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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION Project Number: 1265-31000-096-00
Project Type: Appropriated

Start Date: Jul 24, 2007
End Date: Jul 23, 2012

Objective:
The primary objective is to improve the productive efficiency of dairy animals for traits of economic interest through genetic evaluation and management characterization so that the United States and other countries can meet the dietary needs of their populations. Specific objectives include: Objective 1: Collect genotypes, specifically single-nucleotide polymorphisms (SNPs), and new phenotypes to improve accuracy and comprehensiveness of the national dairy database. Subobjective 1.A: Increase the accuracy of pedigree information by using SNP genotypes to verify and to assign parentage. Subobjective 1.B: Obtain additional data on health and management traits, and improve consistency of national database. Objective 2: Characterize phenotypic measures of dairy practices, and provide the dairy industry with information needed to determine the impact of various herd management decisions on profitability. Objective 3: Improve accuracy of prediction of economically important traits currently evaluated, determine merit and potential for developing genetic predictions for new traits, and investigate methods to incorporate high-density genomic data. Subobjective 3.A: Develop methodology for calculation of genome-enhanced breeding values using SNP genotypes. Subobjective 3.B: Develop methodology for accurate genetic predictions for new traits such as fertility and health. Objective 4. Investigate economic value of traits and correlations among them to most efficiently combine evaluations to select for healthy dairy animals capable of producing quality milk at a low cost in many environments.

Approach:
Objective 1: Extensive data on selected single nucleotide polymorphisms (SNPs) will be stored in a database, and intensive checks for accuracy will be conducted. Subobjective 1.A: A subset of SNPs will be selected for use in parentage verification and determination. Pedigree verification will be performed by comparing SNP genotypes of animals with those of recorded parents. Subobjective 1.B: Data for health and management traits will be obtained from dairy records processing centers. A system for submission and editing of data for new traits will be developed to allow routine data processing. Objective 2: Reports will be developed to describe industry progress and various statistics from the national genetic evaluation system for dairy animals, including statistics for Dairy Herd Information programs; breed reports for cow longevity and culling rate; summaries for reproductive traits; crossbreeding summaries and comparison tables for breed performance; heifer and cow inventories by breed composition; evaluation averages, distributions, and changes; genetic trends; progeny-test profiles; and selection intensity changes. Need for separate rankings for a grazing environment will be investigated. Objective 3: Test-day model methodology will be investigated. After patent issues with Cornell University are resolved, a test-day system will be implemented that provides parity-specific evaluations that account for maturity rate as well as evaluations for lactation persistency. Subobjective 3.A: Prediction of genetic merit using SNP information will be combined with results from the national dairy cattle genetic evaluation system to create an integrated prediction of genetic merit. Subobjective 3.B: Quality of available health data will be determined. Variance components will be estimated for individual and composite traits using threshold sire models. Methodology for genetic evaluation of health traits will be developed. Relationships among health and other traits of economic value will be examined. Environmental and genetic factors that affect gestation length of U.S. dairy cattle will be documented. Methods to improve accuracy of male-fertility evaluations from field data will be examined; effect of genetic and phenotypic factors on bull fertility will be studied. Methods and data for genetic evaluation of components of female fertility will be investigated. Objective 4: Selection goals that improve dairy farm profit most rapidly will be determined by economic analysis. Costs associated with additional health and management variables will be examined to determine if national genetic evaluations for those traits are needed. Optimal indexes for specific target populations will be determined. Interactions of genotype with environment will be investigated. Tools for making breed comparisons will be developed.

Last Modified: 9/10/2014
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