Assignment of Rfp-Y to the chicken major histocompatibility complex/NOR microchromosome and evidence for high-frequency recombination associated with the nucleolar organizer region

cDNA cloning, genomic structure and expression analysis of the goose (Anser cygnoides) MHC class I gene

To provide data for studies on avian disease resistance, goose MHC class I cDNA (Ancy-MHC I) was cloned from a goose cDNA library, it's genomic structure and expression analysis were investigated. The mature peptides of Ancy-MHC I cDNA encoded 333 amino acids. The genomic organization is composed of eight exons and seven introns. Based on the genetic distance, six Ancy-MHC I genes from six individuals can be classified into four lineages. A total of nineteen amino acid positions in peptide-binding domain showed high scores by Wu-kabat index analysis. The Ancy-MHC I amino acid sequence displayed seven critical HLA-A2 amino acids that bind with antigen polypeptides, and have an 85.4-98.9% amino acid homology with each genes, and a 59.8-66.0% amino acid homology with chicken MHC class I. Expression analyses using Q-RT-PCR to detect the tissue-specific expression of Ancy-MHC I mRNA in an adult goose. The result appeared that Ancy-MHC I cDNA was expressed in the liver, spleen, intestine, kidney, lung, pancreas, heart, brain, and skin. The phylogenetic tree appears to branch in an order consistent with accepted evolutionary pathways.

Characterisation of a cluster of TRIM-B30.2 genes in the chicken MHC B locus

We have identified and characterised a cluster of six TRIM-B30.2 genes flanking the chicken BF/BL region of the B complex. The TRIM-B30.2 proteins are a subgroup of the TRIM protein family containing the tripartite motif (TRIM), consisting of a RING domain, a B-box and a coiled coil region, and a B30.2-like domain. In humans, a cluster of seven TRIM-B30.2 genes has been characterised within the MHC on Chromosome 6p21.33. Among the six chicken TRIM-B30.2 genes two are orthologous to those of the human MHC, and two (TRIM41 and TRIM7) are orthologous to human genes located on Chromosome 5. In humans, these last two genes are adjacent to GNB2L1, a guanine nucleotide-binding protein gene, the ortholog of the chicken c12.3 gene situated in the vicinity of the TRIM-B30.2 genes. This suggests that breakpoints specific to mammals have occurred and led to the remodelling of their MHC structure. In terms of structure, like their mammalian counterparts, each chicken gene consists of five coding exons; exon 1 encodes the RING domain and the B-box, exons 2, 3 and 4 form the coiled-coil region, and the last exon represents the B30.2-like domain. Phylogenetic analysis led us to assume that this extended BF/BL region may be similar to the human extended class I region, because it contains a cluster of BG genes sharing an Ig-V like domain with the BTN genes (Henry et al. 1997a) and six TRIM-B30.2 genes containing the B30.2-like domain, shared with the TRIM-B30.2 members and the BTN genes.

Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype

Chicken genome mapping is important for a range of scientific disciplines. The ability to distinguish chromosomes of the chicken and other birds is thus a priority. Here we describe the molecular cytogenetic characterization of each chicken chromosome using chromosome painting and mapping of individual clones by FISH. Where possible, we have assigned the chromosomes to known linkage groups. We propose, on the basis of size, that the NOR chromosome is approximately the size of chromosome 22; however, we suggest that its original assignment of 16 should be retained. We also suggest a definitive chromosome classification system and propose that the probes developed here will find wide utility in the fields of developmental biology, DT40 studies, agriculture, vertebrate genome organization, and comparative mapping of avian species.

B-F DNA sequence variability in Brazilian (blue-egg Caipira) chickens

A total of 100 chickens from the Brazilian (blue-egg Caipira) native breed were studied in relation to exon 2 of the B-F genes of the major histocompatibility complex (MHC) region. After a first screening on 100 birds, 22 animals were selected for amplification, cloning and sequencing experiments of exons 2-4 (a total of 1048 bp) of their DNA. Twenty-three sequences were obtained, of which at least 10 appear novel. Inferred protein sequences were compared with those previously described, totalling 41 different sequences with amino acid changes in 33 of the 88 sites in alpha1, and 34 of the 91 sites in alpha2 domains. Allele expression was investigated in these animals through cloning experiments. The blue-egg Caipira chickens may provide a source of novel B-F alleles for genetic improvement programmes.

Natural selection of the major histocompatibility complex (Mhc) in Hawaiian honeycreepers (Drepanidinae)

The native Hawaiian honeycreepers represent a classic example of adaptive radiation and speciation, but currently face one the highest extinction rates in the world. Although multiple factors have likely influenced the fate of Hawaiian birds, the relatively recent introduction of avian malaria is thought to be a major factor limiting honeycreeper distribution and abundance. We have initiated genetic analyses of class II beta chain Mhc genes in four species of honeycreepers using methods that eliminate the possibility of sequencing mosaic variants formed by cloning heteroduplexed polymerase chain reaction products. Phylogenetic analyses group the honeycreeper Mhc sequences into two distinct clusters. Variation within one cluster is high, with dN > dS and levels of diversity similar to other studies of Mhc (B system) genes in birds. The second cluster is nearly invariant and includes sequences from honeycreepers (Fringillidae), a sparrow (Emberizidae) and a blackbird (Emberizidae). This highly conserved cluster appears reminiscent of the independently segregating Rfp-Y system of genes defined in chickens. The notion that balancing selection operates at the Mhc in the honeycreepers is supported by transpecies polymorphism and strikingly high dN/dS ratios at codons putatively involved in peptide interaction. Mitochondrial DNA control region sequences were invariant in the i'iwi, but were highly variable in the 'amakihi. By contrast, levels of variability of class II beta chain Mhc sequence codons that are hypothesized to be directly involved in peptide interactions appear comparable between i'iwi and 'amakihi. In the i'iwi, natural selection may have maintained variation within the Mhc, even in the face of what appears to a genetic bottleneck.

