UNDERSTANDING COMPOSITION OF BOVINE COLONIC MICROBIOTA AND PREDISPOSITION TO EHEC COLONIZATION AS COMPLEX POLYGENIC TRAITS IN BEEF CATTLE

Objective 1: Develop study populations and collect phenotypic data. We will establish a large animal population (n=1,400) at three different sites (U.S. Meat Animal Research Center [USMARC], Colorado State University and Texas A&M University). Phenotypic data (enterohemorrhagic Escherichia coli [EHEC] shedding, microbiome composition, feed intake, etc. ) will be collected at multiple time points during years 1-4. Microbiome composition will be assessed with 16s rRNA-based pyrosequencing. Objective 2: Collect genotypic data across the study population and perform quantitative trait locus (QTL) analysis. Genotyping will be performed with the bovine high density chip and the genotypic and phenotypic data analyzed using linkage disequilibrium QTL mapping strategies (GWAS). Objective 3: Further localize QTL using a combination of expression QTL (eQTL) and localized high-density mapping. QTL regions will be further localized using eQTL mapping with microarrays and a high density of single-nucleotide polymorphisms (SNPs) located within the QTL regions.