High throughput analysis of MHC class I and class II diversity of Zambian indigenous cattle populations

Abstract

The classical MHC class I and class II molecules play key roles in determining the antigenic-specificity of CD8+ and CD4+ T-cell responses-as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our ability to understand, and potentially, exploit how genetic diversity influences the outcome of immune responses. Cattle remain one of the most economically livestock species, with particular importance to many small-holder farmers in low-and-middle income countries (LMICs). However, our knowledge of MHC (BoLA) diversity in the indigenous breeds that form the mainstay of cattle populations in many LMICs remains very limited. In this study we develop a MiSeq-based platform to enable the rapid analysis of BoLA-DQA and BoLA-DQB, and combine this with similar platforms to analyse BoLA-I and BoLA-DRB repertoires, to study a large cohort of cattle ($800 animals) representing the 3 major indigenous breeds (Angoni, Barotse, Tonga) in Zambia. The data presented confirms the capacity of this high-throughput and high-resolution approach to provide a full characterisation of the MHCI-MHCII genotypes of cattle for which little previous MHC sequence data has been obtained. The cattle in Zambia were found to express a diverse range of MHCI, MHCII and extended MHCI-MHCII haplotypes. The combined MHCI-MHCII genotyping now possible opens new opportunities to rapidly expand our knowledge of MHC diversity Isaac Silwamba and Deepali Vasoya contributed equally to this study.

Large scale transcriptional analysis of MHC class I haplotype diversity in sheep

“…In contrast to the haplotype variation observed for sheep and recently for cattle, [19][20][21] the HLA and chicken MHC regions have haplotypes with a fixed number of MHC class I genes. The HLA class I region includes three classical class I genes, HLA-A, B and C. HLA-A and B are the dominant class-I genes while HLA-C is transcribed at slightly lower levels.…”

“…The development of high through-put, sequencebased MHC typing technologies has been driven by the need to define allelic diversity in HLA class I and class II genes due to their central role in allogeneic tissue transplantation. 18 In this study, we aim to expand on recent development of this technology for cattle [19][20][21] to analyse MHC haplotype diversity in a large cohort of Scottish Blackface sheep.…”

High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure

“…The introduction of next-generation sequencing (NGS) approaches has enabled highresolution and high-throughput MHC genotyping and has fundamentally revolutionized clinical (e.g., [21][22][23]) and research approaches to MHC analysis (e.g., [32,33]). We have recently developed MiSeq-based MHC sequencing approaches to allow the characterization of the MHC genotypes of cattle and applied these to the analysis of MHC diversity in populations of different breeds in various geographical areas [27][28][29]. In this study, we have adapted the NGS MHC genotyping protocol to enable the rapid characterization of the MHCI and MHCII repertoires in horses.…”

“…The equine MHC typing platform was designed based on the system developed for cattle [27][28][29]. In MHCI, the polymorphic region that forms the peptide binding groove is formed by the α1 and α2 domains encoded by exons 2 and 3, which have a combined length of ~540 bp.…”

“…It also affords new opportunities to explore the MHC repertoire of diverse animal species (for example, [24][25][26]). We have recently developed Illumina Miseq-based high-throughput approaches to analyze the combined MHCI and MHCII genotypes of cattle cohorts of various breeds and lineages [27][28][29]. In this study, we developed a parallel system to study the MHC repertoire of horses and applied this to study the MHCI and MHCII alleles expressed in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses.…”