MHC class IIB gene sequences and expression in quails (Coturnix japonica) selected for high and low antibody responses

Two quail lines, H and L, which were developed for high (H) and low (L) antibody production against inactivated Newcastle disease virus antigen, were used to examine differences in the organization, structure and expression of the quail Mhc class IIB genes. Four Coja class IIB genes in the H line and ten Coja class IIB genes in the L line were identified by gene amplification using standard and long-range PCRs and sequencing of the amplified products. RFLP analysis, sequencing and gene mapping revealed that the H line was fixed for a single class IIB haplotype, which we have designated CojaII-02HL- CojaII-01HL. In contrast, evidence was found for two class IIB haplotypes segregating in the L line. Some individuals were found to be homozygous for haplotype CojaII-08L- CojaII-07L and others were found to be heterozygous CojaII-08L- CojaII-07L/ CojaII-02HL- CojaII-01HL. However, expression of CojaII-02HL- CojaII-01HL was not detected in the L line. SRBC immunization induced a measurable antibody response in the serum and a line-specific class IIB gene expression in the peripheral white blood cells. CojaII-01HL was expressed at the highest level in the H line and CojaII-07L in the L line. The expression of the class IIB mRNA reached the highest level at approximately 1 week after the primary antibody response and then declined exponentially. The antibody and class IIB gene expression data obtained in response to SRBC immunization provide further evidence that quails within the L line had reduced immunocompetence compared with those in the H line.

cDNA cloning and genomic structure of the duck (Anas platyrhynchos) MHC class I gene

In order to provide data for studies on disease resistance, duck MHC class I cDNA (Anpl-MHC I) was cloned from a duck cDNA library and the genome structure was investigated. Anpl-MHC I genes encoded 344-355 amino acids. The genomic organization is composed of eight exons and seven introns. Based on the genetic distance, Anpl-MHC I cDNA from six individuals can be classified into four lineages (from Anpl-UAA to Anpl-UDA). A total of 28 amino acid positions in the peptide-binding domain (PBD) showed high scores by Wu-kabat index analysis. The Anpl-MHC amino acid sequence displayed seven critical HLA-A2amino acids that bind with antigen polypeptides, and have an 83.6-88.5% amino acid homology with each lineage, a 55.2-64.6% amino-acid homology with chicken MHC class I (B-FIV21, B-FIV2, Rfp-Y), and a 40.3-42.8% homology with mammalian MHC class I. Nested PCR detected that Anpl-MHC I can be expressed in the brain, heart, kidney, intestines and bursa. Compared with the human HLA-A2 tertiary structure of the PBD, Anpl-MHC I had an insertion or deletion variation in four domains (A-D). The phlyogenetic tree appears to branch in an order consistent with accepted evolutionary pathways.

The dominant MHC class I gene is adjacent to the polymorphic TAP2 gene in the duck, Anas platyrhynchos

We are investigating the expression and linkage of major histocompatibility complex (MHC) class I genes in the duck ( Anas platyrhynchos) with a view toward understanding the susceptibility of ducks to two medically important viruses: influenza A and hepatitis B. In mammals, there are multiple MHC class I loci, and alleles at a locus are polymorphic and co-dominantly expressed. In contrast, in lower vertebrates the expression of one locus predominates. Southern-blot analysis and amplification of genomic sequences suggested that ducks have at least four loci encoding MHC class I. To identify expressed MHC genes, we constructed an unamplified cDNA library from the spleen of a single duck and screened for MHC class I. We sequenced 44 positive clones and identified four MHC class I sequences, each sharing approximately 85% nucleotide identity. Allele-specific oligonucleotide hybridization to a Northern blot indicated that only two of these sequences were abundantly expressed. In chickens, the dominantly expressed MHC class I gene lies adjacent to the transporter of antigen processing ( TAP2) gene. To investigate whether this organization is also found in ducks, we cloned the gene encoding TAP2 from the cDNA library. PCR amplification from genomic DNA allowed us to determine that the dominantly expressed MHC class I gene was adjacent to TAP2. Furthermore, we amplified two alleles of the TAP2 gene from this duck that have significant and clustered amino acid differences that may influence the peptides transported. This organization has implications for the ability of ducks to eliminate viral pathogens.

