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Imagine taking a genetic snapshot of
a calf as soon as it’s born, complete with Expected Progeny
Differences (EPDs) that have more accuracy than those based on
pedigree alone, including predictions for difficult to measure
traits such as feed efficiency.
Think of the mistakes that could be
avoided testing new genetics, and the gains that could be made
exploiting proven ones from animals that haven’t yet reached
breeding age.
The idea isn’t new, nor is the
concept of Whole Genome Selection (WGS) that makes such a thing
possible. What’s new is the fact that the necessary DNA
references (the Bovine Genome Map) and the requisite technology
now exists to enable the concept. That’s what scientists at the
USDA Meat Animal Research Center, the USDA Agricultural Research
Service at Beltsville, MD, the University of Missouri, a private
company called Illumina® and various breed organizations are in
the midst of proving.
Inference of the Whole
To this point, the focus of bovine genomics has revolved
chiefly around identifying which genes affect which traits alone
and in combination, and to what degree. Moreover, it has
revolved around identification of what are called QTLs
(Quantitative Trait Loci), which indicate the proximity of
causal genes where the precise location is not yet known. Though
MARC researchers explain locating and explaining all of the
causal genes for economically relevant traits is still the
ultimate goal, WGS could allow producers to leap-frog into the
future by enhancing genetic predictions today.
“Whole genome selection is an
alternative genomics method to traditional QTL discovery,”
explained Bob Weaber, extension beef specialist with the
University of Missouri at this year’s Range Beef Cow Symposium.
“We know that most production traits are polygenic (affected by
more than one gene). Using a tool like the new Illumina Bovine
SNP 50 assay, with a high-density marker panel, one can divide
up the genome in to small blocks. Cattle have 30 pairs of
chromosomes. Dividing each chromosome into 100 blocks produces
about 16 SNP markers per block. Theoretically, each of those
blocks can be analyzed for association with a broad range of
phenotypes. For a trait like marbling, researchers have
identified nearly 60 different QTLs and there might be 60 or
more of these blocks, out of the 3,000 total blocks in the
genome that account for variation in the trait.
“Once blocks have been
identified, specific genetic effects can be determined for the
variants in genotype within each block. A breeding value can be
estimated, then, by genotyping an animal then summing all of the
effects from each block. Prototype work in dairy cattle has
shown a high correlation between genome breeding value with high
accuracy breeding values we would estimate via traditional
methods.”
In other words, combine a high
enough resolution view of an animal’s genome with knowledge of
what phenotypes are associated with a specific combination of
SNP genotypes, and you come up with an accurate prediction of
breeding value.
The assay Weaber mentions is the
technology which is making WGS possible. Known as the Bovine
SNP50 bead chip, offered by Illumina, it interrogates 54,000
SNPs (Single Nucleotide Polymorphisms)—a DNA sequence in which
the base of a single nucleotide has been replaced by another—per
sample in a single assay. Actually it probes more SNPs than
that, but the 54,000 mentioned have been proven in other studies
to be informative markers for the traits of interest. Up to 12
samples can be assayed with each chip, or about 650,000 SNPs per
chip. We’re talking a single DNA sample and a device plastic
cassette about as long as your index finger.
Increasing Utility of Current Tools
Like EPDs themselves, you don’t have to know the science
behind how and why predictions generated through WSG work, you
just have to know that they do and how to incorporate them into
your selection decision.
With that in mind, scientists at
MARC are developing the infrastructure that would allow WGS data
to be incorporated into existing breed genetic evaluations. The
data will add accuracy to the EPDs producers are already
familiar with, not replace them.
“The U.S. Beef Industry
Whole-Genome Selection Project initiated earlier this year is
likely to accelerate the evolution toward genome-enhanced and
genome-enabled animal-evaluation tools,” says Kent Andersen,
Executive Vice President of the North American Limousin
Foundation (NALF). “For Limousin breeders, other seedstock
producers and commercial producers, genomics research ultimately
could yield appreciably higher accuracy predictions of genetic
merit for all animals – including young, non-parent bulls – and
for an even more comprehensive set of economically relevant
traits (ERTs).”
ERTs are traits that directly
impact income or expenses, such as heifer pregnancy, rather than
indictor traits, such as scrotal circumference which seeks to
get at fertility because of its association with subsequent
fertility in sire daughters.
NALF is one of 16 of the most
heavily used beef breeds in the United States that have been
invited by MARC to provide DNA on their most influential and
currently used sires for genotyping with the new assay. This
will encompass about 2,000 bulls; the breeders and their
associations will be charged nothing. Data on these bulls will
be used along with genotypes from about 3,600 of MARC’s Cycle
population—including 2,600 from its Cycle 7 population—to
develop the initial genetic predictions.
Mark Allan, MARC research
geneticist explains the Cycle 7 population represents F1 matings
conducive to revealing wide swaths of chromosomal segregation
for ERTs. As it turns out, these cattle are also ideal for
identifying relationships between SNPs and ERTs.
“Producers need to view this (WSG) as an additional genetic
selection tool, like EPDs themselves,” emphasizes Allan. “This
is not a solve-all, but rather an additional tool that
compliments EPDs and in the future should be incorporated with
them.”
USDA’s Cooperative State
Research, Education, and Extension Service announced last
November it was leveraging investment in bovine genome mapping
by making $5 million available in Fiscal Year 2008 for a 4-year
research project to investigate methods of using whole genome
enabled animal selection.
“USDA, along with many federal
agencies, states and other organizations, has invested millions
of dollars in efforts to sequence the genomes of the primary
agricultural animals,” said Gale Buchanan, USDA under secretary
for Research, Education and Economics. “The goal of this
project is to move animal genome science from the laboratory to
the field and the marketplace and, in the process, solve real
world problems.” He explained whole genome enabled animal
selection was identified as a high priority research focus.
“Genomics promises to revolutionize the field of animal science
and promote low cost, high tech tools for animal breeders,”
said Dr. Peter Burfening, national program leader for animal
genomics.
“Historically, Limousin breeders
and commercial users have used a variety of information tools
for making selection decisions. They include visual animal
appraisal; pedigrees; phenotypic performance data; EPDs; and
bio-economic selection indexes, such as our mainstream terminal
index,” he said. “While those tools will continue to help
breeders make reliable selection decisions, rapidly evolving
genome-based technology now has the potential to revolutionize
how cattle producers and breed associations approach animal
evaluation.”
There’s plenty of ground to cover before these WGS predictions
become a reality, and folks involved in the project are cautious
about promising too much. So far, though, WGS appears to be a
tool that can jump-start the industry’s ability to harness the
promise of genomics in earnest. |
