1. Future Research in Genomics Curt Van Tassell AIPL Centennial Celebration November 28, 2008

2. USDA Genomics Blueprint

3. Science to Practice Genome-enabled animal selection – 

4. Build a Better Black Box New and Improved! Phenotype?? Genotype!! Predicted Genetic Merit

5. Historic Bulls Predictor Bulls Gap Bulls Predictee Bulls Unproven Bulls Cows Numbers continue to increase

6. Reliability Gain by Breed TraitHOJEBS Net merit2393 Milk23110 Fat33155 Protein2241 Fat %434110 Protein %34295

7. Science to Practice Genome-enabled animal selection –  Precision mating systems –Embryonic selection –Non-additive genetic effects Cow data Precision Management Systems –Merial, Pfizer?? Animal identity and traceability –Low density-SNP project

8. Low Density-SNP Project Collaboration with Illumina 384 SNP assay using pooling –~96 dedicated to pedigree verification/traceability –378 for genetic prediction Stages of development –Alpha – test of multiplex –Beta – 1-3 Groups Genotyping ~20K samples –Commercialization ~300K+/yr Implications –Obviate need for pedigree –Increase heritability of phenotypes?!

9. Discovery Science Gene discovery –Deleterious recessives –Causative mutations

10. Deleterious Recessives

11. Deleterious Recessives: Strategy Identify affected and closely related unaffected: case – control population Identify region as narrowly as possible Obtain DNA for these animals Fragment and label DNA Recover for specific region in genome DNA sequence using next-generation instrument Total cost ~ $10,000 for DNA work Proof of concept –Build infrastructure –Next time more rapid`

12. 12 Causative Mutations

13. Discovery Science Gene discovery –Deleterious recessives –Causative mutations Functional genomics –Ongoing – e.g., gene atlas, microarrays –Next-generation sequencing Host-Pathogen interaction –Mastitis –Rumen microbes “Meta-genomics” Systems biology –The big picture

14. Gene Atlas Vitals 7.2 million tag types ~85% of all tags map to genome 6.5 % of the tag types map to within gene boundaries 61 % of the tags that map within gene boundaries map to a single gene Majority of genes show evidence of alternative splicing

16. Tissue Specificity Only in liver Of juvenile Only in fetal adrenal

17. BGA Gbrowse Views

18. Infrastructure Genomic tools –Selection tools –Inbreeding management Databases and bioinformatics –Build large federated databases –Share information Animal resource populations –Large centralized populations –“Falconer” flock model, NPB Education and training –Critical!!

19. 19 USDA/CSREES/NRI2006-35616-166972006-35205-168882006-35205-16701USDA/ARS1265-31000-081D1265-31000-090-00D5438-31000-073D AIPL Laboratories Paul Van Raden George Wiggans Merial, Ltd Stewart Bauck Bull Studs/NAAB ABS Global Accelerated Genetics Alta Genetics CRI/Genex Select Sires Semex Alliance Taurus Service MARC Tim Smith Mark Allan Renee Godtel Linda Flathman Kevin Tennill Kevin Beavers Bob Lee Steve Simcox Tara McDaneld Missouri Jerry Taylor Bob Schnabel Stephanie McKay Jae Woo Kim Matt McClure Megan Rolf Jared Decker Acknowledgements BARC Tad Sonstegard Lakshmi Matukumalli Paul VanRaden Jeff O’Connell George Wiggans John Cole Steven Schroeder Larry Shade Dan Null Alicia Bertles Illumina Marylinn Munson Cindy Taylor Lawley Christian Haudenschild