Australian Center for Plant Functional Genomics

Bundoora, Australia

Australian Center for Plant Functional Genomics

Bundoora, Australia
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Hill C.B.,Australian Center for Plant Functional Genomics | Taylor J.D.,Australian Center for Plant Functional Genomics | Edwards J.,University of Melbourne | Mather D.,Waite Research Institute | And 3 more authors.
Plant Physiology | Year: 2013

Drought is a major environmental constraint responsible for grain yield losses of bread wheat (Triticum aestivum) in many parts of the world. Progress in breeding to improve complex multigene traits, such as drought stress tolerance, has been limited by high sensitivity to environmental factors, low trait heritability, and the complexity and size of the hexaploid wheat genome. In order to obtain further insight into genetic factors that affect yield under drought, we measured the abundance of 205 metabolites in flag leaf tissue sampled from plants of 179 cv Excalibur/Kukri F1-derived doubled haploid lines of wheat grown in a field experiment that experienced terminal drought stress. Additionally, data on 29 agronomic traits that had been assessed in the same field experiment were used. A linear mixed model was used to partition and account for nongenetic and genetic sources of variation, and quantitative trait locus analysis was used to estimate the genomic positions and effects of individual quantitative trait loci. Comparison of the agronomic and metabolic trait variation uncovered novel correlations between some agronomic traits and the levels of certain primary metabolites, including metabolites with either positive or negative associations with plant maturity-related or grain yield-related traits. Our analyses demonstrate that specific regions of the wheat genome that affect agronomic traits also have distinct effects on specific combinations of metabolites. This approach proved valuable for identifying novel biomarkers for the performance of wheat under drought and could facilitate the identification of candidate genes involved in drought-related responses in bread wheat. © 2013 American Society of Plant Biologists. All Rights Reserved.

Conn S.J.,University of Adelaide | Conn S.J.,European Molecular Biology Laboratory | Conn V.,University of Adelaide | Conn V.,Australian Center for Plant Functional Genomics | And 4 more authors.
New Phytologist | Year: 2011

Magnesium accumulates at high concentrations in dicotyledonous leaves but it is not known in which leaf cell types it accumulates, by what mechanism this occurs and the role it plays when stored in the vacuoles of these cell types. Cell-specific vacuolar elemental profiles from Arabidopsis thaliana (Arabidopsis) leaves were analysed by X-ray microanalysis under standard and serpentine hydroponic growth conditions and correlated with the cell-specific complement of magnesium transporters identified through microarray analysis and quantitative polymerase chain reaction (qPCR). Mesophyll cells accumulate the highest vacuolar concentration of magnesium in Arabidopsis leaves and are enriched for members of the MGT/MRS2 family of magnesium transporters. Specifically, AtMGT2/AtMRS2-1 and AtMGT3/AtMRS2-5 were shown to be targeted to the tonoplast and corresponding T-DNA insertion lines had perturbed mesophyll-specific vacuolar magnesium accumulation under serpentine conditions. Furthermore, transcript abundance of these genes was correlated with the accumulation of magnesium under serpentine conditions, in a low calcium-accumulating mutant and across 23 Arabidopsis ecotypes varying in their leaf magnesium concentrations. We implicate magnesium as a key osmoticum required to maintain growth in low calcium concentrations in Arabidopsis. Furthermore, two tonoplast-targeted members of the MGT/MRS2 family are shown to contribute to this mechanism under serpentine conditions. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Parent B.,Australian Center for Plant Functional Genomics | Tardieu F.,French National Institute for Agricultural Research
New Phytologist | Year: 2012

Rates of tissue expansion, cell division and progression in the plant cycle are driven by temperature, following common Arrhenius-type response curves. We analysed the genetic variability of this response in the range 6-37°C in seven to nine lines of maize (Zea mays), rice (Oryza spp.) and wheat (Triticum aestivum) and in 18 species (17 crop species, different genotypes) via the meta-analysis of 72 literature references. Lines with tropical or north-temperate origins had common response curves over the whole range of temperature. Conversely, appreciable differences in response curves, including optimum temperatures, were observed between species growing in temperate and tropical areas. Therefore, centuries of crop breeding have not impacted on the response of development to short-term changes in temperature, whereas evolution over millions of years has. This slow evolution may be a result of the need for a synchronous shift in the temperature response of all developmental processes, otherwise plants will not be viable. Other possibilities are discussed. This result has important consequences for the breeding and modelling of temperature effects associated with global changes. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Adem G.D.,University of Tasmania | Roy S.J.,Australian Center for Plant Functional Genomics | Roy S.J.,University of Adelaide | Zhou M.,University of Tasmania | And 2 more authors.
BMC Plant Biology | Year: 2014

