The major and a minor class II β-chain (B-LB ) gene flank the Tapasin gene in the B-F /B-L region of the chicken major histocompatibility complex

 We have identified the major histocompatibility complex class II β-chain (B-LB) genes present in the B-F/B-L region of the B complex of nine well-characterized lines of chickens and have cleared up much of the confusion concerning numbers and location of B-LB genes in this region. By amplifying DNA sequences between adjacent genes, we found two B-LB genes that lie on either side of Tapasin. The dominantly expressed 'major' B-LB gene in all haplotypes lies between Tapasin and RING-3, and belongs to the B-LBII family of class II β-chain genes. The poorly expressed 'minor' B-LB gene in all haplotypes lies between B-lec1 and Tapasin, and belongs either to the B-LBII family or to the previously unmapped B-LBVI family of class II β-chain genes. The data suggest that the B-LBII and B-LBVI genes are two lineages of B-LB genes and we propose that they all be termed B-LB genes. The location of a third B-LB gene in the B12 haplotype (and possibly other haplotypes as well) has yet to be determined. The structural organization and expression of the class II β-chain genes in the B-F/B-L region is similar to that of chicken class I (B-F) genes, one functional result of which is differential resistance to disease and response to vaccines. Received: 29 July 1999 / Revised: 27 September 1999     

Mapping of susceptibility to Marek's disease within the major histocompatibility (B) complex by refined typing of White Leghorn chickens

The major histocompatibility (B) complex of a distinct commercial pure White Leghorn chicken line was characterized using serological, biochemical and restriction fragment length polymorphism (RFLP) typing. Line B chickens displayed a high recombination frequency within the B complex. Three recombinant haplo-types were identified. The influence of these haplotypes was determined in relation to the haplotypes B^l9 and B²¹ on their resistance to Marek's disease (MD) in an experimental infection with the virus. Offspring of sires with a recombinant haplotype in combination with B¹⁹ or B²¹, and dams, which were homozygous B¹⁹/B¹⁹ or B²¹/B²¹ were infected. The B type of the offspring had a significant effect upon survival. Animals with B complex types B²¹/B²¹, B¹³⁴/B²¹ and B²³⁴/B²¹ were relatively resistant to MD (24–32% mortality), whereas B¹⁹/B¹⁹ birds were highly susceptible (68% mortality). Animals with a recombinant halpotype B^19r21 (B-G²¹, B-F¹⁹) were equally susceptible to MD as birds with the complete B¹⁹ haplotype. In contrast to earlier publications, resistance was not inherited as a dominant trait. Apparently, B¹⁹ was associated with a dominant susceptibility. The gene(s) associated with the B complex and involved in resistance to MD were localized within the B-F/B-L region. However, the association with a presumably non-coding subregion of B-G could not be excluded.     

Ancestral and recombinant 16-locus HLA haplotypes in the Hutterites

 Prior studies in the Schmiedeleut Hutterites of South Dakota have demonstrated associations between human leukocyte antigen (HLA) haplotype matching and fetal loss (Ober et al. 1992) and mate preferences (Ober et al. 1997), as well as deficiencies of homozygotes for HLA haplotypes (Kostyu et al. 1993). These studies were based on the serologically-defined five-locus HLA-A, -C, -B, -DR, -DQ haplotype. To further elucidate the effects of specific major histocompatibility (MHC) loci or regions on fetal loss and mate choice, we genotyped a sample of Hutterites for 14 MHC loci by DNA or biochemical methods. Typing for additional loci in the HLA-A to HLA-DPB1 region increased the number of recognized Hutterite MHC haplotypes to 67, and further localized the site of cross-over in 9 of 15 recombinant haplotypes. Hutterite MHC haplotype sequences are similar to those observed in outbred Caucasians, suggesting that the influence of HLA haplotypes on fetal loss and mating structure may be general. Received: 1 May 1998 / Revised: 2 December 1998     

Influence of different B-complex recombinants on the outcome of Rous sarcomas in chickens

