Mhc-B haplotypes in "Campero-Inta" chicken synthetic line

Identification of new major histocompatibility complex-B Haplotypes in Bangladesh native chickens

OBJECTIVE

The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck.

METHODS

These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program.

RESULTS

A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes.

CONCLUSION

The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.

Discovery of novel MHC-B haplotypes in Chantecler chickens

The major histocompatibility complex (MHC) is a highly polymorphic cluster of genes which contribute to immune response. Located on chromosome 16, the chicken MHC has great influence over disease resistance and susceptibility. Through the use of a high-density SNP panel which encompasses the MHC-B region, haplotypes can be easily identified. This study aims to use an MHC-B SNP panel to evaluate the MHC-B variability in the Chantecler breed. This breed is native to Quebec, Canada, and is a dual-purpose breed known for its strong resistance to extreme cold temperatures. The Chantecler breed faced a near extinction event in the 1970s, which most likely resulted in a genetic bottleneck and loss of diversity. Despite this, SNP haplotype diversity was observed among 4 Chantecler populations. A total of 8 haplotypes were observed. Of these haplotypes, 6 were previously defined in other breeds, and the other 2 were unique to the Chantecler. Within the populations, the number of haplotypes ranged from 4 to 7, with 3 haplotypes, including the novel BSNP-Chant01, being present in all the groups. This study shows existence of reasonable diversity in the MHC-B region of the Chantecler breed and our results further contribute to understanding the variability of this region in chickens.

Major Histocompatibility Complex-B haplotype and ovarian graft response

Gonadal tissue transfer is considered one of the best methods to preserve genetic variability. Poultry hosts can receive a gonad from a donor of a different genetic background, sustain the growth of this graft, and produce gametes from it. Unfortunately, the host's strong immune response may significantly reduce the gonadal graft's ability to reach maturity. Our study aimed to evaluate the influence of MHC-B alleles in rejecting a gonadal graft of similar or different genetic backgrounds. In the first experiment, ovarian tissue was transplanted to chicks of similar genetic backgrounds, either Lohmann White (LW) with variable MHC-B or Barred Rock (BR) with fixed MHC-B. The sustained growth of donor ovarian tissues occurred in (4/7 hosts) BR (MHC-B matched) hosts only-one of these graft-positive-BR hens produced eggs derived from the donor ovary. No grafts were recovered when the host and the donor had an LW background (0/9; MHC-B mismatched). In the second experiment, ovarian transplantation was done between chicks of either similar or different genetic backgrounds (Brown Leghorn [BL], BR, and BL/BR F1). The 2 pure lines contained only one MHC-B allele, whereas the F1 heterozygotes had both. All host birds were given a daily dose of an immunosuppressant (mycophenolate mofetil) until maturity. The success rate was assessed by microsatellite genotype confirmation of donor-derived ovaries plus physiological and histological analyses of ovarian grafts. In this second experiment, 11 out of 43 ovarian hosts laid eggs. However, all fertilized eggs from these hens were derived from the remnant host ovarian tissue, not from the donor ovaries. A necropsy assessment was done on all 43 host birds. Ten donor grafts were recovered from hosts having matched (6 hosts) and mismatched (4 hosts) MHC-B, and none were functional. Interestingly, 6 of them were enclosed by a serous membrane capsule filled with fluid and had various tissue growth. In addition, clusters of immune cells were observed in all recovered donor grafts. Our results demonstrated that genetic background could greatly influence the success of gonadal transfer in chickens.

Improved high-throughput MHC typing for non-model species using long-read sequencing

The major histocompatibility complex (MHC) plays a critical role in the vertebrate immune system. Accurate MHC typing is critical to understanding not only host fitness and disease susceptibility, but also the mechanisms underlying host‐pathogen co‐evolution. However, due to the high degree of gene duplication and diversification of MHC genes, it is often technically challenging to accurately characterise MHC genetic diversity in non‐model species. Here we conducted a systematic review to identify common issues associated with current widely used MHC typing approaches. Then to overcome these challenges, we developed a long‐read based MHC typing method along with a new analysis pipeline. Our approach enables the sequencing of fully phased MHC alleles spanning all key functional domains and the separation of highly similar alleles as well as the removal of technical artefacts such as PCR heteroduplexes and chimeras. Using this approach, we performed population‐scale MHC typing in the Tasmanian devil (Sarcophilus harrisii), revealing previously undiscovered MHC functional diversity in this endangered species. Our new method provides a better solution for addressing research questions that require high MHC typing accuracy. Since the method is not limited by species or the number of genes analysed, it will be applicable for studying not only the MHC but also other complex gene families.