Nutritional modulation of immune function in broilers

Collaborative research efforts across disciplines typically result in more insight toward the hypothesis being tested due to the omnibus nature of the projects. For example, nutritional experiments evaluating a nutrient response will benefit greatly by incorporating biochemical, physiological, and immunological endpoints for measurement. Clearly, commercial poultry producers do not have the luxury of focusing on specific disciplines when field problems occur. Hence, in practice interplay exists among nutrition, genetics, management, and diseases. Dietary composition impacts immune function of the chicken. As research in the area of nutritional immunology has increased, it is becoming apparent that nutrient needs for immunity do not coincide with those for growth or skeletal tissue accretion. This review is not a comprehensive assessment of nutrient needs for immunity in the chicken. Rather, this review is concerned with nutritional modulation of immunity in broilers that offers insight for nutritionists and researchers to implement nutritional regimens to reduce the severity of disease and to test or validate nutritional regimens that heighten immunity. Nutritional modulation of the hen diet and in ovo nutrient modulation to improve chick immunity and disease resistance are discussed.

Molecular and cytogenetic organization of the 5S ribosomal DNA array in chicken (Gallus gallus)

The 5S ribosomal (r) RNA genes encode a small (approximately 120-bp) highly-conserved component of the large ribosomal subunit. The objective of the present research was to study the molecular and cytogenetic organization of the chicken 5S rDNA. A predominant 2.2-kb gene (5Salpha) consisting of a coding and intergenic spacer (IGS) region was identified in ten research and commercial populations. A variant gene repeat of 0.6kb (5Sbeta) was observed in some of the populations. Genetic linkage analysis and cytogenetic localization by fluorescence in-situ hybridization assigned the 5S rDNA to chromosome 9. The 5S rDNA array was determined to be 80.2 +/- 7.0 kb upon electrophoretic sizing following EcoRV digestion. Sequence analysis of 5Salpha IGS regions revealed considerable conservation between chicken subspecies (98.4% identity) as well as homology with vertebrate Pol III promoter and regulatory sequence motifs. Minor intraindividual sequence variation within 1000 bp of IGS was observed in four cloned Red Jungle Fowl (Gallus gallus gallus) 5Salpha repeats (95.5% identity in this region). Sequence comparisons between IGS regions of 5Salpha and 5Sbeta genes indicated two short continuous (>20bp) and many short non-continuous homologous regions as well as other conserved features such as promoter and termination motifs.

Diversity and locus specificity of chicken MHC B class I sequences

The major histocompatibility complex B (MHC B) region in a standard haplotype of Leghorn chickens contains two closely linked class I loci, B-FI and B-FIV. Few sequences of B-FI alleles are available, and therefore alleles of the two loci have not been compared with regard to sequence diversity or locus specificity. Here, we report eight new B-F alpha 1/alpha 2-coding sequences from broiler chicken MHC B haplotypes, and a unique recombinant between the two B-F loci. The new sequences were combined with existing B-F sequences from Leghorn and broiler haplotypes for analysis. On the basis of phylogenetic analysis and conserved sequence motifs, B-F sequences separated into two groups (Groups A and B), corresponding to B-FIV and B-FI locus, respectively. Every broiler haplotype had one B-F sequence in Group A and the second B-F sequence, if it existed, clustered in Group B. Group B (presumptive B-FI locus) sequences identified in broiler haplotypes resembled the human MHC class I HLA-C locus in their distinctive pattern of allelic polymorphism. Compared with B-FIV, B-FI alleles were less polymorphic and possessed a conserved locus-specific motif in the alpha1 helix, but nevertheless demonstrated evidence of diversifying selection. One B-FI alpha 1/alpha 2-coding nucleotide sequence was completely conserved in four different broiler haplotypes, but each allele differed in the exon encoding the alpha 3 domain.

The properties of the single chicken MHC classical class II alpha chain ( B-LA) gene indicate an ancient origin for the DR/E-like isotype of class II molecules

In mammals, there are MHC class II molecules with distinctive sequence features, such as the classical isotypes DR, DQ and DP. These particular isotypes have not been reported in non-mammalian vertebrates. We have isolated the class II (B-L) alpha chain from outbred chickens as the basis for the cloning and sequencing of the cDNA. We found only one class II alpha chain transcript, which bears the major features of a classical class II alpha sequence, including the critical peptide-binding residues. The chicken sequence is more similar to human DR than to the DQ, DP, DO or DM isotypes, most significantly in the peptide-binding alpha(1) domain. The cDNA and genomic DNA sequences from chickens of diverse origins show few alleles, which differ in only four nucleotides and one amino acid. In contrast, significant restriction fragment length polymorphism is detected by Southern blot analysis of genomic DNA, suggesting considerable diversity around the gene. Analysis of a large back-cross family indicates that the class II alpha chain locus ( B-LA) is located roughly 5.6 cM from the MHC locus, which encodes the classical class II beta chains. Thus the chicken class II alpha chain gene is like the mammalian DR and E isotypes in three properties: the presence of the critical peptide-binding residues, the low level of polymorphism and sequence diversity, and the recombinational separation from the class II beta chain genes. These results indicate that the sequence features of this lineage are both functionally important and at least 300 million years old.

