Download Should I Use DNA Testing? - Beef Improvement Federation

DNA Testing and
Marker Assisted Selection
R. Mark Thallman
U.S. Meat Animal Research Center
Clay Center, NE
Applications of DNA Testing
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•
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Parentage Verification
Parentage Determination (Multisire)
Traceback
Qualitative Traits
• Color, polledness, genetic defects
• Quantitative Traits
• Most production and end product traits
Commercially Available DNA Tests for
Quantitative Traits in Beef Cattle
• GeneStar Marbling
• Genetic Solutions/Bovigen
• GeneStar Tenderness 2
• Genetic Solutions/Bovigen
• TenderGENE
• Frontier Beef Systems/GeneSeek
• IGENITY L
• Merial/Quantum Genetics
• MMIG Mu-Calpain Tender
• MMI Genomics
Overview
• “Should I use DNA testing?”
• “Which DNA tests should I use?”
• “Which traits will DNA tests be most
useful for?”
• “Which animals should I test?”
• “How should I use the test results?”
• “What should breed associations be doing
about DNA testing?”
“Should I Use DNA Testing?”
Benefits of DNA Testing
• Obtain evaluations earlier in the life cycle.
• Increased accuracy of selection, especially
for traits that are expensive to measure, sexlimited, or measured postmortem.
• Get more benefit from each phenotype that
is measured.
• Greater opportunity to select for traits with
antagonistic genetic relationships (e.g., birth
weight and growth rate).
Cost of Testing
“Should I Use DNA Testing?”
• This is a business decision that each
breeder must make individually.
• It depends as much on the breeder’s
role in the industry and marketing
plan as it does on the cost of testing.
“They Just Use it as
a Marketing Tool”
• Not an acceptable excuse for not using technology
“They Just Use it as
a Marketing Tool”
• Not an acceptable excuse for not using technology
• They have said this about weights, EPDs,
ultrasound, and every other new technology for
genetic improvement.
“They Just Use it as
a Marketing Tool”
• Not an acceptable excuse for not using technology
• They have said this about weights, EPDs,
ultrasound, and every other new technology for
genetic improvement.
• If it is used successfully in marketing, it is
influencing breeding decisions.
“They Just Use it as
a Marketing Tool”
• Not an acceptable excuse for not using technology
• They have said this about weights, EPDs,
ultrasound, and every other new technology for
genetic improvement.
• If it is used successfully in marketing, it is
influencing breeding decisions.
• Over time, it seems that the early adopters of
technology have benefited the most.
“Which DNA Tests
Should I Use?”
• A number of detailed questions about
DNA tests should be answered before
deciding which tests to use.
“Which DNA Tests
Should I Use?”
The essential questions about a test are:
• Does it work?
• Does it affect traits that you want to change?
• Does it segregate in your population?
Independent Characterization
of DNA Tests
• Standard resource populations of cattle
with phenotypes for the desired traits
• Independent institution to conduct the
characterization
• The National Beef Cattle Evaluation
Consortium ( NBCEC) has initiated such a
process.
Independent Characterization
of DNA Tests
• The NBCEC provides DNA to the DNA testing
company.
• The DNA testing company runs the test on the
DNA and send the results to the NBCEC.
• The NBCEC analyzes the data and reports
results in a standardized format as described
above.
Benefits of Independent
Characterization of DNA Tests
• Breeders have better information from which to
decide which tests to use.
• DNA testing companies can market tests more
effectively and with greater confidence.
• The process generates information that is
needed in order for DNA testing data to be
included in national cattle evaluation.
“What if a Test Has Not Been
Characterized in My Breed?”
• Ideally, tests would be characterized in every
breed in which they would be used.
• But, that is probably not realistic, so you may need
to use data from another breed of the same
biological type as your breed.
• It does not serve anybody if the cost of bringing a
new test to market is unreasonably high.
• Tests are most likely to be characterized in breeds
that are proactive in providing quality resource
populations for the process and that tend to use
and promote DNA testing technology.
Realistic Expectations for
Independent Characterization
• We are unlikely to have enough data to
answer all of the questions we have as
clearly as we would like.
• Allele frequencies often work against us.
• But some information is better than none.
• If customers come to expect it, it will
become routine.
• The process will improve with time.
BIF Guidelines on DNA Testing
• Independent Characterization
• Standardized format for reporting results
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•
•
•
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Format in which test results are reported
Which animals to test
Data acquisition for NCE
Nomenclature
Incorporation into NCE
Which Traits will be Emphasized?
• Most interest is in traits that are difficult or
expensive to measure:
•
•
•
•
Carcass traits, especially tenderness
Feed efficiency
Reproductive efficiency
Disease resistance
• Tests for such traits are difficult to develop
for the same reasons that they are difficult
to select for conventionally
• It is also difficult to verify that they work
Realistic Expectations
• DNA testing can increase the amount of
information that each phenotype
contributes.
