Gastrointestinal helminths in indigenous and exotic chickens in Vietnam: association of the intensity of infection with the Major Histocompatibility Complex

Ascaridia galli infection in chicken: Pathobiology and immunological orchestra

BACKGROUND

Ascaridia galli is the largest gut-dwelling helminth of chickens, which confers adverse effects on meat and egg production; thus, on the animal protein supply and the economy. Both adult and immature parasites affect gut health, but larval stages play a major role in pathology.

AIMS

Here, we present immunology and pathology of A. galli in chickens.

MATERIALS AND METHODS

Literatures were surveyed through online platforms such as PubMed, Google Scholar and Researchgate.

RESULTS

The larvae cause excessive mucus production, damage to the intestinal gland, hemorrhage, anemia, diarrhea, and malnutrition. The adult worms can cause death by intestinal obstruction and intussusception. Although both cellular and humoral immunity are involved in fighting against ascariasis, the role of naturally acquired immunity is poorly defined. In cellular immunity, Th-2 cytokines (IL-4, IL-5, IL-9, and IL-13), goblet cells (mucin), gut-associated lymphoid tissues, CD8α+ intraepithelial cells, TCRγδ + T cells, and TGF-β4 form a protective band. Type 2 immunity provides protection by forming a network of endogenous damage-associated molecular patterns, chitin, and parasitic antigens. Among antibodies, IgY is the most prominent in chickens and provides temporary humoral protection. During parasitic infection, infiltration of various immune cells is evident, especially in the intestinal epithelium, lamina propria, and crypts of the duodenum and jejunum. In chickens older than 12 weeks, gradual reduction of worm burden is more successful than the younger birds. Female chickens exert a short-lived but higher level of protection by passing IgY to chicks in the form of egg yolk antibodies. In laying conditions, immunity differs between breeds. This review provides an overview of the silent but inevitable pathological changes induced by A. galli and the interaction of host immunity with the parasite.

Molecular identification of helminth parasites of the Heterakidae and Ascarididae families of free-ranging chickens from selected rural communities of KwaZulu-Natal province of South Africa

Free-range chickens are predisposed to diverse parasitic infections during scavenging. Accurate identification of these parasites using morphological characters has been a challenge. Therefore, this study aimed to identify nematodes from the Heterakidae and Ascarididae family infecting free-ranging chickens from KwaZulu-Natal province of South Africa using a combination of morphological and molecular techniques. Forty-two free-ranging adult indigenous chickens were purchased from randomly selected households in Shongweni (n=12), Umzinto (n=10), Gingindlovu (n=10) and Ozwathini (n=10) rural villages and examined for nematodes of the Heterakidae and Ascarididae family. Collected specimen were identified morphologically and confirmed using mitochondrial and nuclear ribosomal markers. Results showed that Ascaridia galli was common, occurring at all sampling locations with an overall prevalence of 58.3%, while Heterakis gallinarum and H. beramporia occurred in three locations. Ascaridia galli had high prevalence in Shongweni (58.3%), followed by Gingindlovu (40%), Ozwathini (20%) and Umzinto (10%). Heterakis gallinarum infection was prevalent in three locations, with an overall prevalence of 90% in Gingindlovu, 80% in Ozwathini and 58.3 % in Shongweni. Heterakis gallinarum and H. beramporia were not recorded in Umzinto. Heterakis beramporia was recorded in low prevalence in Gingindlovu (20%), Ozwathini (10%) and Shongweni (8.3%) villages. Mixed infections of A. galli and H. gallinarum were recorded in Gingindlovu, Ozwathini and Shongweni, and H. gallinarum and H. beramporia in Gingindlovu. Molecular analysis confirmed identification of A. galli, and further showed close relationship with the GenBank-derived South African isolates. Haplotype network further confirmed their ancestral history, where all South African A. galli isolates formed five novel haplotypes corresponding with the structure of the phylogenetic tree. Similar structure was observed with Heterakis isolates, where analysis of the cox1 gene showed that H. gallinarum formed a well-supported monophyletic clade with other Heterakis species. The ITS marker identified three specimens from Gingindlovu, Ozwathini and Shongweni as H. beramporia, which formed strongly supported sister clade to H. indica and this is the first report confirming the occurrence of H. beramporia in South Africa.

