Project Number: 3040-31000-100-11-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Mar 1, 2018
End Date: Jan 31, 2022
1) Analyze a large beef cattle population (n=750) utilizing a combination of functional phenotyping methods to characterize the rumen pan-genome involved in rumen ecosystem function, searching for specific functional features and pathways of the microbiome that may influence feed efficiency; 2) Test rumen microbial functional genes, and genes of the microbiota associated with feed efficiency for genome-wide associations with 70K SNP assays to develop a subset of single nucleotide polymorphisms (SNP) that can be used for selection and for QTL detection.
Cattle (n = 750) under different dietary conditions will be phenotyped for their rumen microbial pan-genome. The gut microbial community functional gene content will be assessed by shotgun sequencing of the total rumen DNA using Illumina HiSeq sequencing. Sequencing will be performed using 150 bp paired-end sequencing at a depth of ~12,000,000 reads per sample. In addition all animals will be genotyped, and performance parameters will be measured. The microbial functional gene composition identified through shotgun metagenome sequencing will be used to determine functional changes in the microbial community composition in high efficiency and low efficiency animals. Consequently, our in-depth analysis of the microbiota “functional phenotypes” will be used for QTL mapping of microbiome functions as well as co-occurring sets of functions that may be associated with increased feed efficiency. Finally, we will analyze the pan-genome of the rumen to identify candidate genes and metabolic pathways that may influence feed efficiency.