in turkeys

Sublines homozygous for each of four MHC haplotypes were developed from randombred control populations of turkeys and challenged with Pasteurella multocida (capsular serogroup a, somatic serotype 3, 4) at 6 wk of age or Newcastle disease virus (NDV; Texas GB strain) at 4 wk of age. In addition, individuals from a randombred control line (RBC2) and a subline (F) of RBC2 long-term selected for increased 16-wk BW were included in most of the challenge trials. The duration of the challenge trials was 2 wk for both organisms. Mortality following challenge with P. multocida or NDV was higher in the F line than in its randombred control. The MHC genotypes differed in mortality following exposure to both organisms but the rankings of the genotypes were not the same for P. multocida and NDV. The increased susceptibility of the F line to both organisms could not be explained by known changes in the frequency of the MHC haplotypes.

Poultry immunogenetics: which way do we go?

A major goal in poultry immunogenetics is the enhancement of innate immunoresponsiveness and resistance to disease. This may be pursued by studying either single genes or polygenic traits. The MHC is perhaps the best-characterized family of host genes that modulates response to a variety of antigens and pathogenic challenges. The association of different MHC alleles with disease resistance has been known for decades. But only recently has analysis at the DNA level opened new avenues of understanding and new opportunities for application of genetic variation in the MHC with immunoresponsiveness. An alternate approach to molecular analysis is selection for a desired phenotype controlled by polygenes. Several studies have illustrated the successful alteration of immunoresponsiveness by genetic selection for antibody production. Recently, a selection program based upon multiple traits of immune response was conducted. Results of this project demonstrated that selection on multiple immune-response traits altered immunophysiology, MHC allelic frequencies, and disease resistance. Several areas for future pursuits in poultry immunogenetics research are proposed.