Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing

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Date
2016Author
Vasoya, Deepali
Law, Andy
Motta, Paolo
Yu, Mingyan
Muwonge, Adrian
Cook, Elizabeth
Li, Xiaoying
Bryson, Karen
MacCallam, Amanda
Sitt, Tatjana
Toye, Philip
Bronsvoort, Barend
Watson, Mick
Morrison, W. Ivan
Connelley, Timothy
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Show full item recordAbstract
The major histocompatibility complex (MHC) region
contains many genes that are key regulators of both innate
and adaptive immunity including the polymorphicMHCI
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 bovineMHCI 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.