download - Animal Improvement Programs Laboratory

gooseliverBiotechnology

Oct 22, 2013 (3 years and 10 months ago)

98 views

G.R. Wiggans

Animal Improvement Programs Laboratory

Agricultural Research Service, USDA

Beltsville, MD

george.wiggans@ars.usda.gov

Georgetown Ag Systems (
1
)

G.R. Wiggans, 2010

Animal
Biotechnology

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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)

G.R. Wiggans, 2010

Georgetown Ag Systems (
5
)

Bovine genome sequence

G.R. Wiggans, 2010

Georgetown Ag Systems (
6
)

Federal support for genomics


Cattle


Sheep


Swine


Poultry


Horses


Aquaculture (fish and other water animals)

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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!

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown Ag Systems (
12
)

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown Ag Systems (
16
)

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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown 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

G.R. Wiggans, 2010

Georgetown Ag Systems (
22
)