G.R. Wiggans
Animal Improvement Programs Laboratory
Agricultural Research Service, USDA
Beltsville, MD
george.wiggans@ars.usda.gov
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G.R. Wiggans, 2010
Animal
Biotechnology
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Application of biotechnology
Identify superior animals early
Increase rate of genetic improvement
Detect abnormalities
Improve understanding of mechanisms of
genetic control
Determine parentage
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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
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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)
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Bovine genome sequence
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Federal support for genomics
Cattle
Sheep
Swine
Poultry
Horses
Aquaculture (fish and other water animals)
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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
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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
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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
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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!
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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
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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
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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
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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
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History of application for US dairy cattle
Dec. 2007
BovineSNP50 BeadChip available
Apr. 2008
First unofficial evaluation released
Jan. 2009
Genomic evaluations official for
Holstein and Jersey
Aug. 2009
Official for Brown Swiss
Sept. 2010
Unofficial evaluations from 3K chip
released
Dec. 2010
3K genomic evaluations become official
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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
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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
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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
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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
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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
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