Abstract
Described here is a new, more efficient method for defining major histocompatibility complex-Y (MHC-Y) genotypes in chickens. The MHC-Y region is genetically independent from the classical MHC (MHC-B) region. MHC-Y is highly polymorphic and potentially important in the genetics of disease resistance. MHC-Y haplotypes contain variable numbers of specialized MHC class I-like genes, along with members of four additional gene families. Previously, MHC-Y haplotypes were defined by patterns of restriction fragments (RF) generated in labor-intensive procedures that were difficult to use to define MHC-Y genotypes for large numbers of samples. The method reported here is much simpler. MHC-Y genotypes are distinguished via patterns of PCR products generated from heritable short tandem repeat (STR) regions found immediately upstream of the MHC class I-like genes located throughout MHC-Y haplotypes. To validate the method, fully pedigreed families were analyzed for STR-defined haplotypes in light of haplotypes defined previously by RF patterns. STR-defined MHC-Y patterns segregate in fully pedigreed families as expected and correspond with haplotypes assigned by RF patterns. The patterns provided in STR chromatograms generated by capillary electrophoresis are distinct for different haplotypes and can be scored easily. Investigations into the influence of MHC-Y genetics on immune responses can now realistically be conducted with large sample sets.
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Acknowledgments
We thank Chris Ashwell, North Carolina State University, for urging us to incorporate capillary electrophoresis in the analysis of the STR patterns revealed by PCR, and Garrett Larson, City of Hope, for instruction in STR analyses. We laud the outstanding support provided by Rosalina Lonergan in the City of Hope Integrated Genomics Core. We thank reviewers for guiding us in improving this manuscript.
Funding
This work reported here is supported by Agriculture and Food Research Initiative Competitive Grant from the United States Department of Agriculture, National Institute of Food and Agriculture, Food Safety Program (Grant 12233246) and funds from a City of Hope donor. This work was made possible by earlier advances funded through previous USDA NIFA awards.
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Zhang, J., Goto, R.M. & Miller, M.M. A simple means for MHC-Y genotyping in chickens using short tandem repeat sequences. Immunogenetics 72, 325–332 (2020). https://doi.org/10.1007/s00251-020-01166-6
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DOI: https://doi.org/10.1007/s00251-020-01166-6