Improving Crop Plants Through Genomics
The Tomato Magazine
By Luis Pons, Agricultural Research
Service Information Staff, Agricultural
In 1968, genomics breakthroughs at
ARS’s U.S. Plant, Soil, and Nutrition
Laboratory (PSNL) in Ithaca, New York,
earned the U.S. Department of Agriculture
its only Nobel Prize to date. Biochemist
Robert Holley received the award for being
part of the team that first determined the
structure and nucleotide sequence of transfer
Today, PSNL scientists are building on
Holley’s legacy, applying genomics and
related sciences such as proteomics and
molecular genetics to improve the nutritional
value of leading crops. The ARS researchers,
whose labs are located on Cornell
University’s main campus, are also out to
boost crop plants’ resistance to disease and
their tolerance to soils lacking nutrients or
containing toxic amounts of metals. And
two PSNL scientists are now part of major
efforts to map and sequence the genomes of
tomato and maize.
A pivotal moment in PSNL’s genomics
research occurred fi ve years ago, when
David J. Schneider was hired as one of
ARS’s fi rst computational biologists— experts at
integrating computer science with biological research. He and molecular
Samuel W. Cartinhour have since helped
make computational and molecular biology
critical components of the lab’s work.
“We are combining computational and
bench-based biological research to help
solve complex problems in agriculture,” says Schneider.
Schneider and Cartinhour apply this
interdisciplinary approach to their research
on plant diseases. Says Schneider, “We’re
studying disease development from the
They’re using the bacterial pathogen
Pseudomonas syringae DC3000 as a model
system for studying virulence-related
genes and pathways.
“We’re relying on
statistical physics, computer science, and
complex-systems theory to identify regions
in a pathogen’s genome that help regulate
gene expression,” says Cartinhour. “We’re
showing that there’s a real role for numbercrunching
Among other projects at Ithaca is one led
by molecular biologists James J. Giovannoni
and Li Li, who are using tomato and cauliflower as models for improving
Five years ago, Giovannoni and colleagues
reported the discovery of RIN, a
tomato gene that regulates ethylene, a plant
hormone that stimulates ripening. This landmark
finding raised the possibility of both
growing better tasting tomatoes that meet
commercial shelf-life needs and geneticallymanipulating ripening in other
fruits, such as
melon and strawberry.
Recently, Giovannoni and colleagues
cloned tomato’s green-ripe (GR) gene,
which inhibits the plant’s ripening responses
to ethylene. The gene greatly affects fruit
development while exerting minimal infl uence
on other plant tissues.
“This may help control ethylene’s effects
on ripening—and bring about longer shelflife
and better quality—while retaining
ethylene’s desirable effects, such as disease
resistance, on other plant tissues,” he says.
“It makes it possible to control ripening in
fruit while maintaining normal plant vigor.”
Giovannoni has also helped discover
two genes that regulate fruit’s response to
light, and he’s found that these genes— LeCOP1LIKE
and HIGH-PIGMENT 1—can be manipulated to alter fruit quality
and nutritional value.
Today, his team is using microarray,
or gene-chip, technology, which enables
quick examination of thousands of genes in
a single experiment. One signifi cant study
showed how microarrays can help characterize
gene expression in tomato-related fruit
species, such as pepper and eggplant, for
which genomic resources are either currently
unavailable or limited.
The fruits studied are part of the plant
family Solanaceae, which—with more than
3,000 members—is the most important
“We showed that tomato
microarrays can be used to characterize gene
expression in four of the most important
Solanaceae crop species,” says Giovannoni.
Giovannoni is also contributing to the
Tomato Sequencing Project. Undertaken by
a consortium involving scientists from 10
countries, this effort is part of an even larger
initiative: The International Solanaceae
Genome Project: Systems Approach to
Diversity and Adaptation.
Cauliflower and Beta-Carotene
Meanwhile, Li is using caulifl ower as a
model system to identify genes and defi ne
molecular She’s focusing on carotenoids, the
fruit-and-vegetable compounds that the body
converts into essential vitamins and uses as
antioxidants for cancer prevention. She’s
using a caulifl ower gene, dubbed “Or” for
the color orange, to induce accumulation of
high levels of beta-carotene in food crops.
The human body uses beta-carotene, the
carotenoid that gives carrots their color, to
make vitamin A.
“Our work is important,
as vitamin A deficiency has been reported
to affect some 250 million children worldwide,” says Li.