The Chicken MHC: Insights into Genetic Resistance, Immunity, and Inflammation Following Infectious Bronchitis Virus Infections

The chicken immune system has provided an immense contribution to basic immunology knowledge by establishing major landmarks and discoveries that defined concepts widely used today. One of many special features on chickens is the presence of a compact and simple major histocompatibility complex (MHC). Despite its simplicity, the chicken MHC maintains the essential counterpart genes of the mammalian MHC, allowing for a strong association to be detected between the MHC and resistance or susceptibility to infectious diseases. This association has been widely studied for several poultry infectious diseases, including infectious bronchitis. In addition to the MHC and its linked genes, other non-MHC loci may play a role in the mechanisms underlying such resistance. It has been reported that innate immune responses, such as macrophage function and inflammation, might be some of the factors driving resistance or susceptibility, consequently influencing the disease outcome in an individual or a population. Information about innate immunity and genetic resistance can be helpful in developing effective preventative measures for diseases such as infectious bronchitis, to which a systemic antibody response is often not associated with disease protection. In this review, we summarize the importance of the chicken MHC in poultry disease resistance, particularly to infectious bronchitis virus (IBV) infections and the role played by innate immunity and inflammation on disease outcome. We highlight how future studies focusing on the MHC and non-MHC genes can potentially bring clarity to observed resistance in some chicken B haplotype lines.

Taxonomy of Echinostoma revolutum and 37-Collar-Spined Echinostoma spp.: A Historical Review

Echinostoma flukes armed with 37 collar spines on their head collar are called as 37-collar-spined Echinostoma spp. (group) or 'Echinostoma revolutum group'. At least 56 nominal species have been described in this group. However, many of them were morphologically close to and difficult to distinguish from the other, thus synonymized with the others. However, some of the synonymies were disagreed by other researchers, and taxonomic debates have been continued. Fortunately, recent development of molecular techniques, in particular, sequencing of the mitochondrial (nad1 and cox1) and nuclear genes (ITS region; ITS1-5.8S-ITS2), has enabled us to obtain highly useful data on phylogenetic relationships of these 37-collar-spined Echinostoma spp. Thus, 16 different species are currently acknowledged to be valid worldwide, which include E. revolutum, E. bolschewense, E. caproni, E. cinetorchis, E. deserticum, E. lindoense, E. luisreyi, E. mekongi, E. miyagawai, E. nasincovae, E. novaezealandense, E. paraensei, E. paraulum, E. robustum, E. trivolvis, and Echinostoma sp. IG of Georgieva et al., 2013. The validity of the other 10 species is retained until further evaluation, including molecular analyses; E. acuticauda, E. barbosai, E. chloephagae, E. echinatum, E. jurini, E. nudicaudatum, E. parvocirrus, E. pinnicaudatum, E. ralli, and E. rodriguesi. In this review, the history of discovery and taxonomic debates on these 26 valid or validity-retained species are briefly reviewed.

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.

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

The major histocompatibility complex-B (MHC-B) in chickens is a cluster of genes located on chromosome 16. The chicken MHC-B is known to be highly associated with resistance to numerous diseases caused by viruses, bacteria, and parasitic pathogens. Since the level of resistance varies with MHC-B haplotypes, identification and classification of different haplotypes within lines is important for sustaining lines. The "Campero-INTA" chicken breed is a meat-type free-range poultry breed that was developed specifically for small producers in Argentina. Campero-INTA was started by selection in populations produced by crosses between a variety of established lines. MHC-B variation was examined in 65 samples obtained in 2002 using the VNTR marker LEI0258, a marker for MHC-B region. These samples plus and an additional 55 samples from 2018 were examined for variation using the MHC-B specific SNP panel that encompasses ∼230,000 bp of the MHC-B region. Eleven MHC-B SNP haplotypes with 6 LEI0258 alleles were identified in the 120 samples representing the Campero-INTA AH (male) line. Seven haplotypes originate from the breeds originally used in the development of Campero-INTA AH line. Two appear to be recombinant haplotypes. The origin of the remaining 2 is not known, but may be associated with genes introduced from crosses with the Fayoumi breed conducted more recently to sustain the line.

Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing

Unraveling the genetic diversity of livestock species is central to understanding their value and importance for conservation and improvement in diverse production environments. In developing countries, information on genetic attributes of many livestock species is unfortunately scanty to support well-informed decision-making upon relevant management strategies. This study aimed at investigating allelic variability, genetic diversity, and genetic relationships of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania using the Major Histocompatibility Complex-linked LEI0258 marker. A total of 400 DNA samples, 40 per ecotype, were genotyped by capillary electrophoresis. Thirty different alleles with sizes ranging from 197 to 569 bp were determined. The number of alleles ranged from 17 (Itunduma) to 21 (Mbeya), with an average of 19.20 alleles per ecotype. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Thirty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polymorphism based on a combination of two repeat regions at 12 and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 13 bp appeared 1 to 28 times, whereas the region at 12 bp appeared 3 to 19 times in all sequenced fragments. The numbers of indels and SNP determined were 7 and 9, respectively. From capillary electrophoresis, the Chunya and Msimbazi ecotypes exhibited the highest genetic diversity (0.937), whereas the lowest value (0.910) was observed from the Mbarali ecotype, with an average of 0.925. The Namtumbo and Wanging'ombe ecotypes showed high inbreeding coefficients (FIS > 0.05), whereas a high excess heterozygote value (FIS = -0.098) was observed from the Njombe ecotype. Two percent of the genetic diversity was due to differences among ecotypes, and the rest was due to differences among individuals within the ecotypes. Despite the overall low genetic differentiation, both fragment and sequencing analyses depicted a high allelic and genetic variability across 10 chicken ecotypes. These results therefore, underscore the importance of establishing appropriate conservation and management strategies to capitalize on observed variability and maintain genetic flexibility across diverse production environments.

Infections and pathology of free-roaming backyard chickens on St. Kitts, West Indies

Free-roaming chickens on Caribbean islands are important sentinels for local avian diseases and those introduced by birds migrating through the Americas. We studied 81 apparently healthy unvaccinated free-roaming chickens from 9 parishes on St. Kitts, an eastern Caribbean island. Using commercial ELISAs, no chickens had antibodies against avian influenza virus, West Nile virus, or Salmonella Enteritidis, although seropositivity was high to infectious bursal disease virus (86%), infectious bronchitis virus (84%), Mycoplasma (37%), and avian avulavirus 1 (Newcastle disease virus, 31%). Examination of small and large intestinal contents revealed cestodes in 79% and nematodes in 75% of the chickens. Although ectoparasites and endoparasites were common (74% and 79%, respectively), only a few chickens had lesions at postmortem examination, mainly intestinal serosal nodules (12%) and feather loss (6%). Histologic examination of 18 organs from each bird revealed lesions in high percentages of organs, mainly the liver (86%), lung (75%), spleen (60%), small intestine (56%), skin (42%), and kidney (40%). Lesions included degenerative, reactive, inflammatory, and neoplastic, and were not correlated with the serologic status of the chickens except in one case of infectious bursal disease. Microscopically, Paratanaisia bragai was seen in the kidneys of 3 chickens and intestinal coccidiasis in 1 chicken. Pulmonary silicate aggregates were common, were present in intestinal serosal nodules, and were suggestive of environmental exposure.

Prevalence and burden of gastrointestinal helminthes among grey-breasted helmet guinea fowls (Numida meleagris galeata) encountered in Gombe state, Nigeria