Comparison of major histocompatibility complex-B variability in Sri Lankan indigenous chickens with five global chicken populations using MHC-B SNP panel

In the present study, we investigated the major histocompatibility complex (MHC)-B haplotypes diversity of Sri Lankan indigenous chickens from three different geographical sites consisting of highly mixed populations using 90 SNPs in the MHC-B region. A total of 48 haplotypes were identified. Those included 37 novel haplotypes and 11 previously identified 'standard' haplotypes. The MHC-linked marker, LEI0258, had 23 alleles showing less diversity than defined by MHC-B SNP haplotypes. Among those identified haplotypes, five standard haplotypes-BSNP-O02, BSNP-M01, BSNP-A04, BSNP-K03, BSNP-T04-were most commonly observed, suggesting past introgression of imported breeds. Comparison of the MHC-B haplotypes of Sri Lankan and four other global populations with previously defined haplotypes indicated the sharing of 23 standard haplotypes with common origins. Novel haplotypes are population-specific and not shared among the geographical boundaries. Backyard indigenous chickens are unselected, highly crossbred, and generally thrive under dynamic environmental conditions. Hence free-range production systems may be responsible for maintaining high diversity in the MHC-B region with novel haplotypes.

MHC-B variation in maternal and paternal synthetic lines of the Argentinian Campero INTA chicken

The Campero-INTA chicken of Argentina was developed to provide a robust bird that can survive under Argentinian pasture conditions with no significant additional nutrition, producing a source of animal protein for small producers or low-income families. In previous work, we described the AH paternal line of Campero and its Major Histocompatibility Complex B region (MHC-B) variation. In this work we analyzed the three remaining synthetic lines used to produce the Campero-INTA production bird: lines AS, A, and E. Because of the association between variation within the MHC of chickens and disease resistance, MHC variation within this breed is of particular interest. MHC variability within the lines used to produce the Campero-INTA chicken was examined using a 90 SNP panel encompassing the chicken MHC-B region plus the VNTR, LEI0258, located within the chicken MHC. Across all 4lines 12 haplotypes were found, with 7 of these being previously reported in North America/European breeds, reflecting the original breed sources for these birds. Three Campero unique haplotypes were found, 2 of which likely originated from MHC recombination events. MHC-B variation for all lines involved with production of the final Campero-INTA bird has now been determined.

Chickens productivity selection affects immune system genes

The quantitative trait loci associated with the immune properties of chickens are of interest from the point of view of obtaining animals resistant to infectious agents using marker-assisted selection. In the process of selecting markers for genomic selection in broiler-type chickens, a non-standard genotype frequency of the RACK1 gene allele (SNP Gga_rs15788101) in the B5 line of broiler-type chicken cross Smena 8 was identified and it was suggested that this gene was involved in selection. Therefore, it was decided to investigate the available polymorphisms in the three genes responsible for the IgY titer (DMA, RACK1 and CD1B). Molecular typing of single nucleotide polymorphisms of three loci revealed an approach to fixation of the unfavorable allele of the DMA gene (SNP Gga_rs15788237), an approach to fixation of the unfavorable allele of the RACK1 gene and the prevalence of the favorable CD1B gene allele (SNP Gga_rs16057130). Analysis of the haplotypes revealed a strong linkage disequilibrium of these genes. This suggests that these genes experience selection pressure. Analysis of the protein-coding sequences of the CD1B and DMA genes of various breeds of chickens revealed a negative selection of these genes. In order to understand whether the fixation of the studied alleles is the result of artificial selection of the B5 line of the cross Smena 8, an analysis of similar loci in layer chickens Hisex White was carried out. The frequencies of the alleles at the loci of the CD1B gene (Gga_rs16057130) and the RACK1 gene (Gga_rs15788101) in the Hisex White chicken genome differ from the frequencies of the alleles obtained for chickens of the B5 line of the cross Smena 8. It can be assumed that the fixation of the allele in the DMA gene (SNP Gga_rs15723) is associated with artificial or natural selection, consistent in broilers and layers. Changes in the loci Gga_rs16057130 and Gga_rs15788101 in the B5 line of the Smena 8 chickens are most likely associated with artificial selection of broiler productivity traits, which can subsequently lead to fixation of alleles at these loci. Artificial breeding of chickens leads to degradation of the variability of genes encoding elements of the immune system, which can cause a decrease in resistance to various diseases. The study of the negative impact of selection of economic traits on immunity should provide means to mitigate negative consequences and help find ways to obtain disease-resistant animals.

