# Presentation: 517416

## 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

- New and Improved!

- Phenotype??

**Genotype!!**

- Predicted Genetic Merit

## Numbers continue to increase

**       ****Historic Bulls**
**       ****Predictor Bulls**
**       ****Gap Bulls**
**       ****Predictee Bulls**
**       ****Unproven Bulls**
**        ****Cows**

***Numbers continue to increase***

## Reliability Gain by Breed

| Trait | HO | JE | BS |
| --- | --- | --- | --- |
| Net merit | 23 | 9 | 3 |
| Milk | 23 | 11 | 0 |
| Fat | 33 | 15 | 5 |
| Protein | 22 | 4 | 1 |
| Fat % | 43 | 41 | 10 |
| Protein % | 34 | 29 | 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

## 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?!

- 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

## 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

## 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

- 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

## Slide 15

## Tissue Specificity

## 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

**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**

**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***