Role of nonclassical class I genes of the chicken major histocompatibility complex Rfp-Y locus in transplantation immunity

The chicken major histocompatibility complex ( MHC) genes are organized into two genetically independent clusters which both possess class I and class IIbeta genes: the classical B complex and the Restriction fragment pattern- Y ( Rfp-Y) complex. In this study, we have examined the role of Rfp-Y genes in transplantation immunity. For this we used three sublines, B19H1, B19H2 and B19H3, derived from a line fixed for B19. Southern blots, PCR-SSCP assays using primers specific for Rfp-Y genes, and Rfp-Y class I allele-specific sequencing show that the polymorphisms observed in B19H1, B19H2 and B19H3 are due to the presence of three different Rfp-Y haplotypes. The Rfp-Y class I ( YF) alleles in these three haplotypes are highly polymorphic, and RT-PCR shows that at least two YF loci are expressed in each subline. The three sublines show Rfp-Y-directed alloreactivity in that Rfp-Y-incompatible skin grafts are rejected within 15 days, a rate intermediate between that seen in B-incompatible rejection (7 days) and that observed for grafts within the sublines (20 days). We conclude that Rfp-Y has an intermediate role in allograft rejection, likely to be attributable to polymorphism at the class I loci within this region.

Analysis of part of the chicken Rfp-Y region reveals two novel lectin genes, the first complete genomic sequence of a class I alpha-chain gene, a truncated class II beta-chain gene, and a large CR1 repeat

The Rfp-Y region lies on the same microchromosome as the B-F/B-L region of the B complex, yet in contrast to the latter it is poorly characterised. To date it has been shown to contain at least two class I alpha-chain ( Y-F) genes, a class II B-chain gene and a C-type lectin-like gene. We describe the sequencing and analysis of some 20 kb of the Rfp-Y region, and identify several new genes. These include two novel C-type lectin-like genes ( Y-Lec1 and Y-Lec2) that differ strongly from the previously described C-type lectin-like gene found in the Rfp-Y region. We describe a complete genomic sequence of a class I alpha-chain ( Y-F) gene and its promoter from the Rfp-Y region. The predicted cDNA from this gene has high homology to the previously reported Y-F cDNAs. The promoter contains an altered enhancer A element. This portion of the Rfp-Y region also contains a truncated class II B-chain ( Y-LB) gene, as well as a large chicken repeat 1 (CR1) element.

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.

Differences in chicken major histocompatibility complex (MHC) class Ialpha gene expression between Marek's disease-resistant and -susceptible MHC haplotypes

The expression of chicken major histocompatibility complex (MHC) class Ialpha genes was investigated in spleen cells from a panel of chickens with well-defined MHC haplotypes, and two class Ialpha transcripts of 1.9 and 1.5 kb were detected in various amounts. In BW1, B130 and B21, the two transcripts were almost equally expressed. In B2, B6, B12 and B19, the ratio between the two transcripts was 4 : 1, with the 1.9 kb transcript having the strongest expression. In B14 and B15, the 1.5 kb transcript was undetectable and the 1.9 kb transcript appeared to be exclusively expressed. Thus, haplotypes considered to have an MHC-determined resistance to Marek's disease (MD) had the highest relative amount of the 1.5 kb transcript, whereas haplotypes considered to be MD-susceptible had the lowest. In order to address a possible correlation between MHC-Ialpha transcriptional patterns and MD resistance, a larger animal material experimentally infected with MD virus (MDV) was examined. The expression of MHC class Ialpha genes was investigated in spleens as well as in other organs, 9 weeks post-infection (p.i.), from animals of the two MD-resistant haplotypes B21 and BW1 as well as from the MD-susceptible haplotype B19. In the spleen cells of infected animals, the relative amount of the 1.5 kb transcript in the haplotypes BW1 and B21 was shown to be significantly higher than that in B19. Interestingly, in infected BW1 and B21 animals, the relative amount of the 1.5 kb transcript was also significantly higher than that in healthy MHC-matched controls. In B19, no differences were detected between uninfected and infected animals. Furthermore, it was shown in BW1 and B21 that the two classical MHC-Ialpha genes located in the MHC region were both able to produce both mRNA transcripts. Hybridization experiments, using specific probes upstream and downstream of the polyadenylation signals in the 3' end of the MHC-Ialpha genes, demonstrated that alternate use of these signals is probably involved in the production of the two mRNA transcripts.

Chromosome mapping of MHC class I in rainbow trout (Oncorhynchus mykiss)

The major histocompatibility complex (MHC) is well-studied in mammals. Much research has addressed the genomic organisation of MHC genes and it is well established that human MHC class I genes are located on chromosome 6. However, information on the organisation of the MHC complex in rainbow trout is only beginning to become available. In the present study it was determined that rainbow trout MHC class I sequences are located on chromosome 18. This is the first reported use of fluorescence in situ hybridisation (FISH) to identify the chromosomal location of genes involved in the immune system of fish.

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.

