Download A REVOLUTION IN DAIRY CATTLE GENETICS Roger D. Shanks

A REVOLUTION IN DAIRY CATTLE GENETICS
Roger D. Shanks
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Genomic selection using a panel of SNPs has the potential to revolutionize dairy cattle
genetics.
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Genomic selection has both positive and negative consequences.
Sound the alarm. “One if by land and two if by sea” stated Henry Wadsworth Longfellow in his
poem “The Midnight ride of Paul Revere”. The redcoats are coming. The redcoats are coming.
Today, the SNPs are coming. SNPs (pronounced snips) are actually already here. A SNP is a
single nucleotide polymorphism. Translating, a SNP is a small change in DNA, the genetic
material of life. The technology is now available to process large amounts of DNA and detect
how individuals vary. The challenge that remains is to associate those small changes in DNA
with changes in performance of economically important traits in cattle. A panel of 50,000 SNPs
is being developed to assist cattle selection. Dr. Curt Van Tassell of USDA is leading the effort
to identify which SNPs are part of the panel. It is my understanding that these SNPs will be
widely dispersed across the genome. It is anticipated that genomic selection can be practiced on
the SNPs that an individual possesses. A SNP is basically a change of a single nucleotide in
DNA. The four nucleotides, also known as bases, are adenine (A), cytosine (C), guanine (G),
and thymine (T). The DNA molecule consists of two paired strings of nucleotides.
WHAT IS POTENTIAL IMPACT OF SNPS?
One historical example will demonstrate advantages of SNPs. Earlier research at Illinois dealt
with a lethal defect called “Deficiency of Uridine Monophosphate Synthase” or DUMPS.
Although DUMPS was a lethal condition, it was not quickly eliminated form the Holstein
population initially. A DNA test based on a change at a single nucleotide polymorphism
facilitated rapid removal of the undesirable DUMPS gene from the population. The following
numerical example documents the extent of benefit.
Consider that you have a herd of 100 Holstein cows, none of which have the DUMPS gene. The
frequency of the DUMPS gene is zero and you would not lose any embryos to DUMPS.
However, if you mate your cows to one bull that is a carrier of DUMPS, half the resulting
offspring would be carriers of DUMPS. They would not have died because two DUMPS genes
are needed for the lethal effect. In the offspring, from mating your 100 cows to one DUMPS
carrier bull, the frequency of the DUMPS gene would be 25%. Half the offspring have one of
two paired genes that are the DUMPS gene. If the offspring were mated to another bull that also
was a carrier of DUMPS, 12.5% of the embryos would die from having two copies of the
DUMPS gene. Obviously, using a DNA based test such as SNP and identifying male carriers of
DUMPS could avoid the second mating to a DUMPS carrier.
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COULD THE DUMPS GENE NATURALLY LEAVE THE POPULATION?
Yes, but it would take awhile. Consider the population of offspring with the frequency of the
DUMPS gene at 25%. If the population was random mated, the frequency of the DUMPS gene
would reduce to 1% after 96 generations. If each generation interval is about 5 years, the
reduction of frequency of DUMPS gene from 25% to 1% would take about 480 years.
To repeat, the frequency of the DUMPS gene could be increased to 25% in one generation, but
waiting for the lethal gene to reduce its frequency to 1% would take almost five centuries.
Selecting for a SNP is an alternative. A SNP identifies which animals are carriers of specific
genes. If the genes are undesirable, the animals with those genes can be eliminated in one
generation.
Using a SNP to eliminate DUMPS from the Holstein population is an easy decision to make.
The benefit of using SNPs to select or eliminate other individuals is an area of future research.
Most SNPs are not associated with a lethal condition. The hope is that many SNPs can be
associated with favorable outcomes. To find these associations, many animals will be needed
that have both SNP and phenotypic data. Selection based on SNP’s is called genomic selection.
It has the potential to revolutionize selection of dairy cattle.
ADVANTAGES OF GENOMIC SELECTION TO FURTHER ANIMAL
IMPROVEMENT
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Decision to keep or cull an animal could be made earlier in an animal’s life.
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Expensive progeny testing would not be required.
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Generation interval could be reduced resulting in more rapid genetic gain.
DISADVANTAGES OF GENOMIC SELECTION TO FURTHER ANIMAL
IMPROVEMENT
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Variability available for future genetic gain would be reduced.
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The rate of genetic gain would diminish over time.
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Incorrect associations between phenotypes and the SNPs could lead to unexpected
results, some of which would be unfavorable.
OTHER POSSIBLE CONSEQUENCES
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Geneticist would have increased job security because the associations between
phenotypes and SNPs would need to be monitored routinely.
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The panel of SNPs could be useful in selecting germ plasm for genetic conservation.
Only diverse gene plasm would need to be stored.
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