Seven major histocompatibility (B) complex recombinants were evaluated for anti-Rous sarcoma response. In experiment 1, the B^R5(F21-G19) recombinant haplotype both homozygous and in heterozygous combinations with B¹⁹ and B²¹ haplotypes were compared to B¹⁹/B¹⁹ and B²¹/B²¹ chickens to determine the relative influence of the B^F versus B^G chromosomal segments on regression of Rous sarcoma virus-induced tumours. In experiment 2, six recombinant haplotypes B^R1(F24-G23), B^R2(F2-G23), B^R3(F2-G23), B^R4(F2-G23), B^R6(F21-G23) and B^R8(F2-G2a,23) present in chickens heterozygous for normal haplotypes B¹⁹, B²³ or B²⁶ were compared for anti-sarcoma response. A total of 1328 chickens were blood typed for B alloanti-gens at 17 days of age, inoculated in the wingweb with Rous sarcoma virus at 6 weeks and monitored for anti-tumour immune response over a 10-week period. Genotypes which shared the same B^F haplotype, but differed in their B^G regions, had similar anti-tumour responses, implicating the B^F but not the B^G region in tumour regression. Chickens carrying B^F2 or B^F21 had a strong anti-tumour response, while B^F24 conferred a weaker response, regardless of the accompanying normal haplotype.     

Chicken Mhc alloantiserum cross-reactivity analysis by hemagglutination and flow cytometry

 The major histocompatibility complex (Mhc) haplotype in the chicken is generally determined by the use of alloantisera in a hemagglutination assay. This method restricts haplotype determination to antigens expressed on the surface of erythrocytes which includes class I (B – F) and class IV (B – G) antigens as well as any other polymorphic molecules on these cells. Alloantisera can result in complex cross-reactivity patterns. We describe here the analysis of 53 alloantisera made within Mhc-congenic lines. Each antiserum was tested by hemagglutination with erythrocytes and by flow cytometry with erythrocytes and peripheral white blood cells of seven Mhc haplotypes; B ² , B ⁵ , B ¹² , B ¹³ , B ¹⁵ , B ¹⁹ , and B ²¹ . Five types of antiserum were identified based on their reactivity to different cell subpopulations of the peripheral blood of the donor haplotype as well as in cross-reactivity for different haplotypes. RBC specific cross-reactive antigens attributed to B – G molecules were demonstrated for the B5 : B19, B12 : B19, and B19 : B21 cross-reactions. Cross-reactive antigens detected on RBC and thrombocytes attributable to B – G molecules on both types of cells were demonstrated for the B2 : B12, B2 : B15, B2 : B19, and B2 : B21 cross-reactions. In addition, cross-reactive antigens occurring on RBC and WBC were attributed to B – F (or RBC and lymphocyte-expressed B – G loci) and included the B12 : B13, B13 : B19, and B15 : B19 cross-reactions. Several antisera with specificity for B cells purportedly identifying B – L epitopes were found but their numbers were limited and cross-reactivities were not defined. The identities described here may be useful in understanding B haplotype similarities and differences in disease resistance and immune response. Received: 18 September 1995 / 15 November 1995     

High KIR diversity in Amerindians is maintained using few gene-content haplotypes

Interaction between killer cell immunoglobulin-like receptors (KIR) and cognate HLA class I ligands influences the innate and adaptive immune response to infection. The KIR family varies in gene content and allelic polymorphism, thereby, distinguishing individuals and populations. KIR gene content was determined for 230 individuals from three Amerindian tribes from Venezuela: the Yucpa, Bari and Warao. Gene-content haplotypes could be assigned to 212 individuals (92%) because only five different haplotypes were present—group A and four group B. Six different haplotype combinations accounted for >80% of individuals. Each tribe has distinctive genotype frequencies. Despite few haplotypes, all 14 KIR genes are at high frequency in the three tribes, with the exception of 2DS3. Each population has an even frequency of group A and B haplotypes. Allele-level analysis of 3DL1/S1 distinguished five group A haplotypes and six group B haplotypes. The high frequency and divergence of the KIR haplotypes in the Amerindian tribes provide greater KIR diversity than is present in many larger populations. An extreme case being the Yucpa, for whom two gene-content haplotypes account for >90% of the population. These comprise the group A haplotype and a group B haplotype containing all the KIR genes, except 2DS3, that typify the group B haplotypes. Here is clear evidence for balancing selection on the KIR system and the biological importance of both A and B haplotypes for the survival of human populations.Electronic Supplementary Material Supplementary material is available for this article at     

