INTERPRETING CATTLE GENOMIC DATA: BIOLOGY, APPLICATIONS AND OUTREACH

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 0211111
• Project Start Date: Oct 1, 2002
• Project End Date: Sep 30, 2008
• Program Code: [(N/A)]- (N/A)

Recipient Organization
CORNELL UNIVERSITY
(N/A)
ITHACA,NY 14853

Performing Department
ANIMAL SCIENCE

Non Technical Summary
DNA technology for marker-assisted selection is maturing. Appropriate use of DNA information for selection requires that information be used in conjunction with pedigree and phenotypic data. Selection for traits such as healthfulness of beef products and cattle health is currently constrained by the lack of data on pedigreed animals. Selection for these traits will be enhanced by the development of DNA marker tools. This project will investigate the inclusion of DNA information into genetic evaluation programs to supplement the current information used to produce expected progeny differences. As well, populations will be developed for the collection of data on the fatty acid and mineral composition of beef and on the health of feedlot animals. These data sets will be used for DNA marker discovery and for the quantitative study of healthfulness of beef and cattle health.

Animal Health Component

90%

Research Effort Categories

Basic

(N/A)

Applied

90%

Developmental

10%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3310	1080	50%
303	3320	1080	50%

Knowledge Area
303 - Genetic Improvement of Animals;

Subject Of Investigation
3320 - Meat, beef cattle; 3310 - Beef cattle, live animal;

Field Of Science
1080 - Genetics;

Keywords

beef

genetic evaluation

healthfulness

feedlot health

Goals / Objectives
1. Determine the location, structure, function and expression of genes affecting health, reproduction, production, and product quality in cattle. 2. Interpret and apply genomics and proteomics information by developing statistical/bioinformatics methods and utilizing molecular tools in cattle. 3. Develop and deliver educational materials about bovine genomics research to consumers and stakeholders.

Project Methods
The National Beef Cattle Evaluation Consortium (NBCEC) addresses development of new genetic evaluation (GE) systems for expected progeny difference (EPDs), development and use of new trait GE, development of economically relevant traits, and producer education. DNA tests are becoming available through commercialization of DNA markers. Appropriate use of this information in conjunction with pedigree and phenotypic data requires DNA markers be incorporated into GE systems. DNA tests represent panels of markers, and it is envisioned that results will be reported as numeric scores representing the additive genetic value (AGV). There are two options that will be explored in incorporating these scores into evaluation programs; a multiple trait approach and an external EPD approach. In the multiple trait approach each panel result will be considered a separate but correlated trait to the trait being measured phenotypically. In the external EPD approach, the AGV will be brought into the GE system using the same procedure describe by Zhang et al. (2002) for including external EPDs for animals not in the data being analyzed. A system for each approach needs to be developed that appropriately estimates the AGV of the animals with DNA tests. Two new traits for genetic evaluation are healthfulness of beef products and health of feedlot cattle. The healthfulness project is to develop tools (i.e., EPDs and DNA markers) for selection of the nutritional/health values of beef. Beef fat is saturated and considered to be less healthy than other fat sources. The central hypothesis for the proposed research is that genetic selection/DNA markers can be used to select animals for enhanced nutritional value. An outcome of this project is that producers will be able to alter nutrient composition of beef (e.g., fatty acid composition, iron content, etc.) through selection, which will enhance its nutritional value, thus improving human health. To achieve this outcome, Iowa State University researchers wil1 determine nutrient composition of beef samples and evaluate any influence these nutrient components have on tenderness/sensory characteristics. Cornell University will perform evaluation to identify genetically superior animals and develop the phenotypic database for this project. We will demonstrate how beef can be enhanced and what the nutritional implications of these changes are so that producers can make informed breeding decisions. Cattle health is an important component to profitability. Over two years, 1600 calves from a single large ranch will be owned by and fed at a cooperating feedlot. Data on incidence of disease, behavior (flight speed and chute behavior), and growth and carcass traits as well as DNA samples will be collected by Colorado State University. It is anticipated that 80 percent of the calves will be identified back to their sire through DNA parentage testing. Whole genome scans will be done on the sick calves and a representative sample of those identified as not being sick in the feedlot growing phase of the study. The NBCEC is involved in producer education through workshops and symposium and train-the-trainer educational events.