Identification and evaluation of major histocompatibility complex antigens in chicken chimeras and their relationship to germline transmission

Chimeric chickens were evaluated as an intermediate for development of transgenic chickens. The transfer of Barred Plymouth Rock (BR) blastodermal cells into White Leghorn (WL) embryos results in BR-->WL chimeras, and some breeder males generate over 30% germline transmission of the BR genotype to offspring based on a feather-color trait. The objectives of the current study were to 1) identify the MHC (B haplotypes) in resident BR and WL lines, 2) establish that B antigens could be detected and quantified in red blood cells (RBC) of chimeras, 3) establish if there is a correlation in chimeras between percentage of RBC with donor B antigens and percentage germline transmission, and 4) evaluate if the MHC genotype influences chimera development. The RBC agglutination data indicated three B haplotypes were present in each line. The B*2-like, and B*19-like genes were unique to the WL line, and B*13-like and B-15-like genes were unique to the BR line, whereas a B*21-like gene was present in both lines. In adult BR-->WL chimeras, as well as 10- to 14 d-old WL-->WL chimeras, donor-type B antigens were detectable and quantifiable on RBC using flow cytometry. In BR-->WL chimeras, the percentage germline transmission was significantly correlated with the percentage of RBC with donor B antigen, as well as percentage of black feathers in the plumage. In a retrospective study using previously developed BR-->WL chimeras, the level of chimerism and germline transmission was higher in B*21/*21 type recipients, but this was not statistically significant in two prospective studies. It was concluded that MHC antigens on RBC can be used for identifying, quantifying, and selecting chicken chimeras developed by the transfer of blastodermal cells.

Variation at the major histocompatibility complex in Savannah sparrows

The class I and class II genes of the major histocompatibility complex (Mhc) encode dimeric glycoproteins responsible for eliciting the adaptive immune response of vertebrates. Recent work with birds suggests that the number, size, and arrangement of these genes can differ markedly across species, although the extent of this variation, and its causes and consequences, are poorly understood. We have used a 157-base-pair (bp) portion of the second exon of a class II B gene to probe the Mhc in a free-living population of Savannah sparrows (Passerculus sandwichensis). Segregation analysis of Mhc bands suggests that class II B genes can be found in two independently assorting clusters, as previously described for domestic chickens (Gallus gallus) and ring-necked pheasants (Phasianus colchicus) but unlike gene organization in mammals. The Mhc in Savannah sparrows appears large (with many class II B genes) and variable; we found 42 unique genotypes among 48 adults breeding on Kent Island, New Brunswick, Canada in 1995. Savannah sparrows are long-distance migrants, and these results support recent predictions that migratory birds should show higher levels of Mhc polymorphism and/or a greater number of genes than sedentary species. Savannah sparrows are also socially polygynous with high levels of extra-pair paternity, suggesting that a history of sexual selection might also influence the size and/or structure of the avian Mhc.

Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: evidence for a stable class I region and MHC haplotype lineages

Cartilaginous fish (e.g., sharks) are derived from the oldest vertebrate ancestor having an adaptive immune system, and thus are key models for examining MHC evolution. Previously, family studies in two shark species showed that classical class I (UAA) and class II genes are genetically linked. In this study, we show that proteasome genes LMP2 and LMP7, shark-specific LMP7-like, and the TAP1/2 genes are linked to class I/II. Functional LMP7 and LMP7-like genes, as well as multiple LMP2 genes or gene fragments, are found only in some sharks, suggesting that different sets of peptides might be generated depending upon inherited MHC haplotypes. Cosmid clones bearing the MHC-linked classical class I genes were isolated and shown to contain proteasome gene fragments. A non-MHC-linked LMP7 gene also was identified on another cosmid, but only two exons of this gene were detected, closely linked to a class I pseudogene (UAA-NC2); this region probably resulted from a recent duplication and translocation from the functional MHC. Tight linkage of proteasome and class I genes, in comparison with gene organizations of other vertebrates, suggests a primordial MHC organization. Another nonclassical class I gene (UAA-NC1) was detected that is linked neither to MHC nor to UAA-NC2; its high level of sequence similarity to UAA suggests that UAA-NC1 also was recently derived from UAA and translocated from MHC. These data further support the principle of a primordial class I region with few class I genes. Finally, multiple paternities in one family were demonstrated, with potential segregation distortions.

Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system

MHC gene organization (size, complexity, gene order) differs markedly among different species, and yet all nonmammalian vertebrates examined to date have a true "class I region" with tight linkage of genes encoding the class I presenting and processing molecules. Three paralogous regions of the human genome contain sets of linked genes homologous to various loci in the MHC class I, class II, and/or class III regions, providing insight into the organization of the "proto MHC" before the emergence of the adaptive immune system in the jawed vertebrates.

Major histocompatibility complex and immunoglobulin loci visualized by in situ hybridization on Xenopus chromosomes

A technique for fluorescent in situ hybridization (FISH) on chromosomes of the amphibian Xenopus laevis is described. Positive results were obtained with cDNA probes of about 1kb when at least three adjacent copies of the gene are present. The immunoglobulin heavy chain locus is in the centre of the long arm of chromosome 1. Previously, family studies showed that bona fide MHC class Ib genes segregated independently. Now we show that MHC class II alpha and beta genes and class Ib genes are on the same acrocentric chromosome, with MHC in the middle of the long arm, the class Ib complex (XNC) at the tip or the same arm. Each locus or complex is found on only one pair of chromosomes confirming the diploidization of these genes in the pseudotetraploid X. laevis.