A genome‐wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease

Marek's disease (MD) is a neoplastic disease in chickens, caused by the Marek's disease virus (MDV). To investigate host genetic resistance to MD, we conducted a genome‐wide association study (GWAS) on 67 MDV‐infected chickens based on a case and control design, including 57 susceptible chickens in the case group and 10 resistant chickens as controls. After searching 38 655 valid genomic markers, two SNPs were found to be associated with host resistance to MD. One SNP, rs14527240, reaching chromosome‐wide significance level (P < 0.01) was located in the SPARC‐related modular calcium‐binding 1 (SMOC1) gene on GGA5. The other one, GGaluGA156129, reaching genome‐wide significance (P < 0.05), was located in the protein tyrosine phosphatase, non‐receptor type 3 (PTPN3) gene on GGA2. In addition, expression patterns of these two genes in spleens were detected by qPCR. The expression of SMOC1 was significantly up‐regulated (P < 0.05), whereas the expression of PTNP3 did not show significance when the case group was compared with the control group. Up‐regulation of SMOC1 in susceptible spleens suggests its important roles in MD tumorigenesis. This is the first study to investigate MD‐resistant loci, and it demonstrates the power of GWASs for mapping genes associated with MD resistance.     

Genetic influences on spontaneous autoimmune thyroiditis in (CS x OS)F2 chickens

Genetic effects on spontaneous autoimmune thyroiditis in chickens were assessed by measuring phenotypic symptoms, the titer of circulating antibody to thyroglobulin, and the pathological change in the thyroids of young chicks. One or more loci within theB complex (the major histocompatibility complex of the chicken) are responsible for the expression of autoimmunity, and evidence is provided for an interaction of theB haplotype with genes at other loci. The influence of theB complex component on genetic susceptibility is more visible in animals with limited susceptibility at other loci and becomes indistinguishable as the frequency of other genes determining thyroid autoimmunity increases.     

Gene order in the major histocompatibility complex of the rat

The loci in the major histocompatibility complex (MHC) of the rat which code for class I and class II antigens—RT1.A and RT1.B, respectively — have previously been separated by laboratory-derived recombinants and by observations in inbred and wild rats. Closely linked to the MHC is the growth and reproduction complex (Grc) which contains genes influencing body size (dw-3) and fertility (ft). These phenotypic markers were used in this study to orient the A and B loci of the MHC. Two recombinants were used for mapping. The BIL(R1) animal is a recombinant between the MHC and Grc, and it carries the haplotype RT1.A ^lB^lGrc⁺. The r10 animal is an intra-MHC recombinant, and it has the haplotype RT1.A ⁿB¹ Grc. These recombinants were characterized serologically, by mixed lymphocyte reactivity, by immune responsiveness to poly (Glu⁵²Lys³³Tyr¹⁵) and by the presence of the dw-3 gene. The data demonstrate that the gene order of the loci is: dw-3-RT1.B-RT1.A.     

Identification of HLA-B44 subtypes associated with extended MHC haplotypes

The HLA class I antigen B44 is found in each of two different extended major histocompatibility haplotypes (allele combinations of HLA-B, HLA-DR, and complement genes BF, C2, C4A, and C4B in linkage disequilibrium). Using isoelectric focusing, two variants of HLA-B44 were identified. The basic variant was found in all cell lines with the extended haplotype HLA-B44, DR7, FC31, and the acidic variant in all cell lines with the extended haplotype HLA-B44, DR4, SC30. The occurrence of each antigen variant with a unique extended haplotype explains previous observations concerning the nonrandom association of B44 variants with DR antigens.     

Subdivision of the S region of the mouse major histocompatibility complex by identification of genomic polymorphisms of the class III genes

The S region of the mouse major histocompatibility complex (MHC) encodes the class III proteins, the second (C2) and fourth (C4) components of complement, and factor B. Previously, the assignment of S-region haplotypes was based on analysis of protein polymorphisms. The recent availability of C2, C4, and factor B cDNA probes prompted a search for restriction fragment length polymorphisms which would serve as additional genetic markers for these loci. DNA was isolated from livers of mice of all standard inbred H-2 haplotypes and of haplotypes pz and bs. These DNA samples were digested with restriction endonucleases and analyzed by Southern blot. By the pattern of restriction fragment length polymorphism observed, specific markers have been identified in factor B of haplotypes f, u, z, bs, r, and v, and in C4 of haplotypes b, q,f,j,p,s, pz, r, and v. These genetic markers were used in the analysis of S-region composition in strains B10.TFR5 (H-2 ^ap5) and C3H.LG (H-2 ^dx), and a possible intra-S-region recombinant was revealed in the H-2 ^dxhaplotype. The genetic markers identified here subdivide the S region and will be of value in defining further the composition of the complement gene complex of the mouse MHC.     

