Allelic polymorphism, gene duplication and balancing selection of the MHC class II DAB gene of Cynoglossus semilaevis (Cynoglossidae)

Tj, Xu; Yn, Sun; Rx, Wang

doi:10.4238/vol10-1gmr960

Cited by 5 publications

(4 citation statements)

References 42 publications

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“…Loci under positive selection, however, can be essential in distinguishing between recently diverged species and populations that are otherwise difficult to distinguish using neutral makers [14], [38]. Characterizing genomic regions under balancing selection could identify advantageous genes and alleles that move between populations, such as loci involved in disease resistance (e.g., [39]). Thus, a necessary first step in any genetic study is to accurately characterize suites of loci that match study objectives and ensure the application of appropriate analytical models and correct interpretation of results.…”

Section: Discussionmentioning

confidence: 99%

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Haynes

Latch

2012

PLoS ONE

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Single nucleotide polymorphisms (SNPs) are growing in popularity as a genetic marker for investigating evolutionary processes. A panel of SNPs is often developed by comparing large quantities of DNA sequence data across multiple individuals to identify polymorphic sites. For non-model species, this is particularly difficult, as performing the necessary large-scale genomic sequencing often exceeds the resources available for the project. In this study, we trial the Bovine SNP50 BeadChip developed in cattle (Bos taurus) for identifying polymorphic SNPs in cervids Odocoileus hemionus (mule deer and black-tailed deer) and O. virginianus (white-tailed deer) in the Pacific Northwest. We found that 38.7% of loci could be genotyped, of which 5% (n = 1068) were polymorphic. Of these 1068 polymorphic SNPs, a mixture of putatively neutral loci (n = 878) and loci under selection (n = 190) were identified with the FST-outlier method. A range of population genetic analyses were implemented using these SNPs and a panel of 10 microsatellite loci. The three types of deer could readily be distinguished with both the SNP and microsatellite datasets. This study demonstrates that commercially developed SNP chips are a viable means of SNP discovery for non-model organisms, even when used between very distantly related species (the Bovidae and Cervidae families diverged some 25.1−30.1 million years before present).

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Section: Discussionmentioning

confidence: 99%

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Haynes

Latch

2012

PLoS ONE

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“…Polymorphism derives from the creek word πολυμορφία ” (polymorphia) and means “many or complex shapes”. The polymorphism found in the MHC class II genes is generally limited to exon 2, which encodes the peptide-binding groove [59]. Due to the high frequency of MHC alleles, most individuals will be heterozygous for each different MHC gene locus.…”

Section: The Major Histocompatibility Complex (Mhc)mentioning

confidence: 99%

Role of MHC-Linked Susceptibility Genes in the Pathogenesis of Human and Murine Lupus

Relle

Schwarting

2012

Clinical and Developmental Immunology

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Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by the production of autoantibodies against nuclear antigens and a systemic inflammation that can damage a broad spectrum of organs. SLE patients suffer from a wide variety of symptoms, which can affect virtually almost any tissue. As lupus is difficult to diagnose, the worldwide prevalence of SLE can only be roughly estimated to range from 10 and 200 cases per 100,000 individuals with dramatic differences depending on gender, ethnicity, and location. Although the treatment of this disease has been significantly ameliorated by new therapies, improved conventional drug therapy options, and a trained expert eye, the underlying pathogenesis of lupus still remain widely unknown. The complex etiology reflects the complex genetic background of the disease, which is also not well understood yet. However, in the past few years advances in lupus genetics have been made, notably with the publication of genome-wide association studies (GWAS) in humans and the identification of susceptibility genes and loci in mice. This paper reviews the role of MHC-linked susceptibility genes in the pathogenesis of systemic lupus erythematosus.

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“…Numerous studies have found multiple DAB loci in other fish species (Kruiswijk, Hermsen, Fujiki, Dixon, Savelkoul & Stet ; Li, Jiang, Han, Su, Yang & He ; Xu, Sun & Wang ). In this study, we found that individuals possessed, at most, four alleles.…”

Section: Discussionmentioning

confidence: 99%

Association between MHC II beta chain gene polymorphisms and resistance to infectious haematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss, Walbaum, 1792)

et al. 2014

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Infectious haematopoietic necrosis virus (IHNV) is a serious pathogenic threat to rainbow trout (Oncorhynchus mykiss) and other salmonids. Major histocompatibility complex (MHC) polymorphisms have been closely linked to disease susceptibility. In this study, polymerase chain reaction-singlestrand conformation polymorphism, cloning and sequencing were used to examine MHC class II b chain gene (DAB) polymorphisms and analyse their association with IHNV in rainbow trout. The DAB exon 2 was amplified from 104 resistant and 91 susceptible fish. Forty-five different alleles were identified, 30 of which were novel. Individuals possessed between one and four alleles, indicating that the genome harbours at least two closely related DAB exon 2 loci. The percentages of amino acid mutations in the peptide binding region (PBR) and non-PBR were 66.67% and 45.28% respectively. The rate of non-synonymous substitutions occurred at a significantly higher frequency than synonymous substitutions, suggesting the existence of balancing selection for maintenance of polymorphisms at the DAB exon 2 locus. The alleles Onmy-DAB*0201 (P < 0.001), Onmy-DAB*0904 (P < 0.001) and Onmy-DAB*1102 (P < 0.01) were associated with susceptibility to IHNV, while Onmy-DAB*0103, Onmy-DAB*0601 and Onmy-DAB*1402 were associated with resistance (P < 0.001). These alleles could be used as molecular markers for IHNV resistance breeding in rainbow trout.

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Allelic polymorphism, gene duplication and balancing selection of the MHC class II DAB gene of Cynoglossus semilaevis (Cynoglossidae)

Cited by 5 publications

References 42 publications

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Identification of Novel Single Nucleotide Polymorphisms (SNPs) in Deer (Odocoileus spp.) Using the BovineSNP50 BeadChip

Role of MHC-Linked Susceptibility Genes in the Pathogenesis of Human and Murine Lupus

Association between MHC II beta chain gene polymorphisms and resistance to infectious haematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss, Walbaum, 1792)

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