A Host-pathogen Approach to Gwas For Enhanced Resistance to Bacterial Mastitis in Dairy Cattle

The primary research objective of this project is to identify bovine genetic variation associated with enhanced risk of E. coli CM in U.S. Holstein dairy cattle, and to use this information to foster the deployment of SNP-based selection tools that identify dairy cattle with reduced susceptibility. To increase the precision and likelihood of detecting associations with susceptibility, we will focus on the lifetime clinical mastitis distribution for a single bacterial pathogen (E. coli), thus creating a very precise animal disease phenotype. Moreover, genome sequencing data generated from the diagnostic isolates that define each E. coli CM case will also be used in a mixed-model approach to estimate the joint effects and/or interactions related to both host and pathogen genomic variation with respect to risk for recurrent E. coli CM in dairy cattle. Completion of these objectives will positively augment modern on-farm prevention and control measures, and therefore, is expected to allow
for a significant reduction in recurrent E. coli CM among dairy cattle. To achieve our overarching primary research objective, we will employ the following specific objectives:Use > 9,000 precisely documented Holstein dairy cows from commercial NY dairies to define the extremes (i.e. tails) of the lifetime E. coli clinical mastitis distribution andselect cows from each extreme (i.e. multiple E. coli CM cases and controls with zero lifetime CM). To increase our sample size, we will also use these data to match single E. coli CM case cows and zero lifetime CM controls by lactation, age, and herd.Holstein cows with one or more (i.e. recurrent) episodes of diagnostically confirmed E. coli CM will be selected as "cases", with enrollment priority given to cows with ≥ 2 confirmed E. coli CM episodes. A CM severity score will also be assigned to case cows (see approach). Precisely monitored cows matched by lactation, age, and herd that display no lifetime evidence of CM will be selected
as "controls." The ratio of controls to cases will be > 1:1 (n = 500 controls and 300 cases), which is determined by the prevalence of single and repeat E. coli CM cases prior to and across the award period.E. coligenomes representing the diagnostic isolates recovered from CM case cows will be sequenced to ≥ 40X average coverage using standard paired-end libraries applied to an Illumina HiSeq 2500 to facilitate E. coli strain classification, and to elucidate genome-wide information regarding strain-specific variation.All cows will be genotyped using the Illumina GGP-HD 135K assay and imputed to 778K density. Bovine 778K genotypes and E. coli variation will be bioinformatically joined for use in a novel genome-wide association analysis (GBLUP; EMMAX; Bayesian Models) that accounts for E. coli strain and/or polymorphism information with respect to risk for E. coli CM episodes and clinical severity (see approach) while also correcting for any pedigree-based stratification among the
cows.Bovine and/or E. coli markers which are statistically predictive for risk of E. coli CM in Holstein dairy cows will be transferred to the stakeholders in a format that is cost-effective, efficient, and readily incorporated within other ongoing efforts to employ genomic selection in beef and dairy cattle (BRD-CAP Project; Bovine Feed Efficiency Project; Heifer Fertility Project; Bovine Functional Assay Project; Dairy Fertility Project).