This cross sectional survey was conducted from July to December 2015 in order to investigate the burden of gastrointestinal helminthes among guinea fowls in Gombe, Northeastern Nigeria. A total of six hundred fowls (viscera) were purchased from six randomly selected slaughter slabs. Out of the 600 birds examined, 479 (79.83%; 95% CI: 76.4, 82.9) were found harbouring one or more gastrointestinal helminthes. Of this, 238 birds (39.7%; 35.8, 43.6) were infected by nematode species and 392 birds (65.3%; 61.4, 69.0) by cestode species. A total of nine nematodes and seven cestodes species were recovered from these birds. There was no any trematode observed among the studied birds. The prevalences of the nematodes identified in descending order were: Ascaridia galli 56.7% (52.7, 60.6); Ascaridia numidae 38.0% (34.2, 42.0); Heterakis gallinarum 17.2% (14.4, 20.4); Heterakis meleagridis 8.3% (6.4, 10.8); Strongyloides avium 3.5% (2.3, 5.3); Subulura brumpti 3.2% (2.0, 5.0); Gongylonema ingluvicola 2.2% (1.3, 3.7) and both Dispharynx spiralis and Tetrameres numidae had 0.7% (0.3, 1.7). While for cestodes: Raillietina tetragona 72.8% (69.1, 76.2); Raillietina echinobothrida 67.3% (63.5, 71.0); Raillietina cesticillus 50% (46.0, 54.0); Raillietina magninumida 25.7% (22.3, 29.3); Hymenolopsis cantaniana 17.3% (14.5, 20.6); Davainea nana 4.2% (2.8, 6.1) and the lowest was observed in Choanotaenia infundibulum with 2% (1.2, 3.5). Infection rates did not differ significantly based on sex (P > 0.05). However, the occurrence of mixed infection as compared with single infection was statistically significant in both cestodes and nematodes (P < 0.001). The results obtained indicated high prevalence of gastrointestinal helminthes among guinea fowls. These birds may serve as important source of helminthes to other commercial birds in the study area.

LEI0258 microsatellite variability and its association with humoral and cell mediated immune responses in broiler chickens

Major histocompatibility complex (MHC) has a profound influence on disease resistance or susceptibility, productivity and important economic traits in chicken. Association of the MHC with a wide range of immune responses makes it a valuable predictive factor for the disease pathogenesis and outcome. The tandem repeat LEI0258 is a genetic marker which is located within the B locus of chicken MHC and strongly associated with serologically defined haplotypes. LEI0258 microsatellite marker was applied to investigate the MHC polymorphism in Ross 308 broiler chicken (N=104). Association of LEI0258 alleles with humoral and cell mediated immune responses to Newcastle disease (ND), Infectious bursal disease (IBD) and Avian influenza (AI) vaccines were also examined. LEI0258 polymorphism was determined by PCR-based fragment analysis, and association of LEI0258 alleles with immune responses were evaluated using multivariate regression analysis and GLM procedures. A total of seven alleles ranging from 195 to 448bp were found, including two novel alleles (263 and 362bp) that were unique in Ross 308 broiler population. Association study revealed a significant influence of MHC alleles on humoral and cellular immune responses in Ross population (P<0.05). Alleles 385 and 448bp were associated with increased peripheral blood lymphocyte proliferation response. Alleles 300, 362 and 448bp had a positive effect on immune responses to Infectious bursal disease vaccine, and allele 263bp was significantly correlated with elevated antibody titer against Newcastle disease vaccine. Results obtained from this study confirmed the important role of MHC as a candidate gene marker for immune responses that could be used in genetic improvement of disease-resistant traits and resource conservation in broiler population.

MHC variability in heritage breeds of chickens

The chicken Major Histocompatibility Complex (MHC) is very strongly associated with disease resistance and thus is a very important region of the chicken genome. Historically, MHC (B locus) has been identified by the use of serology with haplotype specific alloantisera. These antisera can be difficult to produce and frequently cross-react with multiple haplotypes and hence their application is generally limited to inbred and MHC-defined lines. As a consequence, very little information about MHC variability in heritage chicken breeds is available. DNA-based methods are now available for examining MHC variability in these previously uncharacterized populations. A high density SNP panel consisting of 101 SNP that span a 230,000 bp region of the chicken MHC was used to examine MHC variability in 17 heritage populations of chickens from five universities from Canada and the United States. The breeds included 6 heritage broiler lines, 3 Barred Plymouth Rock, 2 New Hampshire and one each of Rhode Island Red, Light Sussex, White Leghorn, Dark Brown Leghorn, and 2 synthetic lines. These heritage breeds contained from one to 11 haplotypes per line. A total of 52 unique MHC haplotypes were found with only 10 of them identical to serologically defined haplotypes. Furthermore, nine MHC recombinants with their respective parental haplotypes were identified. This survey confirms the value of these non-commercially utilized lines in maintaining genetic diversity. The identification of multiple MHC haplotypes and novel MHC recombinants indicates that diversity is being generated and maintained within these heritage populations.

