Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds

Abstract

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.

Keywords:

• Major histocompatibility complex
• positive selection
• natural selection
• selective sweep
• Cattle

Acknowledgments

Support received from the National Agricultural Science Fund (NASF), Indian Council of Agricultural Research, New Delhi, India for carrying out this work is duly acknowledged. The authors wish to thank the Director and Joint Director (Research), ICAR-Indian Veterinary Research Institute, Bareilly, India for providing the necessary facilities during this study.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genotypic data used in the current study are available in the WIDDE database (http://widde.toulouse.inra.fr/widde/) and also at the Dryad data repository (https://doi.org/10.5061/dryad.th092). The remaining genotypic data used in this study are available with the corresponding author.

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.