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IMAGING work delivered enormous agricultural gains

through the mid 1990s. But with yields of

With ‘Phenomics,’ Plant Scientists many crops having hit plateaus, green
thumbs are no longer enough. Modern plant
breeders need the equivalent of a watch-
Hope to Shift Breeding Into Overdrive maker’s magnifying glass and tweezers to
tinker with complex and intertwined traits.
MELBOURNE, AUSTRALIA— Last May, a world, consists of two nodes. One is a High Phenomics, says Uli Schurr, director of IPR,
scrawny grass, Brachypodium distachyon, Resolution Plant Phenomics Centre (HRPPC) promises to usher in “precision agriculture
joined the exclusive club of plants whose in Canberra, which opened last week. A and predictive breeding.”
genomes have been sequenced. Brachy- debut project of the center is an international One trait Australia has in its cross hairs is
podium may look unassuming, but under the collaboration to screen Brachypodium vari- salt tolerance. High salinity affects one-fifth
hood it is a geneticist’s dream. It has a short ants for drought-tolerance and for less lignin of the world’s irrigated land and two-thirds
life cycle and a small genome with one pair of in their cell walls. The second node is the of Australian cereal crops. But selecting
chromosomes (wheat, for instance, has three Plant Accelerator in Adelaide, a screening plants for salt tolerance has generally
pairs) that readily reveals the effects of genetic facility that Tester will run and aims to get flopped. “We can end up with plants like

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modification. In short, the temperate grass is a online by December. mangroves that are salt-tolerant but slow
superb model organism for cereals like wheat “Australia is leading the way,” says David growing and not much use,” says Tester. He
and rice and for biofuels like switchgrass. But Kramer, a spectroscopist at the Institute of and Rana Munns of CSIRO Plant Industry in
Brachypodium’s genome alone cannot revolu- Biological Chemistry at Washington State Black Mountain, Canberra, recently found
tionize plant breeding. University, Pullman. But other countries are that salt tolerance is connected with a plant’s
Enter plant phenomics. Borrowing imag- ramping up fast. In Germany, for example, ability to resume growth after osmotic
ing techniques from medicine, phenomics the Institute for Phytosphere Research (IPR) shock—the shutdown in cell growth occur-
ring fractions of a second after a plant is
Bundle sheath cells exposed to high salt concentrations.
Exploiting that trait, Tester’s lab earlier this
year used a three-dimensional camera to
record minute changes in growth responses
after wheat plants transplanted into salty soil
went into osmotic shock. After crossing vari-
eties and laboriously screening hundreds of
plants, one of Tester’s Ph.D. students, Karthika
Rajendran, appears to have pinpointed a gene
that helps plants resist osmotic shock.
Such mind-numbing screening will be
automated and sped up when the Plant Accel-
erator roars to life. It will have a throughput of
Mesophyll cells 2400 plants a day—10 times the capacity of
current labs. Plants will travel by conveyer
A-maizing transformation. In this maize leaf, laser confocal microscopy reveals a clear distinction between belt to stations that measure growth rate and
high activity of photosystem II in mesophyll cells (pink fluorescence) and low activity in bundle sheath cells color, a sign of tissue health.
(purple)—a distinction typical of C4 plants. The green fluorescence comes mainly from lignin in cell walls. Also expected to get a phenomics boost is


an effort to replace rice’s inefficient C3 photo-
offers plant scientists new windows into the in Jülich in 2007 established the Jülich synthetic pathway with the C4 pathway found
inner workings of living plants: infrared Phenomics Centre, which carries out a vari- in maize and 40 other plant species. For the
cameras to scan temperature profiles, spec- ety of screens and is developing root imag- same input of water and nitrogen, maize pro-
troscopes to measure photosynthetic rates, ing. And the Leibniz Institute of Plant duces twice the carbohydrate content of rice.
lidar to gauge growth rates, and MRI to Genetics and Crop Plant Research in Gater- Researchers have tried to assemble the C4
reveal root physiology. “Phenomics will give sleben is carrying out high-throughput pathway in rice using maize enzymes, but the
plant scientists the tools to unlock the infor- screening on crops such as barley and wheat efforts failed, perhaps because rice’s subcellu-
mation coded in genomes,” says Mark Tester, using instruments such as infrared cameras lar structure prevented the enzymes from
director of the Australian Plant Phenomics to chart transpiration and fluorescent working in synchrony.
Facility (APPF), a new $40 million venture microscopy to assess photosynthesis. Phenomics tools can provide snapshots of
with headquarters in Adelaide. cellular structure and diagnose steps along the
Institutes worldwide are racing to build From feel to phenomics way toward C4 metabolism in live plants. The
facilities with instrument arrays that can scan Plant breeders are known for their “feel”: the International Rice Research Institute (IRRI)
thousands of plants a day in an approach to ability to select subtle traits that enhance a in Los Baños, Philippines, is screening rice
science akin to high-throughput DNA plant’s performance. They might key in on varieties for those with a cellular architecture
sequencing. “This will allow plant physiol- the way a plant curls its leaves, for example, best suited to house the C4 enzyme assembly.
ogy to ‘catch up’ with genomics,” says Tester. or a particular shade of green whose signifi- In C4 plants, mesophyll cells turbocharge
APPF, the first national lab of its kind in the cance escapes the uninitiated. Such craft- photosynthesis by delivering carbon dioxide