MHC, parasites and antler development in red deer: no support for the Hamilton & Zuk hypothesis

The Hamilton-Zuk hypothesis proposes that the genetic benefits of preferences for elaborated secondary sexual traits have their origins in the arms race between hosts and parasites, which maintains genetic variance in parasite resistance. Infection, in turn, can be reflected in the expression of costly sexual ornaments. However, the link between immune genes, infection and the expression of secondary sexual traits has rarely been investigated. Here, we explored whether the presence and identity of functional variants (supertypes) of the highly polymorphic major histocompatibility complex (MHC), which is responsible for the recognition of parasites, predict the load of lung and gut parasites and antler development in the red deer (Cervus elaphus). While we found MHC supertypes to be associated with infection by a number of parasite species, including debilitating lung nematodes, we did not find support for the Hamilton-Zuk hypothesis. On the contrary, we found that lung nematode load was positively associated with antler development. We also found that the supertypes that were associated with resistance to certain parasites at the same time cause susceptibility to others. Such trade-offs may undermine the potential genetic benefits of mate choice for resistant partners.

A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1

BACKGROUND

The major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. MHC genes are especially important in regulating immune responses, but even after over 80 years of research on the MHC, much remains to be learned about how it influences adaptive and innate immune responses. In most species, the MHC is highly polymorphic and polygenic. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. Here, we report (1) the development of a high-density SNP (single nucleotide polymorphism) panel for MHC-B typing that encompasses a 209,296 bp region in which 45 MHC-B genes are located, (2) how this panel was used to define chicken MHC-B haplotypes within a large number of lines/breeds and (3) the detection of recombinants which contributes to the observed diversity.

METHODS

A SNP panel was developed for the MHC-B region between the BG2 and CD1A1 genes. To construct this panel, each SNP was tested in end-point read assays on more than 7500 DNA samples obtained from inbred and commercially used egg-layer lines that carry known and novel MHC-B haplotypes. One hundred and one SNPs were selected for the panel. Additional breeds and experimentally-derived lines, including lines that carry MHC-B recombinant haplotypes, were then genotyped.

RESULTS

MHC-B haplotypes based on SNP genotyping were consistent with the MHC-B haplotypes that were assigned previously in experimental lines that carry B2, B5, B12, B13, B15, B19, B21, and B24 haplotypes. SNP genotyping resulted in the identification of 122 MHC-B haplotypes including a number of recombinant haplotypes, which indicate that crossing-over events at multiple locations within the region lead to the production of new MHC-B haplotypes. Furthermore, evidence of gene duplication and deletion was found.

CONCLUSIONS

The chicken MHC-B region is highly polymorphic across the surveyed 209-kb region that contains 45 genes. Our results expand the number of identified haplotypes and provide insights into the contribution of recombination events to MHC-B diversity including the identification of recombination hotspots and an estimation of recombination frequency.

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

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

Abundant polymorphisms at the microsatellite locus LEI0258 in indigenous chickens

The chicken major histocompatibility complex (MHC) has abundant SNP and indels, and is closely related with host genetic resistance or susceptibility to disease. The LEI0258 locus is the most variable in the MHC region, and is a useful marker in reflecting the variability of MHC. In this study, we applied the LEI0258 microsatellite marker to investigate polymorphism of MHC in Chinese indigenous chickens. The size of LEI0258 fragments in 1,617 individuals from 33 Chinese chicken breeds was detected by capillary electrophoresis, and 213 samples with different fragment sizes were further sequenced. A total of 69 alleles ranging from 193 to 489 bp were found, including 21 novel alleles and 28 private alleles that existed in only one breed. Three alleles, 249 bp (7.04%), 489 bp (6.57%), and 309 bp (6.10%), were the most frequent in the indigenous chickens. A 489-bp novel allele was unique in Chinese local chicken breeds. Three indels and 4 SNP of upstream/downstream of 2 repeat regions (R13/R12) were found. Abundant variations indicate high genetic diversity at the MHC region in indigenous chickens. Rare alleles are vulnerable to genetic drift in small populations, and can be used as molecular markers for monitoring the dynamic conservation of many indigenous breeds.

