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United States Department of Agriculture

Agricultural Research Service

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Research Project: The National Dairy Genetic Evaluation Program


2013 Annual Report

1a. Objectives (from AD-416):
To maintain a high standard of integrity in data collection systems providing data for the National Dairy Genetic Evaluation Program (GEP) database; to provide data to AIPL for use in research and education, including the development of effective procedures for estimating the genetic merit of dairy animals; to provide data and summaries of information to research and extension personnel, and to others for educational purposes as appropriate; to improve the genetic merit and production efficiency of U.S. dairy cattle; and to enhance the world market competitiveness of the U.S. dairy industry.

1b. Approach (from AD-416):
It will be the responsibility of both parties to ensure the integrity of the data submitted by the Cooperators for inclusion in the GEP datatbase and to maintain the credibility of the GEP by establishing quality standards for data submitted to the GEP.

3. Progress Report:
This project is related to in-house objectives 1 (expand national and international collection of phenotypic and genotypic data through collaboration with the Council on Dairy Cattle Breeding and the Bovine Functional Genomics Laboratory), 2 (develop a more accurate genomic evaluation system with advanced, efficient methods to combine pedigrees, genotypes, and phenotypes for all animals), and 3 (use economic analysis to maximize genetic progress and financial benefits from collected data focused on herd management practices, optimal systems for genetic improvement, quantification of economic values for potential new traits such as feed efficiency, economic values of individual traits, and methods to select healthy, fertile animals with high lifetime production). Enhancements to the national database included 1) Mexican cow records; 2) heifer and cow conception rates as new measures of female fertility; 3) genetic evaluations for Brown Swiss mobility; 4) genetic evaluations for Milking Shorthorn milking speed and rear legs (rear view); 5) genetic evaluations for days from calving to first insemination; 6) correction and adjustment of health trait evaluations and reliabilities; 7) update of genetic bases for all traits; 8) updated economic values of all traits for genetic-economic indexes; 9) automated processing of genotypes; 10) genotypes and genomic evaluations based on three low-density marker panels; 11) genotypes based on a high-density marker panel; 12) Holstein genotypes from Italy and the United Kingdom; 13) Brown Swiss genotypes from Switzerland and Interbull; 14) maternal grandsire confirmation and discovery; 15) matching of genomic and pedigree inbreeding; 16) adjustments to genomic evaluations and reliabilities to improve accuracy; 17) breed-specific markers for genotype checks; 18) haplotypes for imputing genotypes; 19) imputed genotypes for dams using combined genotypes of progeny; 20) a web query to track genotype status; and 21) polygenic effects for genomic evaluation. Data were provided by processing centers (yield, health, pedigree, reproduction), breed associations (pedigree, genotype), and artificial-insemination organizations (pedigree, reproduction, genotype). Information available triannually through the laboratory web site included 1) official genetic evaluations for yield, conformation, and fitness traits and economic indexes for almost 20 million U.S. dairy cattle and goats, 2) multinational bull evaluations and conversion formulas, 3) updated graphic displays of phenotypic and genetic trends for yield and fitness traits, and 4) bull fertility rankings. Also available through the web site were animal documentation for five recessive defects for dairy cattle fertility discovered by the Animal Improvement Programs Laboratory in over 300,000 genotyped animals, triannual interim evaluations for progeny-test bulls, and genetic evaluations for yield (semiannual) and conformation (annual) for U.S. dairy goats. Genomic evaluations began to be distributed monthly to industry cooperators (rather than bimonthly) in April 2010 for Holsteins, Jerseys, and Brown Swiss. Calving-ease and stillbirth evaluations for bulls were released triannually to the National Association of Animal Breeders for distribution; conformation evaluations for breeds other than Holstein also were released triannually to appropriate associations for distribution. Test-herd data were used to compare procedural differences among processing centers. Thirty-four scientific peer-reviewed manuscripts, 54 scientific abstracts, 2 book chapters, 20 conference proceeding articles, 26 technical reports, and 154 popular press articles were published related to the National Dairy Genetic Evaluation Program, and 99 presentations were made at regional, national, and international meetings. This memorandum of understanding was terminated effective Dec. 30, 2012, because it was superseded by a Nonfunded Cooperative Agreement between the Cooperator and ARS. That agreement was implemented to increase the level of cooperation through onsite daily interaction between Cooperator and ARS employees using a shared database.

4. Accomplishments

Last Modified: 2/23/2016
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