Finding dollars in DNA - John Deere

By Steve Werblow
Finding dollars in DNA
Genomes are opening the
door to greater productivity.
36 THE FURROW

Almost daily, it seems,
headlines announce that
a new species of plant,
animal, or pathogen has
had its genome sequenced, the code
of each of its genes spelled out and
mapped. Scientists are following
those maps to a treasure trove of
information.
Now they’re sifting through the
data in a race to understand those
genes and put them to work in
improved crops and livestock.
“I don’t think sequencing is
going to be an issue anymore,” says
Kulvinder Gill, a wheat breeder
and geneticist at Washington State
University in the United States. “The
issue is going to be how to use it.”
Big hurry. In Gill’s lab, graduate
students and post-doctorates are
dropping tissue samples from
wheat leaves into tiny test tubes,
multiplying the genetic material
from the samples so there’s enough
to test, analysing the genes piped
out of each little vial, and searching
for markers that could be linked to
genetic success. They’re in a hurry –
the plants those samples were taken
from are about to flower, and Gill
LEFT: Breakthroughs in genetic research
are starting to yield breeding advances.
BELOW: A DNA sample on this glass
slide will be analysed by a high-throughput
sequencer that can identify and unscramble
600 billion base pairs – the building blocks
of genes – in a 12-day run cycle.
wants to use their data to select the
most promising plants to cross.
At another desk, a researcher is
studying the corn genome, looking
for a gene that could confer a new
type of dwarfing characteristic
to wheat. Welcome to breeding,
genomics style.
The tools Gill’s team uses are a
triumph of modern science.
DNA is made up of millions of
pairs of just four chemical bases,
labeled A, C, T, and G. That means
every gene is a string of hundreds
or thousands of those letters. Every
chromosome is a collection of
thousands of genes, along with a
bunch of “junk code” like silenced
genes, old bits of viruses, and other
DNA that doesn’t seem to have a role
in the organism’s growth.
Some genomes, like those in people
and cows, have two copies of each
chromosome, one from mum and one
from dad. Others, like wheat, have six
copies of each. That’s billions of As,
Cs, Ts, and Gs on a gene map. In the
test tube, they’re just alphabet soup.
“Let’s say you took an
encyclopedia, all 26 volumes,” says
Brian Scheffler, who heads the
U.S. Department of Agriculture
Agricultural Research Service’s
Genomics and Bioinformatics Unit in
Stoneville, Mississippi. “Each volume
is a chromosome. Each page is a
gene. Now run them through a paper
shredder – and we’re not talking
strips, we’re talking confetti. Then
you have to put it all back together.”
If that’s not challenging enough,
remember that for plants like cotton,
which has chromosomes from two
different ancestor species in every
cell, you’re reconstructing complete
encyclopedia sets from different
publishers.
That’s why completing a genome
is such a milestone – a good map
makes sequencing the next individual
from that species much easier, and
provides a basis for comparing the
similarities and differences among
chromosomes.
“Resequencing is like doing a
puzzle and having the box top in
front of you,” Scheffler explains.
A day’s work. Technology has
gotten faster and cheaper, easing
the effort. “My Ph.D. thesis would
be about a day’s work for my lab
now,” Scheffler says, adding that
the $100 million rice genome project
completed in 2005 would cost about
$2 million today.
That speed and economy propels
Gill’s real-time breeding choices. It
also allows geneticists to analyse the
genotypes of 5,000 to 7,000 U.S. dairy
cows and bulls per month, using
computerised chips to see which gene
markers are present in each animal.
Breeders have spent years correlating
BELOW: Analysing 60,000 gene markers
in a chicken’s genome allows producers to
choose breeding animals in 20 weeks rather
than 2 years.
illustration: paul lange
THE FURROW 37

those markers – single nucleotide
polymorphisms (SNPs), or “snips”
– against thousands of pedigree
records and performance tests.
As a result, they’ve ratcheted up the
accuracy of predicting genetic fitness
in dairy cattle to 83 percent using
computer-analysed “SNP chips,”
compared to a success rate of 35
percent or 40 percent with pedigrees,
says Curt Van Tassell at the USDA-
ARS Bovine Functional Genomics
Laboratory in Beltsville, Maryland.
Driven by genomic analysis, the
rate of productivity gain in the dairy
industry is expected to double over
the next few years, he adds. “It’s
already being felt as the sons of top
bulls are kicking their dads off the
top of the list quickly,” Van Tassell
notes.
Fast and cheap. A SNP chip
analysis of a bull’s genome costs $300
to $500. That’s cheap – compared to
the $50,000 now spent collecting data
on a bull’s daughters – and faster.
“We can identify an up-andcoming
bull essentially from the date
of birth instead of waiting five or six
years like we did in the past, when
we had to wait for his daughters
to yield milking data,” Van Tassell
explains.
Chicken producers can use
SNP chips, too. At $56 per bird, a
BELOW: Golden capillaries channel
fragments of DNA to an analyser. Teased
apart by a gentle electrical charge, they form
a “genetic fingerprint.”
few thousand birds at a time, the
economics of a 60,000-marker
SNP test are a bit more daunting,
according to poultry and aquaculture
breeder Bill Muir at Purdue
University, Indiana, though genomic
selection has more than doubled the
annual rate of gain in the industry.
“Where this technology has the
greatest potential to bring about
good is traits that are expensive to
measure, difficult to measure, or that
don’t exhibit until later in life,” Muir
says.
Feed efficiency, carcass quality, egg
production, or low-heritability traits
like leg soundness are prime targets.
Muir is developing smaller SNP
chips with markers corresponding to
specific traits like egg production or
feed efficiency. His goal is to bring
the price down to a few dollars.
But don’t confuse the success of
SNP chips or marker-assisted
breeding – using SNPs to track
key bits of DNA through the plant
breeding process technology that’s
already yielded blockbuster hybrids
and Clearfield wheat – with a deep
understanding of how genes actually
work.
“We’re trying to decipher all
the information that’s coming in
and decide what it means,” says
John Soper, vice president of crop
genetics R&D for Pioneer Hi-Bred
International in Johnston, Iowa. “The
scientists working on this will start
to focus on ‘what is a gene really
all about? What is the recipe for a
38 THE FURROW

esistance gene?’ Perhaps the last
piece of the puzzle, the complex
piece of the puzzle, is starting to
understand how genes interact.”
Scheffler agrees.
“When I did my Ph.D., from 1986
to 1989, science moved forward
one gene at a time,” he says. “Now
we’re asking the question, ‘what’s
happening when the whole thing
comes together?’ That’s important
because when you get down to
yield, it’s not just one gene – yield
is multiple genes, multiple levels of
expression.”
Global questions. “Now we can
start pulling things apart,” Scheffler
continues. “We can start asking
global questions like, ’when a plant
is experiencing drought, which genes
have an impact on yield?’ We can
start solving problems we couldn’t
address before.”
Every crop sequenced and every
gene identified brings all breeders a
step closer to the next advance, adds
Gill.
“Once a gene is cloned in rice, it’s
more than likely it will work the
same in wheat,” he says. “We are
going to learn from each other.”
ABOVE: Genomics allows plant
breeders to start managing crosses in
the lab or greenhouse, not the test plot.
BELOW: Kulvinder Gill of Washington
State University says cost-saving genomics
tools can help breeders develop varieties
with genes ideal for specific regions or
niche crops.
THE FURROW 39