LEI0258 microsatellite variability in Khorasan, Marandi, and Arian chickens

Microsatellite LEI0258 is a genetic marker for chicken MHC haplotypes and can be used as an indicator of the influence of population genetics on immune responses. LEI0258 microsatellite variability in three Iranian indigenous chicken populations (Khorasan, Marandi, and Arian) was investigated. In total, 142 Khorasan, 42 Marandi, and 58 Arian chickens were examined. Collectively, 25 different alleles and 79 genotypes could be found. The observed levels of heterozygosity were 81% in Khorasan and Marandi and 34% in Arian chickens. Our results indicate that LEI0258 diversity in Marandi chickens is higher than in the other populations. Allelic diversity in Iranian chickens is relatively higher than in the local chicken breeds reported for Brazil and Vietnam.

Genetic diversity of the major histocompatibility complex region in commercial and noncommercial chicken flocks using the LEI0258 microsatellite marker

Microsatellite marker LEI0258 was used as an indicator to examine the variability of the major histocompatibility complex (MHC) region in 2 commercial layer flocks, 1 experimental layer cross, and 5 noncommercial flocks (used for free-run and free-range meat and egg production). We hypothesized that the populations from noncommercial sources may have more diversity in MHC genes than that in the commercial-source populations. Two related parameters, heterozygosity and the number of alleles harbored by a population, were used to assess the genetic variability. The different combinations of the 22 alleles created 66 genotypes in the 8 chicken populations that were studied. The noncommercial populations, except for the Silkies (SK), harbored more alleles than those in the 2 commercial populations, Lohmann Brown and Lohmann White. The observed heterozygosity of the MHC region was high in all of the populations, except for SK. Considering the 2 parameters we have examined, we can generalize that the intensively selected commercial egg-layer varieties seem to have less genetic variability in their MHC regions compared with that of the noncommercial flocks, which are less intensively selected. The LEI0258 variants can be used as markers to detect most of the MHC haplotypes, but in the different populations the same allele size may not always be associated with the same serologically defined haplotype. The information obtained from this study will be useful for genetic resource conservation and the development of breeding stocks that are suitable for free-range production.

Putative causes and consequences of MHC variation within and between locally adapted stickleback demes

Genes of the major histocompatibility complex (MHC) have been a source of considerable research interest, owing in large part to the growing body of evidence that they may be subject to both natural and sexual selection. However, much remains to be learned about the dynamics of MHC genes in subdivided populations, particularly those characterized by divergent ecological pressures. In this study, we attempt to disentangle the relative roles of both parasite-mediated selection and MHC-mediated mate choice in an open estuarine system inhabited by two parapatric, adaptively divergent threespine stickleback (Gasterosteus aculeatus) demes. We sequenced the putative peptide-binding region (PBR) of an estimated four Class IIβ loci from 127 individuals, identifying 329 sequence variants (276 translated amino acid sequences). Demes differed significantly both in the frequency of MHC alleles and in the communities of helminth parasites infecting resident sticklebacks. Strong signatures of natural selection were inferred from analyses of codon substitutions, particularly in the derived (freshwater) rather than the ancestral (marine) deme. Relationships between parasite load and MHC diversity were indicative of balancing selection, but only within the freshwater deme. Signals of MHC-mediated mate choice were weak and differed significantly between demes. Moreover, MHC-mediated mate choice was significantly influenced by environmental salinity and appeared of secondary importance to tendencies towards assortative mating. We discuss the implications of these findings in respect to ecological adaptation and the potential demographic consequences of possible outcomes of MHC-mediated mate choice.