HLA class II haplotype and sequence analysis support a role for DQ in narcolepsy

 A systematic haplotype and sequencing analysis of the HLA-DR and -DQ region in patients with narcolepsy was performed. Five new (CA)_n microsatellite markers were generated and positioned on the physical map across the HLA-DQB1-DQA1-DRB1 interval. Haplotypes for these new markers and the three HLA loci were established using somatic cell hybrids generated from patients. A four-marker haplotype surrounding the DQB1 ^* 0602 gene was found in all narcolepsy patients, and was identical to haplotypes observed on random chromosomes harboring the DQB1 ^* 0602 allele. Eighty-six kilobases of contiguous genomic sequence across the region did not reveal new genes, and analysis of this sequence for single nucleotide polymorphisms did not reveal sequence variation among DQB1 ^* 0602 chromosomes. These results are consistent with other studies, suggesting that the HLA-DQ genes themselves are among the predisposing factors in narcolepsy. Received: 18 March 1997 / Revised: 23 April 1997     

A polymorphic system related to but genetically independent of the chicken major histocompatibility complex

Analyses of the major histocompatibility complex (Mhc) in chickens have shown inconsistencies between serologically defined haplotypes and haplotypes defined by the restriction fragment patterns of Mhc class I and class II genes in Southern hybridizations. Often more than one pattern of restriction fragments for Mhc class I and/or class II genes has been found among DNA samples collected from birds homozygous for a single serologically defined B haplotype. Such findings have been interpreted as evidence for variability within the Mhc haplotypes of chickens not detected previously with serological methods. In this study of a fully pedigreed family over three generations, the heterogeneity observed in restriction fragment patterns was found to be the result of the presence of a second, independently segregating polymorphic Mhc-like locus, designated Rfp-Y. Three alleles (haplotypes) are identified in this new system.     

Genome scans and gene expression microarrays converge to identify gene regulatory loci relevant in schizophrenia

Multiple linkage regions have been reported in schizophrenia, and some appear to harbor susceptibility genes that are differentially expressed in postmortem brain tissue derived from unrelated individuals. We combined traditional genome-wide linkage analysis in a multiplex family with lymphocytic genome-wide expression analysis. A genome scan suggested linkage to a chromosome 4q marker (D4S1530, LOD 2.17, θ=0) using a dominant model. Haplotype analysis using flanking microsatellite markers delineated a 14 Mb region that cosegregated with all those affected. Subsequent genome-wide scan with SNP genotypes supported the evidence of linkage to 4q33–35.1 (LOD=2.39) using a dominant model. Genome-wide microarray analysis of five affected and five unaffected family members identified two differentially expressed genes within the haplotype AGA and GALNT7 (aspartylglucosaminidase and UDP-N-acetyl-alpha-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase 7) with nominal significance; however, these genes did not remain significant following analysis of covariance. We carried out genome-wide linkage analyses between the quantitative expression phenotype and genetic markers. AGA expression levels showed suggestive linkage to multiple markers in the haplotype (maximum LOD=2.37) but to no other genomic region. GALNT7 expression levels showed linkage to regulatory loci at 4q28.1 (maximum LOD=3.15) and in the haplotype region at 4q33–35.1 (maximum LOD=2.37). ADH1B (alcohol dehydrogenase IB) was linked to loci at 4q21–q23 (maximum LOD=3.08) and haplotype region at 4q33–35.1 (maximum LOD=2.27). Seven differentially expressed genes were validated with RT-PCR. Three genes in the 4q33–35.1 haplotype region were also differentially expressed in schizophrenia in postmortem dorsolateral prefrontal cortex: AGA, HMGB2, and SCRG1. These results indicate that combining differential gene expression with linkage analysis may help in identifying candidate genes and potential regulatory sites. Moreover, they also replicate recent findings of complex trans- and cis- regulation of genes.     