Major histocompatibility complex B variability in Korean native chicken breeds

Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B (MHC-B) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism (SNP) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.

Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms

This study used a single-nucleotide polymorphism (SNP) panel to characterise the diversity in the major histocompatibility complex B region (MHC-B) in 12 chicken populations in Korea. Samples were genotyped for 96 MHC-B SNPs using an Illumina GoldenGate genotyping assay. The MHC-B SNP haplotypes were predicted using 58 informative SNPs and a coalescence-based Bayesian algorithm implemented by the PHASE program and a manual curation process. In total, 117 haplotypes, including 24 shared and 93 unique haplotypes, were identified. The unique haplotype numbers ranged from 0 in Rhode Island Red to 32 in the Korean native commercial chicken population 2 ("Hanhyup-3ho"). Population and haplotype principal component analysis (PCA) indicated no clear population structure based on the MHC haplotypes. Three haplotype clusters (A, B, C) segregated in these populations highlighted the relationship between the haplotypes in each cluster. The sequences from two clusters (B and C) overlapped, whereas the sequences from the third cluster (A) were very different. Overall, native breeds had high genetic diversity in the MHC-B region compared with the commercial breeds. This highlights their immune capabilities and genetic potential for resistance to many different pathogens.

Assessing MHC-B diversity in Silkie chickens

The major histocompatibility complex (MHC) is a highly polymorphic region on chromosome 16, which contains numerous immune response genes, and is known to influence disease susceptibility and resistance in chickens. Variability of MHC-B haplotypes in various well-known and commercially utilized breeds has previously been identified. This study aims to understand MHC-B diversity in the Silkie breed using a high-density SNP panel that encompasses the chicken MHC-B region. DNA was obtained from 74 females and 27 males from a commercial Silkie breeder colony that is maintained through minimal genetic selection practices. A previously described panel of 90 SNPs, all located within the MHC-B region, was used to evaluate MHC-B variability in the commercial Silkie breeder colony. MHC-B haplotypes identified from the individual SNP information in the Silkie colony were compared to published haplotypes from the same region. Of the 27 haplotypes identified in the Silkie population, 8 have been previously described. Nineteen haplotypes are unique to the Silkie population and include one novel recombinant and 2 additional possible novel recombinants. Six haplotypes were found at a frequency greater than 5% of the population, of which 4 are novel. Finally, Hardy Weinberg Equilibrium (HWE) was calculated for the observed haplotypes, which were found to be in HWE. This study shows considerable MHC-B diversity in the Silkie breed and adds further information on variability of the MHC-B region in the chicken.

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.

Development and optimization of a hybridization technique to type the classical class I and class II B genes of the chicken MHC

The classical class I and class II molecules of the major histocompatibility complex (MHC) play crucial roles in immune responses to infectious pathogens and vaccines as well as being important for autoimmunity, allergy, cancer and reproduction. These classical MHC genes are the most polymorphic known, with roughly 10,000 alleles in humans. In chickens, the MHC (also known as the BF-BL region) determines decisive resistance and susceptibility to infectious pathogens, but relatively few MHC alleles and haplotypes have been described in any detail. We describe a typing protocol for classical chicken class I (BF) and class II B (BLB) genes based on a hybridization method called reference strand-mediated conformational analysis (RSCA). We optimize the various steps, validate the analysis using well-characterized chicken MHC haplotypes, apply the system to type some experimental lines and discover a new chicken class I allele. This work establishes a basis for typing the MHC genes of chickens worldwide and provides an opportunity to correlate with microsatellite and with single nucleotide polymorphism (SNP) typing for approaches involving imputation.