A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation

<p>Abstract</p> <p>Background</p> <p>Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as <it>Populus</it>, a woody perennial tree, in order to understand the specific characteristics of these species.</p> <p>Results</p> <p>We present a systems biology model of the regulatory network of <it>Populus </it>leaves. The network is reverse-engineered from promoter information and expression profiles of leaf-specific genes measured over a large set of conditions related to stress and developmental. The network model incorporates interactions between regulators, such as synergistic and competitive relationships, by evaluating increasingly more complex regulatory mechanisms, and is therefore able to identify new regulators of leaf development not found by traditional genomics methods based on pair-wise expression similarity. The approach is shown to explain available gene function information and to provide robust prediction of expression levels in new data. We also use the predictive capability of the model to identify condition-specific regulation as well as conserved regulation between <it>Populus </it>and <it>Arabidopsis</it>.</p> <p>Conclusions</p> <p>We outline a computationally inferred model of the regulatory network of <it>Populus </it>leaves, and show how treating genes as interacting, rather than individual, entities identifies new regulators compared to traditional genomics analysis. Although systems biology models should be used with care considering the complexity of regulatory programs and the limitations of current genomics data, methods describing interactions can provide hypotheses about the underlying cause of emergent properties and are needed if we are to identify target genes other than those constituting the "low hanging fruit" of genomic analysis.</p

A cross-species transcriptomics approach to identify genes involved in leaf development

<p>Abstract</p> <p>Background</p> <p>We have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development in <it>Populus</it>. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.</p> <p>Results</p> <p>Transcription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.</p> <p>Conclusion</p> <p>This work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.</p

The genetics and genomics of drought response in Populus

The genetic nature of tree adaptation to drought stress was examined by utilising variation in the drought response of an F2 mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) known to be highly divergent for a vast range of phenotypic traits. Phenotyping, QTL analysis and microarray experiments were combined to demonstrate that “genetical genomics” can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying and contrasting responses to drought across genotypes including for leaf coloration, expansion, and abscission were observed and QTL for these traits were identified. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of abscission were defined and microarray experiments were conducted on these genotypes and the grandparents. The different groups induced a different set of genes; 215 and 125 genes differed in their expression response in control and drought respectively, suggesting species adaptation at the gene expression level. Genes preferentially expressed in drought resistance genotypes overlapped with genes expressed in dormant tissues whereas genes involved in meristem function had a lower expression. Co-location of differentially expressed genes with drought specific and drought responsive QTLs was identified and these represent candidate genes contributing to the variation in drought response.</p

The genetics and genomics of drought response in Populus

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The physiological, transcriptional and genetic responses of an ozone-sensitive and an ozone tolerant poplar and selected extremes of their F2 progeny

Relatively little is known about the transcriptional response or genetic control of response and adaptation of trees to tropospheric ozone exposure. Such understanding is needed as up to 50% of forests, globally, may be subjected to phytotoxic concentrations of ozone. The physiological, transcriptional and genetic response to ozone was examined in Populus trichocarpa and P. deltoides, which show extreme sensitivity and tolerance to ozone, respectively. Using an inbred F(2) mapping population derived from these two species, we mapped quantitative trait loci (QTL) for traits associated with ozone response, examined segregation of the transcriptional response to ozone and co-located genes showing divergent responses between tolerant and sensitive genotypes with QTL. QTL were identified linking detrimental effects of ozone with leaf and biomass traits and differential responses were found for key genes involved in ethylene production and response

Comparative physiology of allopatric Populus species : geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g(S)) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta C-13) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects

Spatiotemporal delivery of bone morphogenetic protein enhances functional repair of segmental bone defects

Osteogenic growth factors that promote endogenous repair mechanisms hold considerable potential for repairing challenging bone defects. The local delivery of one such growth factor, bone morphogenetic protein (BMP), has been successfully translated to clinical practice for spinal fusion and bone fractures. However, improvements are needed in the spatial and temporal control of BMP delivery to avoid the currently used supraphysiologic doses and the concomitant adverse effects. We have recently introduced a hybrid protein delivery system comprised of two parts: a perforated nanofibrous mesh that spatially confines the defect region and a functionalized alginate hydrogel that provides temporal growth factor release kinetics. Using this unique spatiotemporal delivery system, we previously demonstrated BMP-mediated functional restoration of challenging 8 mm femoral defects in a rat model. In this study, we compared the efficacy of the hybrid system in repairing segmental bone defects to that of the current clinical standard, collagen sponge, at the same dose of recombinant human BMP-2. In addition, we investigated the specific role of the nanofibrous mesh tube on bone regeneration. Our results indicate that the hybrid delivery system significantly increased bone regeneration and improved biomechanical function compared to collagen sponge delivery. Furthermore, we observed that presence of the nanofiber mesh tube was essential to promote maximal mineralized matrix synthesis, prevent extra-anatomical mineralization, and guide an integrated pattern of bone formation. Together, these results suggest that spatiotemporal strategies for osteogenic protein delivery may enhance clinical outcomes by improving localized protein retention

The genetics and genomics of the drought response in Populus

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response