2007 Annual Report 1a.Objectives (from AD-416) Develop statistical, quantitative genetic, genomic, biometric, and computing technologies for use in combining genotypic information from DNA from bulls provided by artificial insemination organizations with phenotypic data on yield and fitness traits. 1b.Approach (from AD-416) Research is directed at developing genomic tools to estimate effects of chromosome segments or individual genes. Previous joint research have used widely spaced markers and found loci with large effects, but confirmed that genetic variation for most traits is quantitative, with many loci distributed across the genome individually exerting small effects. Planned research will estimate the trace inheritance of the many smaller genetic effects by using available single nucleotide polymorphisms (SNPs). Research is directed toward predicting transmitting abilities (PTA) more accurately by simultaneously predicting effects of many genetic loci using dense marker genotypes. Phenotypic data used for this will be from the national genetic evaluations for traits currently evaluated. Data will be expressed as daughter yield deviations or as de-regressed PTAs to avoid reanalysis of all raw records. Use of dense markers to estimate chromosome segment effects avoids most of the recombination between markers and causative genes that reduced the accuracy of previous within-family analyses. Predictions for young bulls will be more reliable when DNA samples for these are obtained in a later phase of the research. 3.Progress Report This report documents research conducted under a specific cooperative agreement between ARS and the University of Maryland's College of Medicine (Baltimore, MD). Additional details of research can be found in the report for the parent project 1265-31000-085-00D, "Improving Genetic Prediction of Economic Merit of Dairy Animals". Research conducted under the agreement is related to objective 2 (improved accuracy of yield evaluations). Monitoring activities for the project included two meetings in Beltsville, MD, with the Cooperator's principal investigator to discuss research approaches, establishment of an office for that investigator at the Animal Improvement Programs Laboratory to allow frequent, direct interaction with Laboratory researchers, and weekly meetings beginning in August to discuss programming responsibilities. The Cooperator's principal investigator has begun preliminary research on developing procedures for combining DNA with phenotypic data. Methods to explain genomic estimates of breeding value were developed by Laboratory scientists. A simulation was used to investigate methods for estimation of breeding values efficiently from dense genomic data. Programs to compute average reliability and accuracy of genomic evaluations were applied to simulated data for 50,000 markers and to actual data for 34,000 markers from the Bovine HapMap Consortium. Varying numbers of full siblings and actual pedigree structures were compared. Two oral presentations were made at the annual meeting of the Federation of Animal Science Societies, and two abstracts were prepared and published in the meeting proceedings. A proceedings paper was prepared and submitted for the annual meeting of the International Bull Evaluation Service in Dublin, Ireland.