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at 10 times atmospheric con- reduced photosynthetic rates. The problem is

centration to sugar-producing that the switches that set the photosynthetic
bundle sheath cells that sur- rate are poorly understood. To penetrate this
round the veins. For this trans- mystery, Kramer plans to use the equivalent of
fer to work, there can be no a car engine dynamometer: a spectrometer that
more than three to four cells gauges the photosynthetic engine. The cogs of
between the veins. IRRI’s ini- the engine—carotenoids, plastocyanins, and
tial screens are for rice vari- cytochrome complexes—emit unique spectral
eties with narrower spacing signatures in their excited states.
between the veins. Promising Kramer hopes to probe the “wear and tear”
varieties will be shipped to costs of photosynthesis with an “idea spec-
HRPPC, which will use fluo- trometer,” a device his group designed that is
rescence microscopy and other inspired by the “tricorder” of Star Trek fame.
tools to interrogate the plants. At the moment, the spectrometer, the size of a
One approach is to look for a fluo- Energy efficient? Chlorophyll fluores- pint of beer, must be wired to a leaf; the goal is
cence, a measure of photosynthesis, in
rescent signature from a complex to be able to wave it over a plant like the fic-
Arabidopsis seedlings and a wheat ear

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of light-absorbing molecules (inset). Blue depicts high photo-
tional tricorder. Kramer says he would freely
called photosystem II: If these synthetic rate, red depicts low. Large provide the device to colleagues to compile a
molecules’ activities are muted in numbers of plants can be screened for global database of plant performance. “We
bundle sheath cells, it means the stress response, for example, or for can push our crop plants harder,” says Kramer.
plant is becoming more C4-like. high yield. “The question is how far.”
Kramer’s lab in Pullman, Kramer and other adherents think the
meanwhile, is examining the split-second (Arundo donax), a potential biofuel source, emerging discipline of phenomics will help
reactions that capture some energy of imping- is many times that of rice. Most crops are foment the next green revolution. We now
ing sunlight while dissipating more than 80% less efficient and “far too conservative for have the tools “to make quantum leaps in
to prevent damage. “If we could reduce this biofuels use,” Kramer says. “They’re play- crop breeding,” says plant physiologist
regulatory loss by 1%, we might double ing it too safe.” Robert Furbank, director of HRPPC.
yields,” he says. Breeders have never seriously attempted to “These are the tools we need to feed and
Plants vary in how much light they dissi- rev up the photosynthetic rate, says Kramer. fuel the world.” –ELIZABETH FINKEL
pate. The photosynthetic rate of giant cane Indeed, some high-yield rice varieties have Elizabeth Finkel is a writer in Melbourne, Australia.


Data Integrity Report Sends Journals Back to the Drawing Board

It seemed like a good idea: With digital vened 17 experts in fields from physics to field, says co-chair Phillip Sharp, a molecu-
data routine in nearly every scientific field, sociology to look at issues of treating, shar- lar biologist at the Massachusetts Institute of
and growing concerns about doctored ing, and archiving research data. Technology (MIT) in Cambridge. So the
images and demands to share data, why not Their conclusions, described in a report* committee couldn’t be too specific, Sharp
convene a set of experts to come up with this week (see Editorial, p. 368), boil down says. For example, says co-chair and emeri-
general data-handling guidelines? But a to three “principles” that are as uncontro- tus MIT physicist Daniel Kleppner, astro-
National Academies panel found this task versial as motherhood and apple pie: physicists don’t really have issues with
impossible. Instead, its report, released Researchers are responsible for ensuring the image manipulation because they work with
today, offers broad principles for dealing integrity of their data; data from published public data sets, and if someone doctors an
with data but calls on disciplines to work papers should be publicly accessible; and image, colleagues “can go right back and
out the details themselves. data should be properly archived. look” and catch it.
One trigger for the study was a particu- The report also offers 11 recommenda- Journal editors seem a bit disappointed.
larly egregious case of scientific fraud: the tions urging scientists, institutions, jour- The National Institutes of Health’s Kenneth

faking of stem cell data by South Korean nals, and other players to develop standards Yamada, an editor of The Journal of Cell
researcher Woo Suk Hwang, including cut- and provide proper training. The sugges- Biology, which has worked out ways to
and-pasted cell images in a 2005 paper in tions include a few new points—for exam- screen for manipulated images that other
Science. Faced with other examples of data ple, data-sharing should include not just the journals have followed, calls the report’s
manipulation, a group of journal editors raw data but also the computer programs principles “an excellent foundation on
asked the academies for advice in 2006. used to analyze it. But there are no detailed which fields can build.” But he suggests a
Academies officials added a second contro- guidelines. “Phase Two” academies study focusing on
versy they considered related: demands The problem was that every time a pan- digital imaging in biology. Katrina Kelner,
from a global-warming skeptic in Congress elist made a detailed proposal, another managing editor, research journals at
for data from the scientists who published member would say it would not work in their Science, who calls the report “welcome”
the so-called hockey stick paper in 1998 in and the principles “useful,” expects jour-
*Ensuring the Integrity, Accessibility, and Stewardship
Nature that shows rising global tempera- of Research Data in the Digital Age, The National nals themselves may have to work out the
tures since 1900. Then the academies con- Academies Press specifics. –JOCELYN KAISER

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Published by AAAS

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