2013 Annual Report
1a.Objectives (from AD-416):
The objective of this agreement is to improve the productivity, efficiency, conformation, and health of the national dairy herd as well as the composition and quality of resulting products for the benefit of dairy producers and the consuming public by transferring the research knowledge of USDA-ARS scientists to cooperator on the appropriate genetic models and computational procedures for the analysis of the Phenotypic and Genomic Data contained in the cooperator Database controlled by cooperator.
1b.Approach (from AD-416):
A. Collect phenotypic, genomic, and proteomic data.
B. Edit collected data for accuracy prior to inclusion in the cooperator database and maintain data in a database to support calculation of genetic evaluations (CGE).
C. Analyze collected data through the CGE to produce estimates of genetic merit.
D. Distribute estimates of generic merit.
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). Since January 2013, genomic evaluations have included genotypes from a new high-density genotyping chip (GeneSeek Genomic Profiler HD BeadChip). Statistical reports on Dairy Herd Information participation, herd averages, dairy records processing center activity, milk somatic cell counts, State and national standardized lactation averages, reasons that cows exit the herd, and reproductive status were released in March 2013. A nonfunded Cooperative Agreement was signed by USDA's Agricultural Research Service and the Council on Dairy Cattle Breeding (CDCB) on March 27, 2013, to transfer control of the evaluation service from government to industry. The CDCB has established a fee schedule for genetic evaluations. Those fees are being used to employ people assisting in receiving data, maintaining the national lactation and genotype databases, delivering evaluations, and performing related service work. Two consultants were hired by CDCB to serve as interim administrator and information technology specialist and are located at the laboratory. Laboratory researchers and staff are continuing to develop improved methods of analysis using the shared databases and are working closely with CDCB to enhance evaluation accuracy and to transition the evaluation system from the Federal government to the dairy industry. Beginning in April 2013, the source of genetic evaluations was changed from USDA-AIPL to USDA-CDCB, and many Laboratory web pages and programs were transferred to the new CDCB web site for delivery and documentation of genetic evaluations. Ayrshire genomic evaluations were calculated and released for the first time in April 2013. Weights to combine direct genomic values with traditional parent averages or predicted transmitting abilities were revised in April 2013 for Holsteins based on updated genomic validation results; this revision improved consistency between traditional and genomic evaluations. To improve selection accuracy and reduce rounding error in genomic evaluations for calving ease, service-sire and daughter calving ease began to be expressed to one decimal position in April 2013 instead of as whole numbers; young bulls also began to be included in estimating marker effects for traditional service-sire calving ease and stillbirth rate. Access to genomic evaluations for young males had been restricted to artificial-insemination organizations but became available to all breeders worldwide in April 2013. Release rules for young males were modified slightly, and breed associations began to receive monthly updates for young males. Genotypes from version 2 of the GeneSeek Genomic Profiler BeadChip were included in May 2013 genomic evaluations. Multitrait across-country exchange of genomic evaluations (GMACE) for Holsteins is targeted for implementation at Interbull in August 2013.