Plant Yields Secret Of Origins
ITHACA, N.Y. A weedy,
inedible member of the mustard
family, related to broccoli and
cauliflower, has become the first
plant to yield the secrets of its
primordial origins.
In a computational research
effort at Cornell University, the
plant, Arabidopsis thaliana, was
shown to contain genetic evi
dence of its emergence between
50 million and 200 million years
ago.
The finding, noted Cornell re
searchers, will be invaluable to
those using Arabidopsis as a
genetic model for other plant
species, unlocking genes for im
portant traits in agricultural
crops such as corn, tomatoes,
and wheat.
The researchers report on
their discovery in the latest edi
tion of the journal Science (Dec.
15,2000).
A decade ago, Arabidopsis
was widely adopted by plant sci
entists as an easily manipulated
model for other plants because it
is simple to grow in the labora
tory, has a short life cycle and
has a small genome only
about 140 million base pairs of
DNA compared with wheat,
which might have as many as 16
billion pairs. This year, the
entire DNA sequence of the
plant was completed, and for the
first time researchers were able
to understand the sequence of
the 25,000 genes necessary for
an organism to function as a
flowering plant.
Using this genome sequence
which is in the public domain
on the Internet the Cornell
researchers used computers to
sort through the plant’s DNA
and find its genetic roots.
“We can take the entire
genome of one plant and look
• back at it,” said Steven D.
Tanksley, the Liberty Hyde
Bailey professor of plant breed
ing at Cornell and an author on
the paper. “We are going back
into genetic time, and we can see
what the ancient genome looked
like. If we can understand what
the ancestral gene content in one
plant is, then we can use that to
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learn the gene content in other
plants.”
Tanksley and the lead
researcher, Todd Vision, a Cor
nell visiting scientist, explained
that for many plant genomes
there is a lot of empty material
between the proteins. Tanksley
suggested that understanding a
genome is like driving along a
highway. On the East Coast, you
do not have to drive far before
you reach another city, while out
west, there are long distances be
tween cities.
The point of the analogy is
that scientists can gather more
general genetic information
from Arabidopsis in a shorter
period of time. Said Tanksley,
“Arabidopsis is the East Coast
of DNA sequencing.”
The researchers used a com
puter program called BLAST to
classify the thousands of genes
in Arabidopsis into gene fami
lies. BLAST (an acronym for
Basic Local Alignment Search
Tool) is a sequence similarity
program designed to support
analysis of nucleotide and pro
tein databases. It was developed
at the National Center for
Biotechnology Information, part
of the National Institutes of
Health, in Bethesda, Md. The re
searchers then used novel algor
ithms to find large chunks of the
chromosomes that were dupli
cated long ago.
In the process of duplication,
all the genetic material in a spe
cies doubles, creating what is
known as a polyploid. The re
searchers inferred that Arabi
dopsis was an ancient polyploid
because it contained evidence of
multiple duplications.
Although duplicated chromo
somes diverged from one an
other and became scrambled
over the eons„the research team
was able to find 103 duplicated
chromosome segments that
ranged in age from 50 million to
200 million years. “We figured
out where gene family members
are located and used that infor
mation to find the ancient dupli
cated segments,” said Vision,
who is a molecular biologist at
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the Center for Agricultural
Bioinformatics (CAB) at Cor
nell. The CAB is supported by
the USDA Agricultural Re
search Service in partnership
with the College of Agriculture
and Life Sciences and the
Theory Center at Cornell.
With help from the dating es
timates obtained by paleobotan
ists, the team was able to look at
the duplicated gene sequences
and deduce when the genome
duplications in Arabidopsis oc
curred. The team found that a
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DOYLESTOWN (Bucks Co.)
Food companies in the Dela
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few large duplication events
were responsible for the pattern
they saw.
“Our work was entirely com
putational, but a lot of other re
searchers’ laboratory work went
into it before that,” said Vision.
He draws an analogy between
finding prehistoric genetic rela
tionships and the development
of language.
Many words in Romance lan
guages such as Spanish, Italian,
French, and Portuguese are de
rived from Latin. “We can see
the roots of the modern words as
being derived from Latin,” he
said. “In our case, we are find-
cakes, cookies, candy and condi
ments, among other commodi
ties.
Following the International
Food Show, a seminar will be of
fered featuring August “Gus”
Schumacher, under secretary of
agriculture for USDA; Jim Cu
orato, director of commerce for
Philadelphia; and Jim Kenney,
Philadelphia city councilman
at-large. At the conclusion of the
seminar, the group will travel to
Doylestown, where they will
tour Delaware Valley College.
Delaware Valley College is
noted nationally as a leader in
agricultural education.
Founded in 1896, the college
is a comprehensive four-year in
stitution of higher learning with
nearly 1,400 men and women
enrolled full-time in more than
35 academic programs, ranging
from agribusiness, agricultural,
RIGIDPLY...
ing the genetic roots of the genes
before they duplicated and
diverged.”
The paper, “The Origins of
Genomic Duplications in Arabi
dopsis,” was authored by
Vision, Tanksley, and Daniel G.
Brown of the Whitehead Insti
tute at the Massachusetts Insti
tute of Technology. Brown
participated in the research
while completing his doctoral
degree, which he earned from
the Department of Computer
Science at Cornell last spring.
The research was funded by the
USDA Agriculture Research
Service and grants from the Na
tional Science Foundation and
the Office of Naval Research.
biological and physical sciences,
to business administration, com
puter information systems, Eng
lish and secondary education. In
addition, 700 students are en
rolled on a part-time basis in
Del Val’s Continuing Education
program, working to advance
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The International Food Show
is sponsored through a collabo
ration of the Pennsylvania De
partment of Agriculture, Food
Export USA-Northeast, The
Delaware River Port Authority
and the International Agrimar
keting Center of Delaware
Valley College.
For more information, call
Ron Davis, international con
sultant at Bell Exports, at (215)
829-9090, or Jim Diamond, Dr.
James E. Diamond, co-director
of the International Agrimarket
ing Center of Delaware Valley
College at (215) 489-2400.
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