Background: Salinity tolerance is a physiologically multi-faceted trait attributed to multiple mechanisms. Three barley (Hordeum vulgare) varieties contrasting in their salinity tolerance were used to assess the relative contribution of ionic, osmotic and oxidative stress components towards overall salinity stress tolerance in this species, both at the whole-plant and cellular levels. In addition, transcriptional changes in the gene expression profile were studied for key genes mediating plant ionic and oxidative homeostasis (NHX; RBOH; SOD; AHA and GORK), to compare a contribution of transcriptional and post-translational factors towards the specific components of salinity tolerance.Results: Our major findings are two-fold. First, plant tissue tolerance was a dominating component that has determined the overall plant responses to salinity, with root K+ retention ability and reduced sensitivity to stress-induced hydroxyl radical production being the main contributing tolerance mechanisms. Second, it was not possible to infer which cultivars were salinity tolerant based solely on expression profiling of candidate genes at one specific time point. For the genes studied and the time point selected that transcriptional changes in the expression of these specific genes had a small role for barley's adaptive responses to salinity.Conclusions: For better tissue tolerance, sodium sequestration, K+ retention and resistance to oxidative stress all appeared to be crucial. Because these traits are highly interrelated, it is suggested that a major progress in crop breeding for salinity tolerance can be achieved only if these complementary traits are targeted at the same time. This study also highlights the essentiality of post translational modifications in plant adaptive responses to salinity. © 2014 Adem et al.; licensee BioMed Central Ltd.

Cotsaftis O.,Australian Center for Plant Functional Genomics | Plett D.,Australian Center for Plant Functional Genomics | Johnson A.A.T.,Australian Center for Plant Functional Genomics | Johnson A.A.T.,University of Melbourne | And 7 more authors.
Molecular Plant | Year: 2011

Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. The aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity per se. Transcript profiles of several gene families with known links to salinity tolerance are described (e.g. HKTs, NHXs). The putative function of a set of genes identified through their salt responsiveness, transcript levels, and/or chromosomal location (i.e. underneath QTLs for salinity tolerance) is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance. © The Author 2010. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPP and IPPE, SIBS, CAS.

Preuss C.P.,Australian Center for Plant Functional Genomics | Preuss C.P.,University of Adelaide | Huang C.Y.,Australian Center for Plant Functional Genomics | Huang C.Y.,University of Adelaide | And 3 more authors.
Plant Physiology | Year: 2010

Remobilization of inorganic phosphate (Pi) within a plant is critical for sustaining growth and seed production under external Pi fluctuation. The barley (Hordeum vulgare) transporter HvPHT1;6 has been implicated in Pi remobilization. In this report, we expressed HvPHT1;6 in Xenopus laevis oocytes, allowing detailed characterization of voltage-dependent fluxes and currents induced by HvPHT1;6. HvPHT1;6 increased efflux of Pi near oocyte resting membrane potentials, dependent on external Pi concentration. Time-dependent inward currents were observed when membrane potentials were more negative than 2160 mV, which was consistent with nH+:HPO42-(n>2) cotransport, based on simultaneous radiotracer and oocyte voltage clamping, dependent upon Pi concentration gradient and pH. Time- and voltage-dependent inward currents through HvPHT1;6 were also observed for SO42-, and to a lesser degree for NO3- and Cl-, but not for malate. Inward and outward currents showed linear dependence on the concentration of external HPO42-, similar to low-affinity Pi transport in plant studies. The electrophysiological properties of HvPHT1;6, which locates to the plasma membrane when expressed in onion (Allium cepa) epidermal cells, are consistent with its suggested role in the remobilization of Pi in barley plants. © 2010 American Society of Plant Biologists.