Molecular characterization of three Mhc class II B haplotypes in the ring-necked pheasant

We investigated the class II B genes in free-ranging population of the ring-necked pheasant Phasianus colchicus by a combination of restriction fragment length polymorphism (RFLP), polymerase chain reaction (PCR), and DNA sequencing. Special attention was paid to the variation in the second exon, which encodes the peptide-binding ₁-domain. The population was introduced, but it still exhibited major histocompatibility complex polymorphism with at least three segregating class II B haplotypes and consequently six genotypes. We found two class II B genes associated with each haplotype. The class II B genes of birds had until then only been molecularly characterized in the domestic chicken. the pheasant genes were highly variable, although one of the amplified sequences was found in two different haplotypes. Taken together, the most polymorphic positions (residues 37 and 38) were not identical in any of the predicted protein sequences, but all except one of the motifs had already been foud in the domestic chicken. Structurally important features in mammalian class II B genes were generally conserved also in the pheasant sequences, but the loss of a potential salt bridge constituent (Arg₇₂) in several sequences may suggest a slightly different structure of the adjacent parts of the peptide-binding groove. The pheasant genes are most closely related to the so called B-LBII family in the chicken, indicating that this represents a major line of development among avian class II B genes.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X75403-X75407. Correspondence to: H. Wittzell, Department of Theoretical Ecology, Ecology Building, Lund University, S-223 62 Lund, Sweden.     

Tumor induction by the LTR,v-src,LTR DNA in four B (MHC) congenic lines of chickens

We report that the cloned DNA harboring the long terminal repeat (LTR), v-src, LTR proviral structure is tumorigenic in chickens of the Prague congenic lines. The growth rate of these tumors is by far the highest in the recombinant CC.R1 line, the B haplotype of which is composed of the B-F/L ⁴ and B-G ¹² subregions originating from different naturally occurring haplotypes. Some of the tumors induced by the LTR, v-src, LTR DNA are repeatedly transplantable in syngeneic chickens, maintain unaltered provirus, and express v-src mRNA. Differences in the response to challenge with Rous sarcoma virus (RSV) and LTR, v-src, LTR DNA on a given experimental model are compared and possible involvement of an interaction between B-F/L and B-G region gene is considered. Regression of the LTR, v-src, LTR DNA-induced tumors did not prevent the formation and growth of tumors induced subsequently by RSV.     

Heterogeneity of human C4 gene size

In this article we present a study showing that the human C4 genes differ in length because of the presence or absence of a 6.5 kb intron near the 5 end of the gene. DNA from individuals of known HLA, factor B, and C4 haplotypes was analyzed for restriction fragment length polymorphism (RFLP) by Southern blot analysis with C4-specific cDNA probes. The RFLP patterns obtained showed that the C4 genes are either 22.5 kb or 16 kb in length. They are referred to as long and short C4 genes, respectively. A population study was carried out to examine the distribution of the gene size according to C4 allotypes and haplotypes. Long C4 genes included all C4A genes studied and also some C4B allotypes, e. g., B1 on most C4 A3B1 haplotypes. Similarly, C4B null genes were found to be of the long form. Other C4B allotypes tested were found to be coded for by short C4 genes, including B2, B1 in C4 A6B1 and C4 AQOB1 (with a single C4B gene haplotype).Abbreviations used in this paper C4 fourth component of complement - C2 second component of complement - BF factor B - MHC major histocompatibility complex - RFLP restriction fragment length polymorphism - EDTA ethylenediaminetetraacetic acid - SDS lauryl sulfate, sodium salt     

Identification of the Tapasin gene in the chicken major histocompatibility complex

 The Tapasin molecule plays a role in the assembly of major histocompatibility complex (Mhc) class I molecules in the endoplasmic reticulum, by mediating the interaction of class I-β₂-microglobulin dimers with TAP. We report here the identification of the Tapasin gene in the chicken Mhc (B complex). This gene is located at the centromeric end of the complex, between the class II B-LBI and B-LBII genes. Like its human counterpart it comprises 8 exons, but features a significantly reduced intron size as compared to the human gene. Chicken Tapasin codes for a transmembrane protein with a probable endoplasmic reticulum retention signal. Exons IV and V, and possibly exon III, code for separate domains that are related to the immunoglobulin (Ig) superfamily (this relationship was so far unrecognized for human Tapasin domain IV which has lost its two cysteines). Two different cDNAs corresponding to the Tapasin gene were isolated, possibly related to alternative splicing events; the Ig-like domain encoded by exon IV is missing in one of the cDNAs, suggesting either that this domain is not necessary for the protein to perform its function, or that the two alternatively spliced cDNAs are translated into two functionally different forms of the protein. Received: 8 July 1998 / Revised: 5 October 1998