At least one class I gene in restriction fragment pattern-Y (Rfp-Y), the second MHC gene cluster in the chicken, is transcribed, polymorphic, and shows divergent specialization in antigen binding region

MHC genes in the chicken are arranged into two genetically independent clusters located on the same chromosome. These are the classical B: system and restriction fragment pattern-Y (Rfp-Y), a second cluster of MHC genes identified recently through DNA hybridization. Because small numbers of MHC class I and class II genes are present in both B: and Rfp-Y, the two clusters might be the result of duplication of an entire chromosomal segment. We subcloned, sequenced, and analyzed the expression of two class I loci mapping to Rfp-Y to determine whether Rfp-Y should be considered either as a second, classical MHC or as a region containing specialized MHC-like genes, such as class Ib genes. The Rfp-Y genes are highly similar to each other (93%) and to classical class Ia genes (73% with chicken B: class I; 49% with HLA-A). One locus is disrupted and unexpressed. The other, YFV, is widely transcribed and polymorphic. Mature YFV protein associated with beta(2)m arrives on the surface of chicken B (RP9) lymphoma cells expressing YFV as an epitope-tagged transgene. Substitutions in the YFV Ag-binding region (ABR) occur at four of the eight highly conserved residues that are essential for binding of peptide-Ag in the class Ia molecules. Therefore, it is unlikely that Ag is bound in the YFV ABR in the manner typical of class Ia molecules. This ABR specialization indicates that even though YFV is polymorphic and widely transcribed, it is, in fact, a class Ib gene, and Rfp-Y is a region containing MHC genes of specialized function.

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.

A polymorphic major histocompatibility complex class II-like locus maps outside of both the chicken B-system and Rfp-Y-system

Chickens have two major regions encoding major histocompatibility complex (MHC) class Ialpha genes and MHC class IIss genes, the serological and functional B-system and the Rfp-Y-system. Recently, they have been shown to assort in a genetically independent way although still located on the same microchromosome. Moreover, the monomorphic MHC class IIalpha gene maps at a third locus located 5 cM from the nearest class IIss genes, located in the B-system (Kaufman et al., 1995). A pedigree family was studied in three generations in order to assign MHC class IIss restriction fragments observed in Southern blot analyses to either the B-system, the Rfp-Y-system or the B-Lalpha locus. In this study, we demonstrate by classical genetic testing of chickens within this fully pedigreed family the existence of an MHC class II-like polymorphic restriction fragment that segregates independently of the B-system, the Rfp-Y-system and of the B-Lalpha locus.

Patterns of ribosomal gene variation in elite commercial chicken pure line populations

The nucleolus organizer region (NOR) encodes the tandemly repeated 18S, 5.8S and 28S ribosomal (r) RNA genes. The NORs of broiler and layer commercial chicken pure lines were studied to establish the type and extent of genetic variation at this important locus. The parameters studied were gene copy number, repeat size, and diversity of NOR-types. The populations were organized into three groups for analysis including brown-egg broiler (13 lines), brown-egg layer (six lines), and white-egg layer (eight lines). The ribosomal gene copy number average of the white-egg layer populations was significantly lower (329 genes) than that of the brown-egg layers (372 genes); the brown-egg broiler ribosomal gene average was intermediate (350 genes). The white-egg layer populations exhibited a ribosomal repeat unit average size of 36 kb, significantly different from the brown-egg layer and brown-egg broiler average repeat unit size of 32.5 and 33.9 kb, respectively. NOR array size was similar among the three groups (6 mb). The brown-egg broiler populations exhibited polymorphic NOR patterns, intra- and interline, whereas the white-egg layer populations were essentially monomorphic for NOR-type; brown-egg layers exhibited an intermediate level of NOR diversity. Some NOR array characteristics may be a function of breed origin as brown-egg commercial populations, both broilers and layers, have similar breed origins and exhibited similarities for predominant repeat unit size as compared with white-egg layer populations. However, the finding that brown-egg broiler lines typically exhibit a greater number of segregating NOR-types than brown-egg layer lines suggests that the selection schemes of broiler vs. layer pure line populations may also have influenced the degree of variation at this gene complex.

The chicken B locus is a minimal essential major histocompatibility complex

Here we report the sequence of the region that determines rapid allograft rejection in chickens, the chicken major histocompatibility complex (MHC). This 92-kilobase region of the B locus contains only 19 genes, making the chicken MHC roughly 20-fold smaller than the human MHC. Virtually all the genes have counterparts in the human MHC, defining a minimal essential set of MHC genes conserved over 200 million years of divergence between birds and mammals. They are organized differently, with the class III region genes located outside the class II and class I region genes. The absence of proteasome genes is unexpected and might explain unusual peptide-binding specificities of chicken class I molecules. The presence of putative natural killer receptor gene(s) is unprecedented and might explain the importance of the B locus in the response to the herpes virus responsible for Marek's diseases. The small size and simplicity of the chicken MHC allows co-evolution of genes as haplotypes over considerable periods of time, and makes it possible to study the striking MHC-determined pathogen-specific disease resistance at the molecular level.

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.

