Recipient Organization
AGRICULTURAL RESEARCH SERVICE
(N/A)
BROOKINGS,SD 57006
Performing Department
(N/A)
Non Technical Summary
Liver abscesses in feedlot cattle are prevalent across the United States costing the industry millions of dollars in livers that cannot be used for food, increased time to process carcasses, and cattle productivity losses. The occurrence of liver abscesses will continue to increase as the industry reduces in-feed antibiotic use. We hypothesize that some cattle are more prone to abscess because of their genetics, and that cellular markers that will correlate with the development of liver abscesses. Our first objective is identify genomic markers that predict the likelihood of an animal developing liver abscesses.Our second objective is to evaluate circulating cell types, cytokines, and metabolites in the blood, and gene expression, liver enzyme function, bacterial communities, feed intake and body weight gain to identify biological or cellular profiles that correlate with the development of liver abscesses and the timing at which they occur during the feeding period. Deliverables will include genetic variants that correlate with susceptibility to liver abscesses to allow selection of animals that are less prone to developing them, and diagnostic tools to identify animals that are developing liver abscesses and may need to be managed differently. These data will be useful as a novel approach to reduce the incidence of liver abscesses in the US without the use of antibiotics and provide an opportunity to improve feed efficiency and beef production.
Animal Health Component
20%
Research Effort Categories
Basic
80%
Applied
20%
Developmental
0%
Goals / Objectives
The goals of this project are to characterize both the genomic variation of animals with liver abscesses and the temporal molecular profiles that correlate with the development of liver abscesses. Specifically, we propose to evaluate the genome for DNA variation; the transcriptome and metabolome of blood and liver for molecular profiles over time; the blood for hematology, liver function enzymes, and cytokine profiles; the rumen content for variation in the microbiome; along with feed efficiency, rumen pH, and ultrasound data to obtain a more complete evaluation of the development of liver abscesses.?
Project Methods
The U.S. Meat Animal Research Center has been collecting liver abscess phenotypes on cattle and to date, currently has liver scores on over 10,000 steers. Most of these animals have low pass sequence data or have been genotyped with high density genotyping arrays. In Objective 1, we will impute all of the animals with scores to whole genome sequence (WGS) using pedigree information and reference haplotypes. This data will provide us with genotypes on over 30 million SNP. The genotypes obtained from whole genome sequence will be used to perform a genome wide association analysis. Variants considered in the GWAS will be a subset of the imputed SNP, selected using genome annotation. The GWAS model will include the fixed effects of contemporary group, breed and sire line. We expect to find 50 or more SNP with at least moderate effects for liver abscesses. We will evaluate these genetic markers for effects on liver abscess score, as well as for the frequency of hetero- and homozygosity among the animals that developed liver abscesses. The markers identified as influential in the training population will be used to weight the genotypes in objective 2 that will be used to produce liver abscess prediction scores.In Objective 2, over two years, we will perform two feeding studies using moderate (MOD) or aggressive (AGGR) adaptation (step-up) rations. We will use 100 ten-month-old composite breed steers. To ensure 100 animals on study, 130 animals will be trained to use the Insentec feeding system to obtain individual animal feed intake records. The training will occur over a five-week period on a grower diet. Once steers have been trained to use the facility, they will be assigned to one of two groups (n=50/group). Animals will be stratified by age and initial weight and randomly assigned to treatment within stratification. One group will be placed on the MOD diet and will be adapted to a 90% corn-based high concentrate diet using four steps over 28 days with a new diet provided every 7 days. The second group will be placed on the AGGR diet and will be stepped up over 14 days of adaptation with a new diet that will be provided alternating every 3 and 4 days (i.e., Step 1 fed for 3 days, Step 2 fed for 4 days, etc.). The diets will not contain tylosin phosphate. Steers will be fed the 90% concentrate finish diet for 147 days.A rumen bolus to monitor rumen pH will be inserted into the reticulum of each animal after training has been completed and before the first adaptation step up has begun. While on the finishing diet, steers will be weighed, blood samples will be collected, and livers will be evaluated by ultrasound every three weeks. A liver biopsy sample will be collected 3 times during the studies and rumen content sample will be collected from each animal at 4 time points. These samples will be used to perform RNA-sequencing and global metabolomics to obtain transcriptomic and metabolomic profiles of the liver and whole blood; hematology parameters from the blood; liver function enzymes and cytokine profiles with the serum and plasma; and microbiome profiles of rumen content. We will also use liver ultrasound, feed intake, feed behavior, weight gain, rumen pH, and health records to generate a better whole animal picture of the changes that occur as liver abscesses develop. In addition, we will perform low-pass sequencing on these animals to use for liver abscess prediction with the genotypes associated with liver abscesses identified in Objective 1.