Progress 10/01/02 to 09/30/08

Outputs
OUTPUTS: DNA technology for marker-assisted selection is maturing. Appropriate use of DNA information for selection requires that information be used in conjunction with pedigree and phenotypic data. Selection for traits such as healthfulness of beef products and cattle health is currently constrained by the lack of data on pedigreed animals. Selection for these traits will be enhanced by the development of DNA marker tools. The National Beef Cattle Evaluation Consortium (NBCEC) addresses development of new genetic evaluation (GE) systems for expected progeny difference (EPDs), development and use of new trait GE, development of economically relevant traits, and producer education. DNA tests are becoming available through commercialization of DNA markers. Appropriate use of this information in conjunction with pedigree and phenotypic data requires DNA markers be incorporated into GE systems. Methodology for the inclusion of molecular information into genetic evaluations has been developed. This system was tested combining phenotypic information for tenderness of beef products with molecular scores from DNA markers. Three new traits for genetic evaluation are healthfulness of beef products, adaptation, and health of feedlot cattle. The healthfulness project is to develop tools (i.e., EPDs and DNA markers) for selection of the nutritional/health values of beef. For adaptation, we are developing phenotypic (reproduction and stayability) and DNA resources on populations of cattle at large ranches located around the U.S. Stayability will be defined as the probability a female stays in the herd through three pregnancies. Cattle health is an important component to profitability. Over two years, 1600 calves from a single large ranch will be owned by and fed at a cooperating feedlot. Data on incidence of disease, behavior (flight speed and chute behavior), and growth and carcass traits as well as DNA samples will be collected by Colorado State University. From all three projects, the phenotypes and DNA resources are available for future validation of DNA tests. This includes approximately 3000 phenotyped animals for each project. The NBCEC conducts educational programs. Two such meetings held this year were a symposium on beef cattle genetic evaluation held in conjunctions with the American Society of Animal Science Annual Meeting in Indianapolis, IN, and the Genetic Prediction Workshop, which was co-sponsored with the Beef Improvement Federation, held in Kansas City, MO. PARTICIPANTS: Breed associations (Angus, Limosuine, Gelbvieh, Charolais, Red Angus and others) DNA companies: Igenity, Bovigen (now Phizer Animal Genetics) TARGET AUDIENCES: Beef Breed Associates, Seed Stock Commercial Producers and Feed Lot Managers. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Methodology for the inclusion of molecular information into genetic evaluations has been developed. Companies providing DNA technology services, such as diagnostic testing for economically-relevant traits, report their outcomes as numeric scores in the units of those traits. Using a multiple-trait analytical approach, a method has been devised to merge this numeric score into a genetic evaluation system that uses phenotypes and pedigrees. A change in action is that now genetic evaluation software for multibreed genetic evaluation is now being used by industry-owned entities providing genetic evaluation services. Previously, genetic evaluations were run for various breed associations at the core institutions of the NBCEC. DNA technology for marker-assisted selection is maturing. As such, it is anticipated that results from the quantitative trait loci discovery projects will alter producers' approach to selecting replacement breeding animals.

Publications

• Thallman, R. M., K. J. Hanford, R. L. Quaas, S. D. Kachman, R. J. Tempelman, R. L. Fernando, L. A. Kuehn, and E. J. Pollak. 2009. Estimation of the Proportion of Genetic Variation Accounted for by DNA Tests. Proceedings, Beef Improvement Federation Annual Meeting, pp 184-209.
• Thallman,R. M. and E. J. Pollak. 2008. Logistics for Working Together to Facilitate Genomic/Quantitative Genetic Prediction. 9th Genetic Prediction Workshop, Dec. 8-10, 2008. Kansas City, MO. Pages 101-108.
• Garrick, D. J. 2009. The nature and scope of some whole genome analyses in US beef cattle. Proceedings, Beef Improvement Federation Annual Meeting, pp 92-102

Progress 10/01/06 to 09/30/07

Outputs
OUTPUTS: We joined this project in the summer of 2007. From that time to the end of September 2007, we organized several populations of cattle to be used to meet the objectives of our project. In the area of reproduction, we have identified a population of females for which we will collect data and DNA samples for a study of heifer pregnancy. These heifers were weaned in August 2007 and will be pregnancy checked for our first data in September 2008. For the feedlot health program, we have secured 1600 steers that are currently being fed at Lamar, Colorado. We have collected information on temperament, stress indicators, immunological parameters, and incidence of bovine respiratory disease. For the healthful of beef products, we have identified several populations of Angus cattle that will be slaughtered in December 2007 and the summer of 2008. We have held several meetings of investigators relative to these projects to finalize the experimental design and protocol. PARTICIPANTS: Collection of data did not start prior to September 2007. As such, our collaborators have not yet participated beyond planning. For the healthfulness project, our collaborators include Jim Reecy (Iowa State University), Raluca Mateescu and Deb VanOverbeke (Oklahoma State University), and Alison Van Eenennaam (University of California, Davis). For the animal health project, our collaborators include Mark Enns and Hana Van Campen (Colorado State University), Guy Loneragan (West Texas A&M), Bob Weaber (University of Missouri), Janine Salak-Johnson (University of Illinois), and Chris Chase (South Dakota State University). For the reproductive study, our collaborators include Milt Thomas (New Mexico State University) and Jim Reecy (Iowa State University). For statistical analysis across projects, our collaborator is Rohan Fernando (Iowa State University). TARGET AUDIENCES: Our target audience is beef producers (seedstock and commercial). The development of diagnostic DNA tests will impact the actions taken by these producers to select cattle and make genetic changes.

Impacts
As we have only joined this project recently, we have yet to have an outcome based on results from our project. The target for this project is to develop DNA diagnostic tests with the phenotypes collected. The approach of developing DNA diagnostic tests for these traits is desirable because the beef industry does not routinely collect phenotypic information that could be used in routine genetic evaluations to produce expected progeny differences. Our plan is to use the 50K SNP panel for this research.

Publications

• No publications reported this period