title: Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing.
abstract: The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Deepali
authors: D
authors: Vasoya
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Andy
authors: A
authors: Law
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Paolo
authors: P
authors: Motta
authors: International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya.
authors: Mingyan
authors: M
authors: Yu
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Adrian
authors: A
authors: Muwonge
authors: International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya.
authors: Elizabeth
authors: E
authors: Cook
authors: Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Xiaoying
authors: X
authors: Li
authors: Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.|Trinity College Dublin, College Green, Dublin, 2, Ireland.
authors: Karen
authors: K
authors: Bryson
authors: Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Amanda
authors: A
authors: MacCallam
authors: Department of Animal and Veterinary Sciences, The University of Vermont, 311 Terrill, 570 Main, Burlington, VT, 05405-0148, USA.
authors: Tatjana
authors: T
authors: Sitt
authors: International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya.
authors: Philip
authors: P
authors: Toye
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Barend
authors: B
authors: Bronsvoort
authors: Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: Mick
authors: M
authors: Watson
authors: Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
authors: W Ivan
authors: WI
authors: Morrison
authors: Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK. timothy.connelley@ed.ac.uk.
authors: Timothy
authors: T
authors: Connelley
mesh_terms: D000818:Animals; D002417:Cattle / Q000235:genetics*; D019295:Computational Biology; D040961:Genetic Drift; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015395:Histocompatibility Antigens Class I / Q000235:genetics*; D016133:Polymerase Chain Reaction
chemical_list: D015395:Histocompatibility Antigens Class I
keywords: Cattle; MHCI; Next-generation sequencing