• DNA testing can reduce the number of
phenotypes needed.
• DNA testing can not replace phenotypes.
Which Traits will be Emphasized?
• There is some merit in developing and using
DNA tests for which phenotypes are
routinely recorded.
• One of the benefits of DNA testing is the
ability to break antagonistic genetic
correlations.
• There could be benefit in tests associated
with birth weight without affecting growth
rate.
“Which Animals Should I Test?”
• Influential sires
• Herd sire candidates
• Donor prospects
• Optimal testing strategy depends on whether
the favorable allele is at high or low
frequency
“How Should I Use the Test
Results?”
Current Genetic Evaluation
Pedigree
NCE
Phenotypes
Phenotypes
EPDs
Accurate
Evaluation
of Genetic
Merit
Phenotypes
Progeny
• Currently, genetic merit is evaluated in the form of EPDs, which
are computed from phenotypes on the individual and its relatives.
The Myth:
Pedigree
Phenotypes
DNA Tests
Phenotypes
Phenotypes
Progeny
Easy,
Highly
Accurate
Evaluation
of Genetic
Merit
EPDs
• For a long time, breeders have been told that an animal’s genetic
potential will be determined by simply testing a DNA sample,
without any need for pedigree, phenotypes, progeny or EPDs.
Consequences of the Myth:
• Leads to the expectation that DNA
testing will simplify cattle breeding
Pedigree
Phenotypes
Easy,
Highly
Accurate
Evaluation
of Genetic
Merit
DNA Tests
Phenotypes
Phenotypes
Progeny
EPDs
A More Realistic Vision
Pedigree
Phenotypes
DNA tests
Phenotypes
DNA tests
NCE
More
Marker Accurate
Adjusted Evaluation
of Genetic
EPDs
Merit
Phenotypes
DNA tests
Progeny
• Under this scenario, phenotypes and DNA tests on the individual
and its relatives are combined, through National Cattle Evaluation
(NCE), to produce marker-adjusted EPDs, upon which selection
decisions are made.
Inclusion of DNA Test Results in
National Cattle Evaluation
Conv.
ID EPD
1
50
Residual Test
A
Acc.
EPD
.90
36
+10
Test
B
+5
MAEPD
52
2
35
.90
44
-10
0
34
3
47
.20
49
-10
0
39
4
46
.20
47
0
-5
42
5
45
.20
42
+10
+5
57
6
44
.20
44
0
0
44
Inclusion of DNA Test Results in
National Cattle Evaluation
Conv.
ID EPD
1
50
Residual Test
A
Acc.
EPD
.90
36
+10
Test
B
+5
MAEPD
52
2
35
.90
44
-10
0
34
3
47
.20
49
-10
0
39
4
46
.20
47
0
-5
42
5
45
.20
42
+10
+5
57
6
44
.20
44
0
0
44
The Myth of Additivity:
Pedigree
Phenotypes
DNA
Tests
+
Phenotypes
EPDs
Marker
Effects
Added to
EPDs
Phenotypes
Progeny
• DNA test results affect low accuracy EPDs much more
than they do high accuracy EPDs.
“They Don’t Use DNA Test
Results Optimally”
• It is difficult to include DNA test results in
NCE until we have sufficient data to work
with.
• But, we won’t get a lot of data until it starts
going into NCE.
• So, we are starting to think about where we
are going and starting to work on the things
we can do now.
• This is not a legitimate excuse not to use the
technology.
Single
Gene
Selection
Weighting the Information Obtained
from Multiple DNA Tests
• Hopefully, there will be too many tests
available for breeders to make breeding
decisions based on raw test results.
• Need to weight the relative emphasis on each
gene by its effect and the relative importance of
the trait.
• Each DNA test will be related to several traits.
• For the foreseeable future, DNA tests will only
account for some of the genetics of any trait; we
will still need EPDs.
Weighting the Information Obtained
from Multiple DNA Tests
• Breeding decisions will be based on output of
National Cattle Evaluation (NCE), rather than
on individual test results.
• NCE will have to be enhanced to accommodate
DNA testing.
“What Should Breed Associations
be Doing About DNA Testing?”
• Establish procedures for direct
acquisition of DNA test results into
breed databases.
• Develop policies that prevent selective
reporting of results.
• Educate breeders on proper use.
What Can You Do Now?
• Make it Standard Operating Procedure to
have DNA tests independently characterized
• Generate data – use DNA testing to the
extent that it fits in your business
• Contribute to systems that allow test results
to flow directly through breed associations
into the NCE system
Conclusions
• We have some difficult issues to
deal with in the next few years
• All roads to genetic improvement
go through National Cattle
Evaluation
• DNA testing will become an
important component of genetic
improvement