|BAKSHY, KIRANMAYEE - Fujifilm/cellular Dynamics
|HEIMEIER, DOROTHEA - The Pirbright Institute
|SCHWARTZ, JOHN - The Pirbright Institute
|GLASS, ELIZABETH - Roslin Institute
|WILKINSON, SAMANTHA - Roslin Institute
|SKUCE, ROBIN - Agri-Food And Biosciences Institute
|ALLEN, ADRIAN - Agri-Food And Biosciences Institute
|YOUNG, JULIANA - Former ARS Employee
|HAMMOND, JOHN - The Pirbright Institute
|Smith, Timothy - Tim
Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2021
Publication Date: 6/1/2021
Citation: Bakshy, K., Heimeier, D., Schwartz, J.C., Glass, E.J., Wilkinson, S., Skuce, R.A., Allen, A.R., Young, J., McClure, J.C., Cole, J.B., Null, D.J., Hammond, J.A., Smith, T.P.L., Bickhart, D.M. 2021. Development of polymorphic markers in the immune gene complex loci of cattle. Journal of Dairy Science. 104(6):6897-6908. https://doi.org/10.3168/jds.2020-19809.
Interpretive Summary: Dairy producers desire healthy cattle that are resistant to disease. The fewer days that a cow is sick, the more likely she is to produce large amounts of high quality milk. One way to accomplish this is to select cows that are resistant to disease based on their genetics. This study provides the first look at regions of the cattle genome that could be used for this intent.
Technical Abstract: The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity, productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly, and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial clone inserts spanning three of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. While we did not identify any significant association of bTB phenotypes with these new genetic markers, two markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.