A PCR method for typing B-L beta II family (class II MHC) alleles in broiler chickens

Certain haplotypes of the major histocompatibility (B) complex are strongly associated with resistance or susceptibility to several infectious diseases in Leghorn chickens. Identification of chicken haplotypes based on the nucleotide sequence of B complex loci could provide more precise identification of haplotypes than traditional serological methods. We report the development and application of polymerase chain reaction with sequence specific primers (PCR-SSP) to type broiler chicken B haplotypes based on the DNA sequence of B-L beta II family genes. Five well-defined standard B haplotypes from White Leghorns and 12 recently characterized B haplotypes from a broiler breeder line were used to develop the test system. The B-L beta II family loci were amplified from genomic DNA by B-L beta II family specific primers and then characterized by PCR-SSP. In total, ten pairs of primers, derived from the sequences of expressed B-L beta II family alleles, were used in the PCR typing test to discriminate the chicken B haplotypes identified previously by serological means. The PCR-SSP showed that each haplotype had a different amplification pattern, except those haplotypes known or suspected to have the same B-L beta alleles. Cloning and sequencing of the family specific PCR products indicated that two loci in the B-L beta II family, presumably B-L beta I and B-L beta II, were amplified. Finally, B-L beta PCR-SSP typing was used in combination with B-G RFLP analyses to characterize unusual (variant) B serotypes; the results indicate that some of these are natural recombinants within the B complex.

The chromosomal duplication model of the major histocompatibility complex

The major histocompatibility complex (MHC) is a genetic region that has been extensively studied by immunologists, molecular biologists, and evolutionary biologists. Nevertheless, our knowledge of how the MHC acquired its present-day organization is quite limited. The recent discovery that the mammalian genome contains regions paralogous to the MHC has led us to the proposal that the MHC region of jawed vertebrates arose as a result of ancient chromosomal duplications. Here, I review the current status of this proposal.

Gene organisation determines evolution of function in the chicken MHC

Some years ago, we used our data for class I genes, proteins and peptide-binding specificities to develop the hypothesis that the chicken B-F/B-L region represents a "minimal essential MHC". In this view, the B locus contains the classical (highly expressed and polymorphic) class I alpha and class II beta multigene families, which are reduced to one or two members, with many other genes moved away or deleted from the chicken genome altogether. We found that a single dominantly expressed class I gene determines the immune response to certain infectious pathogens, due to peptide-binding specificity and cell-surface expression level. This stands in stark contrast to well-studied mammals like humans and mice, in which every haplotype is more-or-less responsive to every pathogen and vaccine, presumably due to the multigene family of MHC molecules present. In order to approach the basis for a single dominantly expressed class I molecule, we have sequenced a portion of the B complex and examined the location and polymorphism of the class I (B-F) alpha, TAP and class II (B-L) beta genes. The region is remarkably compact and simple, with many of the genes expected from the MHC of mammals absent, including LMP, class II alpha and DO genes as well as most class III region genes. However, unexpected genes were present, including tapasin and putative natural killer receptor genes. The region is also organised differently from mammals, with the TAPs in between the class I genes, the tapasin gene in between the class II (B-L) beta genes, and the C4 gene outside of the class I alpha and class II beta genes. The close proximity of TAP and class I alpha genes leads to the possibility of co-evolution, which can drive the use of a single dominantly expressed class I molecule with peptide-binding specificity like the TAP molecule. There is also a single dominantly expressed class II beta gene, but the reason for this is not yet clear. Finally, the presence of the C4 gene outside of the classical class I alpha and class II beta genes suggests the possibility that this organisation was ancestral, although a number of models of organisation and evolution are still possible, given the presence of the Rfp-Y region with non-classical class I alpha and class II beta genes as well as the presence of multigene families of B-G and rRNA genes.

Ribosomal RNA gene copy number and nucleolar-size polymorphisms within and among chicken lines selected for enhanced growth

Ribosomal (r) DNA genotypes (rRNA gene copy number) and nucleolar phenotypes (nucleoli number and size) were studied in dam and sire commercial broiler pure lines from three primary breeder sources. Thirteen lines were studied to determine whether directionally selected broiler pure lines contain higher numbers of rRNA genes than a control line unselected for performance traits. Eight of the 13 lines exhibited rRNA gene copy averages between 261 and 331 copies, three lines had averages between 365 and 380, and two lines had average copy numbers equal to or greater than 450 rRNA genes. The overall source copy number average from one breeder company exhibited a value (402 rRNA genes) significantly different from the control value (300 rRNA genes). Nucleoli number and relative-size were examined in 9 of the 13 lines to establish ploidy and determine the population incidence of nucleolar size polymorphisms. All of the individuals examined for nucleolar phenotype expressed two nucleoli, indicating that gene copy number variation in those lines was generally unrelated to haploidy, aneuploidy, or polyploidy. A high frequency of individuals exhibited nucleolar size polymorphisms (line values of 57 to 87%). The results suggest that multiple nucleolus organizer region (NOR) types are segregating within and among broiler pure lines and that these NOR types contain variable numbers of rRNA genes that differ in nucleogenesis capacity.

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.

