May 6, 2008 It's a familiar notion that an individual might interpret and respond to stressful events in a unique way based on previous experience and genetic predispositions. A new study by researchers at the Duke Institute for Genome Sciences & Policy (IGSP) finds that the same can be said of the individual cells in a plant. They respond in a variety of ways to too much salt or too little iron, both widespread environmental challenges for agricultural crops around the world.
In fact, the researchers show that such differences of “interpretation”—measured as shifts in the activity of genes across the genome—hold all the way down to the level of root cells, depending upon their precise type and developmental stage.
“High salinity and low iron are both important problems for food security, particularly in developing countries,” said Philip Benfey, director of the IGSP Center for Systems Biology at Duke. “The genomic differences we see between various tissues, cell types and developmental stages relate to the plants’ physiological response to these conditions.”
Benfey said the new evidence might provide clues for developing crop plants better equipped to deal with high salt levels and capable of incorporating more iron in times of scarcity. It also speaks to a more general principle: that a cell’s identity largely determines how it will cope with circumstances outside.
Salt contamination is a problem for more than half the world’s arable land and a particular one in parts of Southeast Asia now recovering from the tsunami of 2005, Benfey said. On the other hand, iron-deprived crops present problems for people in developing countries who depend heavily on vegetables for the essential nutrient.
In the many previous studies of plants’ response to salt, iron and other stresses, “the plant is generally taken as a single, homogeneous entity,” Benfey said. “We’ve asked if that is appropriate, and the answer is a very loud and clear no.”
Benfey, along with post-doctoral researchers José Dinneny and Terri Long, examined cells taken from the roots of the model mustard plant Arabidopsis after the plants were exposed to either high salt or low iron. In one set of experiments, the cells were sorted according to the specific type of root tissue they represented, from the outermost layer in to the core. In another, they separated the root cells based on their age. (Because roots grow from dividing stem cells at the tip, root cells are developmentally older the closer they are to the stem.)
Genomic profiles of root cells taken from the various zones revealed highly specific reactions to each of the stresses. Out of the thousands of plant genes, only 244—those that set cells’ identity—held steady with either stress.
The results show that the vast majority of plant genes rise and fall in activity as a reaction to the prevailing environment. A smaller set of core identity genes control those reactions.
So, what might the findings in plants mean for the age-old nature versus nurture debate?
“It shows that there are core genes and there are responsive genes--there is both a hard-wired part and a part that is extremely sensitive to the environment,” Benfey said. And, he added, the precise divide between the two might depend on where exactly you happen to look.
Collaborators on the study include Jean Wang, Jee Jung, Daniel Mace, Solomon Pointer and Siobhan Brady, all of Duke; and Christa Barron and John Schiefelbein of the University of Michigan, Ann Arbor.
The results appeared on April 25th, 2008, in Science Express, the early online edition of the journal Science. The work was funded by the National Science Foundation.
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