Future Research in Genomics

Future Research in Genomics

Future Research in Genomics Curt Van Tassell AIPL Centennial Celebration November 28, 2008 USDA Genomics Blueprint Science to Practice Genome-enabled animal selection Build a Better Black Box Phenotype?? Genotype!! New and Improved!

Predicted Genetic Merit Numbers continue to increase Holstein Genome Selection (August 2008) 1800 1600 1400 Predictor Bulls 1200 Gap Bulls Predictee Bulls 1000

Unproven Bulls 800 Cows 600 400 200 Birthyear 2008 2006

2004 2002 2000 1998 1996 1994 1992 1990 1988

1986 1984 1982 1980 1978 1976 1974 1972

1970 1968 1966 1964 1962 1960 1957 1955 0

1952 Animal Count Historic Bulls Reliability Gain by Breed Trait HO JE BS Net merit Milk Fat Protein Fat %

Protein % 23 23 33 22 43 34 9 11 15 4 41 29 3

0 5 1 10 5 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 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?! Discovery Science Gene discovery Deleterious recessives Causative mutations Deleterious Recessives 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` Causative Mutations 12 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 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 Tissue Specificity Only in fetal adrenal Only in liver Of juvenile BGA Gbrowse Views 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!! Acknowledgements BARC MARC

Tad Sonstegard Tim Smith Lakshmi MatukumalliMark Allan Paul VanRaden Renee Godtel Jeff OConnell Linda Flathman George Wiggans Kevin Tennill John Cole Kevin Beavers Steven Schroeder Bob Lee Larry Shade Steve Simcox Dan Null Tara McDaneld

Alicia Bertles Illumina Missouri Jerry Taylor Marylinn Munson Bob Schnabel Cindy Taylor Lawley Stephanie McKay Christian Haudenschild Jae Woo Kim Matt McClure Megan Rolf Jared Decker USDA/CSREES/NRI

2006-35616-16697 2006-35205-16888 2006-35205-16701 USDA/ARS 1265-31000-081D 1265-31000-090-00D 5438-31000-073D 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 19

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