|Leakey, Andrew D B - UNIVERSITY OF ILLINOIS|
|Bernard, Stephanie - LAWRENCE BERKELEY NAT LAB|
|Markelz, R J Cody - UNIVERSITY OF ILLINOIS|
|Placella, Sarah - UNIV OF CAL - BERKELEY|
|Rogers, Alistair - BROOKHAVEN NATL LAB|
|Smith, Melinda - YALE UNIVERSITY|
|Sudderth, Erika - UNIV OF CAL - BERKELEY|
|Weston, David - OAK RIDGE NATL LAB|
|Wullschleger, Stan - OAK RIDGE NATL LAB|
|Yuan, Shenghua - YALE UNIVERSITY|
Submitted to: Global Change Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 16, 2008
Publication Date: May 1, 2009
Citation: Leakey, A.D.B., Ainsworth, E.A., Bernard, S.M., Markelz, R., Ort, D.R., Placella, S.A., Rogers, A., Smith, M.D., Sudderth, E.A., Weston, D.J., Wullschleger, S.D., Yuan, S. 2009. Gene expression profiling – opening the black box of plant ecosystem responses to global change. Global Change Biology. 15(5):1201-1213. Interpretive Summary: Genomic techniques are increasingly used in the field of ecology. The new field of plant genomic ecology involves experimentation under environmentally realistic conditions to study the fundamental, molecular responses of plants to changes in growth conditions. A number of new techniques and approaches are available to genomic ecologists. Those tools are described in this manuscript, along with the advantages and limitations. The results from recent genomic ecology studies are described to illustrate the power of this approach, and to reveal how gene expression studies have been tailored for use in an ecological context.
Technical Abstract: The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the "black box" of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.