She says the Or gene promotes high
beta-carotene accumulation in various
tissues in the caulifl ower plant that
normally don’t have carotenoids. “It can help us understand
how carotenoid synthesis and accumulation are
regulated in plants and in turn can help us better understand the
health benefi ts of carotenoids.”
The Maize Genome
PSNL’s genomics work includes development of statistical and
genetic tools for identifying natural variation in agronomically
important traits in maize. Scientists are also contributing to the
genome sequencing of maize.
Plant geneticist Edward S. Buckler is working with ARS plant
geneticists Michael McMullen in the Plant Genetics Research
Unit at Columbia, Missouri, and Jim Holland in the Plant Science
Research Unit at Raleigh, North Carolina, and Stephen Kresovich,
director of Cornell’s Institute for Genomic Diversity.
“We’re analyzing many related families of corn as well as unrelated,
genetically diverse corn lines,” says Buckler. “We are looking
for genes and novel alleles, or variations, that control maize’s
complex quantitative traits, such as yield, fl ower development, and
“By using this approach, the best genetic variants can be
discovered, and their position within the genome can be resolved to a
single gene,” he adds. “This can help us identify genes that
can spur a wide array of traits, such as kernel quality, nutritional
content, and tolerance of soil-related stresses.”
PSNL computational biologist Doreen H. Ware, who works
at the nonprofi t Cold Spring Harbor Laboratory in New York, is
contributing genome annotation and bioinformatic tools to the
sequencing of the maize genome. This project is being funded
by the National Science Foundation (NSF), USDA, and the U.S.
Department of Energy.
Tolerating Bad Soil
Plant physiologist Leon V. Kochian, research leader of PSNL’s
Plant, Soil, and Nutrition Research Unit, is using similar genomic
and molecular genetic techniques in work—partially funded by
NSF—to improve crop-plant cultivation on marginal, and even
highly acidic, soils that limit crop production worldwide.
With the genomic tools used on maize and rice—some of which
are being developed by Buckler and Ware—Kochian and his team
have identified genes and associated mechanisms that help plants
tolerate soil acidity and toxic metals.
“We’ve zeroed in on aluminum tolerance in maize and sorghum,” Kochian says. “Aluminum
is what limits root-system growth in acid soils. These crops are ideal
for this project because
in sorghum, aluminum tolerance is a simple trait, while in maize,
the tolerance is complex.”
Kochian’s group and researchers at Brazil’s EMBRAPA
Maize and Sorghum Research Center have cloned Alt SB, the major sorghum
aluminum-tolerance gene. And recently, he and colleagues
confi rmed the importance of a gene called AtALMT1 to aluminum
tolerance in Arabidopsis. They also found that a second, still
unidentifi ed, gene plays a major role in that plant’s aluminum
in acidic soil.
Targeting Insect Vectors
In PSNL’s Plant Protection Research Unit, plant pathologist
Stewart Gray is using genomics to fi nd genes that regulate
plant virus transmission by insect vectors.
He’s focused on how aphids transmit barley yellow dwarf
and potato leafroll, the most economically important viruses
of wheat, barley, oats, and potatoes worldwide.
“We want to
identify both the virus genes and the aphid genes that regulate
transmission of the virus between insect and host,” says Gray.
Recently, Gray identifi ed and characterized the two virus
genes that regulate how a virus moves through its aphid vector.
Now his group is out to identify the corresponding genes
in aphids regulating the insects’ interaction with the virus.
Also, Gray and Iowa State University scientists are
determining the complete nucleotide sequences of up to 100
biologically important barley yellow dwarf and cereal yellow
dwarf isolates from around the world. His lab is also part of a
scientific consortium that’s sequencing the aphid genome.
Meanwhile, Holley’s legacy will continue on into the lab’s
future. Planning is under way to transform the PSNL into the
Robert W. Holley Center for Agriculture and Health. This
center would house all PSNL scientists within a new, $40
Editor’s Note: This research is part of Plant Genetic Resources,
Genomics, and Genetic Improvement (#301), Plant Biological and
Molecular Processes (#302), Plant Diseases (#303), Crop Protection
and Quarantine (#304), and Crop Production (#305), five ARS
National Programs described on the World Wide Web at www.nps.ars.usda.gov.
To reach scientists mentioned in this article, contact Luis Pons, USDAARS
Information Staff, 5601 Sunnyside Ave., Beltsville, MD 20705-5129;
phone (301) 504-1628, fax (301) 504-1486. “Improving Crop Plants
Genomics” was published in the January 2007 issue of Agricultural
© 2007 Columbia
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