Chopin J.,University of South Australia | Laga H.,University of South Australia | Huang C.Y.,Australian Center for Plant Functional Genomics | Heuer S.,Australian Center for Plant Functional Genomics | Miklavcic S.J.,University of South Australia
PLoS ONE | Year: 2015

The morphology of plant root anatomical features is a key factor in effective water and nutrient uptake. Existing techniques for phenotyping root anatomical traits are often based on manual or semi-automatic segmentation and annotation of microscopic images of root cross sections. In this article, we propose a fully automated tool, hereinafter referred to as RootAnalyzer, for efficiently extracting and analyzing anatomical traits from root-cross section images. Using a range of image processing techniques such as local thresholding and nearest neighbor identification, RootAnalyzer segments the plant root from the image's background, classifies and characterizes the cortex, stele, endodermis and epidermis, and subsequently produces statistics about the morphological properties of the root cells and tissues. We use RootAnalyzer to analyze 15 images of wheat plants and one maize plant image and evaluate its performance against manually-obtained ground truth data. The comparison shows that RootAnalyzer can fully characterize most root tissue regions with over 90%accuracy. © 2015 Chopin et al.

Harris J.C.,Australian Center for Plant Functional Genomics | Hrmova M.,Australian Center for Plant Functional Genomics | Lopato S.,Australian Center for Plant Functional Genomics | Langridge P.,Australian Center for Plant Functional Genomics
New Phytologist | Year: 2011

Plant development is adapted to changing environmental conditions for optimizing growth. This developmental adaptation is influenced by signals from the environment, which act as stimuli and may include submergence and fluctuations in water status, light conditions, nutrient status, temperature and the concentrations of toxic compounds. The homeodomain-leucine zipper (HD-Zip) I and HD-Zip II transcription factor networks regulate these plant growth adaptation responses through integration of developmental and environmental cues. Evidence is emerging that these transcription factors are integrated with phytohormone-regulated developmental networks, enabling environmental stimuli to influence the genetically preprogrammed developmental progression. Dependent on the prevailing conditions, adaptation of mature and nascent organs is controlled by HD-Zip I and HD-Zip II transcription factors through suppression or promotion of cell multiplication, differentiation and expansion to regulate targeted growth. In vitro assays have shown that, within family I or family II, homo- and/or heterodimerization between leucine zipper domains is a prerequisite for DNA binding. Further, both families bind similar 9-bp pseudopalindromic cis elements, CAATNATTG, under in vitro conditions. However, the mechanisms that regulate the transcriptional activity of HD-Zip I and HD-Zip II transcription factors in vivo are largely unknown. The in planta implications of these protein-protein associations and the similarities in cis element binding are not clear. © 2011 Australian Centre for Plant Functional Genomics. New Phytologist © 2011 New Phytologist Trust.

Miklavcic S.J.,University of South Australia | Miklavcic S.J.,Australian Center for Plant Functional Genomics | Nyden M.,University of South Australia | Linden J.B.,University of South Australia | Schulz J.,University of South Australia
RSC Advances | Year: 2014

A recent publication [Lindén et al., RSC Adv., 2014, 4, 25063-25066] describing a material with extreme efficiency and selectivity for adsorbing copper opens up the possibility of large scale purification technologies and new materials for prevention of biological growth, both in bulk and on surfaces. On the molecular scale, the material's efficiency and selectivity depends on competitive metal ion diffusion into a nanometer thin polymer film and on competitive binding of metal ions to specific ligand sites. We present and explore two reaction-diffusion models describing the detailed transport and competitive absorption of metal ions in the polymer matrix studied in [Lindén et al., RSC Adv., 2014, 4, 25063-25066]. The diffusive transport of the ions into an interactive, porous polymer layer of finite thickness, supported by an impermeable substrate and in contact with an infinite electrolyte reservoir, is governed by forced diffusion equations, while metal ion binding is modelled by a set of coupled reaction equations. The qualitative behavior observed in experiments can be reproduced and explained in terms of a combination of (a) differing ion diffusive rates and, effectively, (b) an ion exchange process that is superimposed on independent binding processes. The latter's origin is due to conformational changes taking place in the polymer structure in response to the binding of one of the species. The results of simulations under a diverse set of parameter conditions are discussed in relation to experimental observations. © The Royal Society of Chemistry 2014.

DuPont Company, Australian Center For Plant Functional Genomics and DuPont Pioneer | Date: 2013-01-17

Polynucleotide molecules encoding transcription factors, promoter elements, binding partners and methods of use in increasing drought tolerance, yield, and abiotic stress tolerance are disclosed. ERF transcription factors and Cor410b promoter sequences are disclosed.

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