GeorgetownAgSystems_grw1111111111111.ppt

animal biotechnology

1. G.R. Wiggans
Animal Improvement Programs Laboratory
Agricultural Research Service, USDA
Beltsville, MD
[email protected]
Georgetown Ag Systems (1) G.R. Wiggans, 2010
Animal
Biotechnology

2. G.R. Wiggans, 2010Georgetown Ag Systems (2)
Application of biotechnology
Identify superior animals early
Increase rate of genetic improvement
Detect abnormalities
Improve understanding of mechanisms of
genetic control
Determine parentage

3. G.R. Wiggans, 2010Georgetown Ag Systems (3)
Applications in genetic
improvement
Find easily detected genetic differences among
animals
Develop SNP (single nucleotide polymorphism)
panels to detect those differences
Relate SNP differences to productivity
differences
Rank animals on their economic merit
Use best animals as parents of the next
generation

4. G.R. Wiggans, 2010Georgetown Ag Systems (4)
What is genomics?
Study of how the genome (DNA) of any
species is organized and expressed as
traits
New technologies allow examination of an
organism’s genome as a whole rather
than 1 gene at a time
Livestock and poultry genomes sequenced
to understand how various genes function
(functional genomics)

5. G.R. Wiggans, 2010Georgetown Ag Systems (5)
Bovine genome sequence

6. G.R. Wiggans, 2010Georgetown Ag Systems (6)
Federal support for genomics
Cattle
Sheep
Swine
Poultry
Horses
Aquaculture (fish and other water
animals)

7. G.R. Wiggans, 2010Georgetown Ag Systems (7)
How do we use genomics?
Identify DNA sequences associated with
disease resistance and production traits
Animals can be evaluated as soon as DNA
can be obtained (even before birth)
Best animals to be parents can be
determined earlier and more accurately

8. G.R. Wiggans, 2010Georgetown Ag Systems (8)
Dairy cattle selection before
genomics
Slow!
Progeny testing for production traits takes 3 – 4
years from insemination
Bull will be at least 5 years old before first
evaluation is available
Expensive!
Progeny testing costs $25,000 – 50,000/bull
Only 1 in 8 – 10 bulls graduate from progeny test
At least $200,000 invested in each active bull

9. G.R. Wiggans, 2010Georgetown Ag Systems (9)
Background: Genetic markers
Segment of DNA at a unique
physical location in the genome
that varies sufficiently between
individuals that its inheritance
can be tracked through families
Markers not required to be part
of a gene

10. G.R. Wiggans, 2010Georgetown Ag Systems (10)
Genetic markers
Allow inheritance to be
followed in a region across
generations
SNPs are the markers of
choice
Need lots – 3 million in the
genome!

11. G.R. Wiggans, 2010Georgetown Ag Systems (11)
Cattle SNP collaboration – iBMAC
Develop 60,000-bead Illumina iSelect
assay
Agricultural Research Service, USDA
−Beltsville Agricultural Research Center
•Bovine Functional Genomics Lab.
•Animal Improvement Programs Lab.
−Meat Animal Research Center
University of Missouri
University of Alberta
Starting 60,800 beads – 54,000 usable SNPs

12. G.R. Wiggans, 2010Georgetown Ag Systems (12)

13. G.R. Wiggans, 2010Georgetown Ag Systems (13)
Illumina
Marylinn Munson
Cindy Lawley
Christian Haudenschild
BARC
Curt Van Tassell
Lakshmi Matukumalli
Tad Sonstegard
Missouri
Jerry Taylor
Bob Schnabel
Stephanie McKay
Alberta
Steve Moore
USMARC – Clay Center
Tim Smith
Mark Allan
13
USDA/NRI/CSREES
2006-35616-16697
2006-35205-16888
2006-35205-16701
USDA/ARS
1265-31000-081D
1265-31000-090D
5438-31000-073D
Merial
Stewart Bauck
NAAB
Gordon Doak
ABS Global
Accelerated Genetics
Alta Genetics
CRI/Genex
Select Sires
Semex Alliance
Taurus Service
iBMAC Consortium Funding agencies
Participants

14. G.R. Wiggans, 2010Georgetown Ag Systems (14)
Genomic evaluation – US dairy
cattle
Cooperating organizations
Breed associations (Holstein, Jersey, Brown Swiss)
Artificial-insemination organizations
−Own bulls
−Collect and market semen
Full sharing of genotypes and research with Canada
Trading of genotypes with Switzerland, Germany
and Austria – expect to share with more countries
Over 60,000 animals genotyped starting in 2008

15. G.R. Wiggans, 2010Georgetown Ag Systems (15)
Getting DNA samples
Animals selected
Artificial-insemination organizations identify male
and female calves to genotype
Farmers request breed association to arrange for
genotyping
Animal nominated at Animal Improvement Programs
Laboratory – insures pedigree information is in
database
Sample sent to genotyping laboratory
Hair follicles (most common)
Blood Nasal swab
Semen  Ear punch

16. G.R. Wiggans, 2010Georgetown Ag Systems (16)
History of application for US dairy
cattle
Dec. 2007BovineSNP50 BeadChip available
Apr. 2008First unofficial evaluation released
Jan. 2009Genomic evaluations official for
Holstein and Jersey
Aug. 2009Official for Brown Swiss
Sept. 2010Unofficial evaluations from 3K chip
released
Dec. 20103K genomic evaluations become
official

17. G.R. Wiggans, 2010Georgetown Ag Systems (17)
International implications
All major dairy countries investigating genomic
selection
International Bull Evaluation Service (Interbull)
working on how genomic evaluations should be
integrated
EuroGenomics – European collaboration to share
genotypes
Large number of predictor animals increases
prediction accuracy
Importing countries changed rules to allow for
genomically evaluated young bulls

18. G.R. Wiggans, 2010Georgetown Ag Systems (18)
Developed countries
100 years of records
Phenotypes
Pedigree
Progeny testing for
50 years
Plentiful crop
systems
Animals developed
for temperate
climate
Developing countries
No records
No pedigree
Marginal production
systems – tropical
No national testing
systems to evaluate
germplasm
No cash for investing
in value-added
animals
Challenges of technology transfer

19. G.R. Wiggans, 2010Georgetown Ag Systems (19)
Priorities from Gates Foundation
Develop tools and reagents that are applicable
to underdeveloped areas
Collect DNA for breeds to understand current
genetic distances and admixture
Identify critical populations for preservation
and selection – high density chip
Enhance local adapted breeds using
combinations of crossbreeding and selection –
low density chip

20. G.R. Wiggans, 2010Georgetown Ag Systems (20)
Identified a set of parentage
markers for testing at
University of Lahore
Sequenced a native breed
animal for SNP discovery
in water buffalo
Lead role in Water Buffalo Genome Project
(Italy)
Great training opportunity
PAKUS – Water buffalo genomics

21. G.R. Wiggans, 2010Georgetown Ag Systems (21)
Summary
Genomics is revolutionizing animal
breeding
Genomic selection used extensively in
dairy cattle breeding
High quality genotypes support detection
of parentage and other errors
International collaboration has been
important for the success

22. G.R. Wiggans, 2010Georgetown Ag Systems (22)