Molecular identification of the bovine major histocompatibility complex I and II genes of a bos taurus africanus (sanga) cattle breed of Zambia

Abstract

The Major Histocompatibility Complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity and is the most polymorphic locus in the mammalian genome. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation pivotal in determining the nature of immune responses. Currently, our knowledge of the bovine MHCI and II repertoire is limited, with only the Holstein-Friesian breed having been studied intensively. Traditional methods of MHC genotyping are of low resolution and laborious, however, next-generation sequencing (NGS) technologies have enabled high throughput and much higher resolution MHC typing in a number of species. In this study alleles of the BoLA class I and BoLA class II (DRB3, DQA and DQB) loci, from 347 Tonga cattle whole blood from four discrete sampling locations were sequenced using the Illumina MiSeq NGS platform. Analysis of the sequence data was performed with Bioinformatic scripting/tools (FastQC, Flash, Fastx, BLAST, and Perl). During the course of this study, a total of 137 MHC class I haplotypes were identified, of which 37 were novel. Together these novel haplotypes included 13 novel alleles and sequences matching 88 known alleles. Furthermore, 67 novel MHC class II haplotypes were defined by co-occurrence of the same DRB3, DQA and DQB alleles. Together these MHCII haplotypes included 108 novel alleles and sequences matching 121 known alleles. The results of this study have dramatically expanded the known bovine MHC repertoire of African cattle. This is the first report presenting a detailed study of the allelic and haplotype distribution of Bovine MHCI and II genes in a Bos taurus africanus cattle breeds. These results will provide a wealth of information for rationalising the development of improved and novel vaccines against infectious diseases of livestock, help in developing improved Livestock breeding strategies and will be a major contributor to upgrading the current Immuno polymorphism database - MHC database of known bovine MHC alleles. Key words: Major histocompatibility complex; Tonga cattle; next generation sequencing; Bioinformatics