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Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes

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Abstract

The polymorphism of major histocompatibility complex (MHC) class II DQ and DR genes in five common equine leukocyte antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine bacterial artificial chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next generation sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.

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Abbreviations

BAC:

Bacterial artificial chromosome

ELA:

Equine leukocyte antigen

MHC:

Major histocompatibility complex

UTR:

Untranslated region

WGS:

Whole genome sequence

NGS:

Next generation sequencing

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Acknowledgements

This research was conducted with support from US National Institutes of Health grant HD-049545, the Harry M. Zweig Memorial Fund for Equine Research, the Dorothy Russell Havemeyer Foundation, Inc., and the Morris Animal Foundation grant D13EQ-026. This study was made possible in part by NPRP Grant 6-1303-4-023 from the Qatar National Research Fund (a member of Qatar Foundation). The findings achieved, herein, are solely the responsibility of the authors. We would like to thank Jim Hardy, Scott Hoffay, and Emily Silvela for the management of Cornell Equine Genetics Center research herd and Dr. Joel Malek for overseeing genome sequencing efforts.

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Authors and Affiliations

  1. Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA

    Donald Miller, Rebecca L. Tallmadge & Douglas F. Antczak

  2. Equine Analysis Systems, 5472 Leestown Road, Lexington, KY, 40511, USA

    Matthew Binns

  3. Children’s Hospital of Oakland Research Institute, Oakland, CA, 94609, USA

    Baoli Zhu

  4. Weill Cornell Medicine—Qatar, Doha, Qatar

    Yasmin Ali Mohamoud & Ayeda Ahmed

  5. University of Florida, Gainesville, FL, 32611, USA

    Samantha A. Brooks

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  1. Donald Miller
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  2. Rebecca L. Tallmadge
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  8. Douglas F. Antczak
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Correspondence to Douglas F. Antczak.

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Animal care was performed in accordance with the guidelines set forth by the Institutional Animal Care and Use Committee of Cornell University.

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Miller, D., Tallmadge, R.L., Binns, M. et al. Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes. Immunogenetics 69, 145–156 (2017). https://doi.org/10.1007/s00251-016-0964-4

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  • DOI: https://doi.org/10.1007/s00251-016-0964-4

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