Development of polymorphic markers in the immune gene complex loci of cattle

Publication history: Accepted - 18 January 2021; Published online - 6 March 2021The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and 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 chromosome inserts spanning 3 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. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 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.Hammond, Heimeier, and Schwartz were supported by United Kingdom Research and Innovation, Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) funding awards BB/M027155/1, BBS/E/I/00007031, BBS/E/I/00007038, BBS/E/I/00007039, BBS/OS/GC/000015B, and BBS/OS/GC/200016. Glass was supported by UKRI-BBSRC funding awards BB/J004227/1, BB/J004235/1, and BB/P013740; Glass, Skuce, and Allen were also supported by UKRI-BBSRC BB/E018386/1, BB/E018335/1 and 2, and BB/L004054/1; Glass was also supported by UKRI-BBSRC award BB/M027155/1 and BB/P013740/1. Wilkinson was supported by UKRI-BBSRC BB/L004054/1. We gratefully acknowledge the Agri-Food and Biosciences Institute (AFBI, Northern Ireland) who collected and provided samples in the form of phenotyped bTB case/control samples for use within this project. Bickhart, Bakshy, McClure, and Null were supported by appropriated projects 5090-31000-026-00-D, Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency, and 8042-31000-001-00-D, Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection, of the Agricultural Research Service (ARS) of the USDA. Cole and Null were supported by appropriated project 8042-31000-002-00-D, “Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals of ARS-USDA. Cole was also partially supported by the grant “Reducing Mastitis in the Dairy Cow by Increasing the Prevalence of Beneficial Polymorphisms in Genes Associated with Mastitis Resistance” from the Minnesota Agricultural Experiment Station Rapid Agricultural Response Fund. Smith was supported by appropriated project 3040-31000-100-00-D, “Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production,” of ARS-USDA. Bickhart, Bakshy, Young, and Smith were supported by USDA NIFA grant number 2015-67015-22970, “US-UK Collaborative project: “Reassembly of cattle immune gene clusters for quantitative analysis.