download - Animal Improvement Programs Laboratory

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

G.R. Wiggans, 2010

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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

G.R. Wiggans, 2010

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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

G.R. Wiggans, 2010

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