MHC haplotype and susceptibility to experimental infections (Salmonella Enteritidis, Pasteurella multocida or Ascaridia galli) in a commercial and an indigenous chicken breed

In three independent experimental infection studies, the susceptibility and course of infection of three pathogens considered of importance in most poultry production systems, Ascaridia galli, Salmonella Enteritidis and Pasteurella multocida were compared in two chicken breeds, the indigenous Vietnamese Ri and the commercial Luong Phuong. Furthermore, the association of the Major Histocompatibility Complex (MHC) with disease-related parameters was evaluated, using alleles of the LEI0258 microsatellite as markers for MHC haplotypes. The Ri chickens were found to be more resistant to A. galli and S. Enteritidis than commercial Luong Phuong chickens. In contrast, the Ri chickens were more susceptible to P. multocida, although production parameters were more affected in the Luong Phuong chickens. Furthermore, it was shown that the individual variations observed in response to the infections were influenced by the MHC. Using marker alleles of the microsatellite LEI0258, which is located within the MHC region, several MHC haplotypes were identified as being associated with infection intensity of A. galli. An association of the MHC with the specific antibody response to S. Enteritidis was also found where four MHC haplotypes were shown to be associated with high specific antibody response. Finally, one MHC haplotype was identified as being associated with pathological lesions and mortality in the P. multocida experiment. Although not statistically significant, our analysis suggested that this haplotype might be associated with resistance. These results demonstrate the presence of local genetic resources in Vietnamese chickens, which could be utilized in breeding programmes aiming at improving disease resistance.

Mhc class II diversity and balancing selection in greater prairie-chickens

The major histocompatibility complex (Mhc) of domestic chickens has been characterized as small and relatively simple compared with that of mammals. However, there is growing evidence that the Mhc of many bird lineages may be more complex, even within the Order Galliformes. In this study, we measured genetic variation and balancing selection at Mhc loci in another galliform, the greater prairie-chicken. We cloned and sequenced a 239 bp fragment of Mhc Class II beta-chain (BLB) exon 2 in 14 individuals. There was a total of 10 unique sequences and a minimum of four BLB loci. The d(N)/d(S) ratio at peptide-binding codons was significantly greater than one, suggesting balancing selection is acting on the BLB. We also recovered two YLB sequences, which clustered tightly with YLB sequences from three other species: domestic chicken, black grouse and common quail. The relatively large number of loci revealed in our study suggests that even closely related galliforms differ in the level of Mhc variation and structure.

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates

BACKGROUND

The major histocompatibility complex (MHC) is a key model of genetic polymorphism. Selection pressure by pathogens or other microevolutionary forces may result in a high rate of non-synonymous substitutions at the codons specifying the contact residues of the antigen binding sites (ABS), and the maintenance of extreme MHC allelic variation at the population/species level. Therefore, selection forces favouring MHC variability for any reason should cause a correlated evolution between substitution rates and allelic polymorphism. To investigate this prediction, we characterised nucleotide substitution rates and allelic polymorphism (i.e. the number of alleles detected in relation to the number of animals screened) of several Mhc class II DRB lineages in 46 primate species, and tested for a correlation between them.

RESULTS

First, we demonstrate that species-specific and lineage-specific evolutionary constraints favour species- and lineage-dependent substitution rate at the codons specifying the ABS contact residues (i.e. certain species and lineages can be characterised by high substitution rate, while others have low rate). Second, we show that although the degree of the non-synonymous substitution rate at the ABS contact residues was systematically higher than the degree of the synonymous substitution rate, these estimates were strongly correlated when we controlled for species-specific and lineage-specific effects, and also for the fact that different studies relied on different sample size. Such relationships between substitution rates of different types could even be extended to the non-contact residues of the molecule. Third, we provide statistical evidence that increased substitution rate along a MHC gene may lead to allelic variation, as a high substitution rate can be observed in those lineages in which many alleles are maintained. Fourth, we show that the detected patterns were independent of phylogenetic constraints. When we used phylogenetic models that control for similarity between species, due to common descent, and focused on variations within a single lineage (DRB1*03), the positive relationship between different substitution rates and allelic polymorphisms was still robust. Finally, we found the same effects to emerge in the analyses that eliminated within-species variation in MHC traits by using strictly single population-level studies. However, in a set of contrasting analyses, in which we focused on the non-functional DRB6 locus, the correlation between substitution rates and allelic variation was not prevalent.

CONCLUSION

Our results indicate that positive selection for the generation of allelic polymorphism acting on the functional part of the protein has consequences for the nucleotide substitution rate along the whole exon 2 sequence of the Mhc-DRB gene. Additionally, we proved that an increased substitution rate can promote allelic variation within lineages. Consequently, the evolution of different characteristics of genetic polymorphism is not independent.