Rfp-Y region polymorphism and Marek's disease resistance in multitrait immunocompetence-selected chicken lines

Although the influence of the chicken classical MHC in resistance to many diseases is well established, the role of the recently identified, genetically independent, MHC-like region known as Rfp-Y is unclear. The objectives of this study were to analyze the frequencies of DNA polymorphisms of the Rfp-Y region in White Leghorn lines, which were divergently selected in replicate for multitrait immunocompetence, and to determine the association of these polymorphisms with Marek's disease (MD) resistance. Chicks, either with or without herpes virus of turkey (HVT) vaccination, were challenged with 500 ffu of a very virulent Marek's disease virus (Md5) at 2 d of age. The MD-related data were collected for 10 wk. PvuII-digested genomic DNA was hybridized with an Rfp-Y region-specific probe, 18.1. Three Rfp-Y polymorphisms were observed. The frequency of one Rfp-Y polymorphism was significantly different between divergently selected multitrait immunocompetence lines in one replicate only; therefore, the impact of multitrait immunocompetence selection on Rfp-Y polymorphisms is inconclusive. The PvuII defined Rfp-Y region polymorphisms had no association with either innate or vaccine-induced MD resistance to Md5 virus challenge.

The "minimal essential MHC" revisited: both peptide-binding and cell surface expression level of MHC molecules are polymorphisms selected by pathogens in chickens

Birds, like mammals, have a highly polymorphic MHC that determines strong allograft rejection. However, in contrast to mammals, there are a number of viral diseases for which resistance and susceptibility are determined by particular chicken MHC haplotypes. We have found that certain common chicken MHC haplotypes express only one class I molecule at high levels. The selection on a single MHC gene should be strong, in contrast to the situation in mammals. We have determined the peptide motifs for the dominant class I molecules from a number of chicken MHC haplotypes and found that they can explain the outcome of infections with a small virus. However, the strongest MHC association is the resistance of the chicken B21 haplotype to classical Marek's disease virus, a relatively large pathogen for which any MHC molecule should find peptides. In 40 chicken lines, the level of class I expression correlates with the level of MHC-determined susceptibility to Marek's disease, the most susceptible B19 with the highest expression and the most resistant B21 with the lowest expression. Thus, cell surface expression level of class I molecules appears to be a polymorphism under selection by infectious pathogens, just like peptide-binding specificity. We speculate that these expression level differences are another manifestation of the simple MHC of chickens, which in human and mouse haplotypes are averaged out.

Major histocompatibility complex class II DNA polymorphisms in chicken strains selected for Marek's disease resistance and egg production or for egg production alone

The objective of this study was to investigate frequencies of major histocompatibility complex (MHC) class II restriction fragments in two groups of White Leghorn strains. Each group consisted of an unselected control, a strain selected for egg production traits, and a strain selected for egg production traits and Marek's disease (MD) resistance. PvuII-digested genomic DNA was hybridized with a chicken genomic MHC class II probe. The MHC class II DNA fragment frequencies in the selected strains differed from those in the related unselected control and in the strain selected using the same criteria from a different base population. Based on the sizes of the breeding populations, particularly those in the control strain and in the strain selected for egg production, it was considered unlikely that the observed changes of the MHC class II fragment frequencies were due to random genetic drift. The data suggested that some MHC class II bands are associated with production traits or with MD resistance, and that these associations tend to be unique to each genetic background. Hence, MHC class II genes are likely candidates for the investigation of quantitative trait loci in egg production and disease resistance traits such as those for which the studied strains were selected.

Immunoresponsiveness in chickens: association of antibody production and the B system of the major histocompatibility complex

Lines of White Leghorn chickens were selected for high or low antibody response to sheep erythrocytes for five generations. The base population from which the experiment started was composed of individuals all of which were heterozygous at the MHC haplotypes B13 and B21. Body weights, egg production traits, and genotypes at the B system were monitored for all individuals in each generation. By Generations 4 and 5 there was separation of the two replicate lines selected for high titer from the two replicate lines selected for low titer. Over the course of the experiment, higher antibody titers and lower BW were associated with B21 and lower antibody titers and higher BW were associated with B13, although these relationships did not occur in every instance. Conclusions were that the B system was associated with antibody response, but that the chickens did not depend entirely upon that association for protection against foreign proteins. Also, the importance of having replicate lines in a selection experiment was shown.

Association between the Rfp-Y haplotype and the incidence of Marek's disease in chickens

Certain haplotypes at the major histocompatibility (B) complex (Mhc) of the chicken provide an easily demonstrated influence on tumor formation following infections with Marek's disease virus (MDV). Recognition that there is a second histocompatibility complex of genes in the chicken, Rfp-Y, comprised of Mhc class I and class II genes, some of which are at least transcribed, evokes the question of whether this gene complex might also influence the outcome of MDV infections. To test this hypothesis, pedigree-hatched chicks in families from the original Rfp-Y-defining stock in which three Rfp-Y and two B system haplotypes are segregating were challenged with the RB1B strain of MDV. Birds with the Y3/Y3 genotype were found to have 2.3 times the risk of developing a tumor compared with birds with other Rfp-Y genotypes combined (P <0.02). Additionally, birds carrying the BR9/B11 genotype had 2.3 times the risk of tumor formation, relative to birds with the B11/B11 genotype (P <0.02). We found no evidence for an interaction between genotypes within the B and Rfp-Y systems. These data provide evidence that Rfp-Y haplotypes, as well as B haplotypes, can significantly influence the outcome of infection with MDV.