Download Application of Molecular Technologies in Beef Production

Application of Molecular
Technologies in Beef Production
Dan W. Moser, Ph.D
Department of Animal Sciences and Industry
Kansas State University, Manhattan
1
Molecular Technologies
• DNA assessment of identity and
parentage
• Selection for specific genes
• Marker assisted selection
2
Genes and Chromosomes
• Chromosome
– Structure in cell nucleus which stores and
transmits genetic information in the form
of DNA
• Gene
– Sequence of DNA bases on a chromosome
that causes a characteristic
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Genes and Chromosomes
• Any chromosome contains many genes,
but parts of the chromosome may
contain no genes
• The precise locations of most genes are
unknown
• Current estimates place the number of
human genes at 50,000; bovine, perhaps
30,000
4
Genes and Chromosomes
• Chromosomes are arranged into homologous
pairs, chromosomes of similar size and
structure that contain genes for the same
traits
• With 60 chromosomes, cattle have 30
homologous pairs
• A parent contributes one randomly chosen
chromosome from each homologous pair to
its offspring
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Genes and Chromosomes
• The various possible forms of a gene are
called alleles
• When an individual has two identical
alleles for the same trait, they are
homozygous (AA, bb, etc.)
• When an individual has two contrasting
alleles for the same trait, they are
heterozygous (Aa, Bb, etc.)
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DNA Typing
• May be used to establish identity or
parentage
• Useful in determining animal origin
• May become a component of national
ID programs
• Particularly beneficial in seedstock
operations
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DNA Typing for Parentage
• Confirm parentage for pedigree records
and genetic evaluation
• Quality control for carcass data
collection
• Identify sires of calves from multiple
sire pastures
• Allow multiple sires to be used
simultaneously in embryo transfer
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Qualitative Traits
• Qualitative traits fall into a few distinct
classes
–
–
–
–
Red or black
Diluted or non-diluted
Horned or polled
Double-muscled or normal
• Qualitative traits are determined by a one or a
few genes
• These genes usually affect one trait
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Qualitative Traits
• Since few genes are involved, those
genes should be easier to discover
• Some genetic tests for qualitative traits
are available
– Red/Black coat color
– Double-muscling
– Numerous breed-specific genetic diseases
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Quantitative Traits
• Quantitative traits are those that show
a continuous distribution
– Weights and measures
– All performance traits
• Quantitative traits are influenced by
multiple genes
• Each gene has a relatively small effect
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Quantitative Traits
• Quantitative traits are the result of
genes for factors that control growth,
development, reproduction, lactation,
fat deposition, etc.
–
–
–
–
Hormones
Hormone receptors
Growth factors
Other proteins
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Quantitative Traits
• At least four gene tests for beef cattle
are commercially available:
–
–
–
–
GeneSTAR marbling (Thyroglobulin)
GeneSTAR tenderness (Calpastatin)
TenderGENE tenderness (Calpain)
Merial igenity L appetite (Leptin)
• Expect the number of such tests to
continue to increase
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Potential Pitfalls
• The effects of alleles may vary under
different environmental conditions
• Alleles may interact with alleles at other
locations
• One allele may be partially or
completely dominant to the other
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Potential Pitfalls
• Nearly every gene will likely have an
effect on more than one trait
• Some alleles with favorable effects for
one trait may have unfavorable effects
for other traits
• Not all alleles may be detected
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Multiple Alleles
from Thallman, 2001
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Genes vs. Markers
• These tests are direct tests, tests for
variation in the genes that have been
proven to have a certain effect
• Direct tests will work for all animals,
and can identify animals as
homozygous favorable, heterozygous,
or homozygous unfavorable
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Genetic Markers
• Markers – known sequences believed to
be near actual genes
• Statistically associated with a
phenotype
• Markers are used to find genes, but
could be used in some cases for
selection before the gene is known
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Chromosomes
Paternal Chromosome
Maternal Chromosome
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Genes on Chromosomes
Genes
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Genes on Chromosomes
Heterozygous
Homozygous
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Markers on Chromosomes
Markers
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Markers Flanking a Gene
Markers flanking a gene
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Genetic Markers
• Once a marker has been shown to have
an effect for a particular sire, his
progeny can be sorted into those that
received the favorable or unfavorable
allele
• Marker-assisted selection is useful only
for progeny of heterozygous sires
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Compare Progeny Groups
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Compare Progeny Groups
Tender
Tough
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Using Marker Results
tender
tough
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Genetic Markers
• Markers work well within families, but
may not have the same effect in other
families or breeds, due to
recombination (crossover)
• The closer the marker is to the gene, the
more consistent its effect
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Recombination
Paternal
Maternal
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Recombination
Worst-case Scenario
Tough gene
“Tender” markers
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Implementing MarkerAssisted Selection
• Collect DNA on sire
• Collect DNA and phenotypes on (50?)
progeny
• Determine markers that have significant
effects for that sire
• Select future progeny of sire based on
marker results
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Genetic Markers
• Marker-assisted selection is being used
in the swine and dairy industries
• AI companies could test their most
popular bulls for various markers, and
report which marker tests can be used
on progeny of those bulls
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Interpreting Test Results


0
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Interpreting Test Results
GeneSTAR Marb 
GeneSTAR Tnd  
TenderGENE - -
igenity L T t
NCBA Tndr3 - -
LeanGene1 + +
CAB/OSU Marb + -
LeanGene2 + -
MeanGene + +
LeanGene3 + +
Ov. Rate 1 + -
GrowGene A + +
CalvEze + -
GrowGene B - -
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Interpreting Test Results
Calving Ease EPD
2.9
.45
Wean Wt EPD
39
.65
Milk EPD
25
.50
Yearling Wt EPD
80
.65
Carc Wt EPD
14
.65
Marb EPD
0.31
.65
%RP EPD
0.14
.75
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Interpreting Test Results
• The most logical and useful way to
report test results is to include tests in
EPD calculation
• Direct gene and/or marker tests can be
included in National Cattle Evaluation
(NCE) programs
• Raises issues as to which tests should or
should not be used in NCE
36
Gene-Adjusted EPDs
• More accurate, especially for young animals
• Require that gene test results for all tested
animals be available, not just those with
favorable results
• Require independent, unbiased evaluation of
the test
• Selecting which tests to use will be difficult
37
Gene or Marker Selection
• Most beneficial for traits that are
difficult to measure, and for evaluating
young animals
• EPDs evaluate the effects of all genes on
a trait
• Bulls with desirable, high accuracy
EPDs should not be discounted because
of a “bad” gene test result
38