Cargando…
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 innat...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705597/ https://www.ncbi.nlm.nih.gov/pubmed/26743767 http://dx.doi.org/10.1186/s12711-015-0181-x |
_version_ | 1782409042565529600 |
---|---|
author | Fulton, Janet E. McCarron, Amy M. Lund, Ashlee R. Pinegar, Kara N. Wolc, Anna Chazara, Olympe Bed’Hom, Bertrand Berres, Mark Miller, Marcia M. |
author_facet | Fulton, Janet E. McCarron, Amy M. Lund, Ashlee R. Pinegar, Kara N. Wolc, Anna Chazara, Olympe Bed’Hom, Bertrand Berres, Mark Miller, Marcia M. |
author_sort | Fulton, Janet E. |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0181-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4705597 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-47055972016-01-09 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 Fulton, Janet E. McCarron, Amy M. Lund, Ashlee R. Pinegar, Kara N. Wolc, Anna Chazara, Olympe Bed’Hom, Bertrand Berres, Mark Miller, Marcia M. Genet Sel Evol Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12711-015-0181-x) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-07 /pmc/articles/PMC4705597/ /pubmed/26743767 http://dx.doi.org/10.1186/s12711-015-0181-x Text en © Fulton et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Fulton, Janet E. McCarron, Amy M. Lund, Ashlee R. Pinegar, Kara N. Wolc, Anna Chazara, Olympe Bed’Hom, Bertrand Berres, Mark Miller, Marcia M. 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 |
title | 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 |
title_full | 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 |
title_fullStr | 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 |
title_full_unstemmed | 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 |
title_short | 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 |
title_sort | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705597/ https://www.ncbi.nlm.nih.gov/pubmed/26743767 http://dx.doi.org/10.1186/s12711-015-0181-x |
work_keys_str_mv | AT fultonjanete ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT mccarronamym ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT lundashleer ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT pinegarkaran ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT wolcanna ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT chazaraolympe ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT bedhombertrand ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT berresmark ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT millermarciam ahighdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT fultonjanete highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT mccarronamym highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT lundashleer highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT pinegarkaran highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT wolcanna highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT chazaraolympe highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT bedhombertrand highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT berresmark highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 AT millermarciam highdensitysnppanelrevealsextensivediversityfrequentrecombinationandmultiplerecombinationhotspotswithinthechickenmajorhistocompatibilitycomplexbregionbetweenbg2andcd1a1 |