Australian Centre for Plant Functional Genomics publications

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A GRASP-based approach for the Pure Parsimony Haplotype Inference problem
(IEEE, 2010) Suchecki, R.; Chardaire, P.; Huber, K.; 2nd Computer Science and Electronic Engineering Conference (8 Sep 2014 - 9 Sep 2014 : Colchester, UK)
The availability and study of haplotype data is of considerable interest to a wide range of areas including general health care, personalized medicine, and pharmacogenetics. The inner workings of contemporary sequencing techniques however imply that genotype data is generated from a chromosome rather than haplotype data. The reconstruction of the latter from this kind of data lies at the heart of the well studied Pure Parsimony Haplotype Inference problem (PPHI). In this paper, we present a proof of concept that a GRASP-based approach for solving PPHI has the potential of yielding an attractive tool that complements existing approaches. The usage of this strategy for solving PPHI is novel. To assess its suitability, we have implemented it in basic form in the novel and freely available HAPLOGRASP approach which we assessed in terms of simulated and real data. Our findings are highly encouraging.
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A practical algorithm for reconstructing level-1 phylogenetic networks
(IEEE, 2011) Huber, K.T.; van Iersel, L.; Kelk, S.; Suchecki, R.
Recently, much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks-a type of network slightly more general than a phylogenetic tree-from triplets. Our algorithm has been made publicly available as the program Lev1athan. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponential-time exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, Lev1athan runs in polynomial time and always constructs a level-1 network. If the data are consistent with a phylogenetic tree, then the algorithm constructs such a tree. Moreover, if the input triplet set is dense and, in addition, is fully consistent with some level-1 network, it will find such a network. The potential of Lev1athan is explored by means of an extensive simulation study and a biological data set. One of our conclusions is that Lev1athan is able to construct networks consistent with a high percentage of input triplets, even when these input triplets are affected by a low to moderate level of noise.
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Actinobacterial endophytes for improved crop performance
(C S I R O Publishing, 2007) Franco, C.; Michelsen, P.; Percy, N.; Conn, V.; Listiana, E.; Moll, S.; Loria, R.; Coombs, J.; Australian Centre for Plant Functional Genomics (ACPFG)
Increasing numbers of endophytic bacteria are being isolated and identified revealing a rich vein of microbial interaction within a variety of crop plants. In addition, cultivation-independent studies have exposed a broader diversity, with many of the species belonging to culturable genera. Microscopic evidence of endophytic colonisation has been shown in some cases, proving ‘true’ endophytic status and providing an understanding of how these microorganisms gain entry and deploy through their host.
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Al-induced efflux of organic acid anions is poorly associated with internal organic acid metabolism in triticale roots
(Oxford Univ Press, 2003) Hayes, J.; Ma, J.; Australian Centre for Plant Functional Genomics (ACPFG)
The secretion of organic acid anions from roots has been identi®ed as a mechanism of resistance to Al. However, the process leading to the secretion of organic acid anions is poorly understood. The effect of Al on organic acid metabolism was investigated in two lines of triticale (X Triticosecale Wittmark) differing in Al-induced secretion of malate and citrate and in Al resistance. The site of Al-induced secretion of citrate and malate from a resistant line was localized to the root apices (terminal 5 mm). The levels of citrate (root apices and mature root segments) and malate (mature segments only) in roots increased during exposure to Al, but similar changes were observed in both triticale genotypes. The in vitro activities of four enzymes involved in malate and citrate metabolism (citrate synthase, phosphoenolpyruvate carboxylase, malate dehydrogenase, and NADP-isocitrate dehydrogenase) were similar for sensitive and resistant lines in both root apices and mature root segments. The response of these enzymes to pH did not differ between tolerant and sensitive lines or in the presence and absence of Al. Moreover, cytoplasmic and vacuolar pH were not affected by exposure to Al in either line. Together, these results indicate that the Aldependent ef¯ux of organic acid anions from the roots of triticale is not regulated by their internal levels in the roots or by the capacity of the root cells to synthesize malate and citrate.
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An atlas of gene expression from seed to seed through barley development
(Springer-Verlag, 2006) Druka, A.; Muehlbauer, G.; Druka, I.; Caldo, R.; Baumann, U.; Rostoks, N.; Schreiber, A.; Wise, R.; Close, T.; Kleinhofs, A.; Graner, A.; Schulman, A.; Langridge, P.; Sato, K.; Hayes, P.; McNicol, J.; Marshall, D.; Waugh, R.
Assaying relative and absolute levels of gene expression in a diverse series of tissues is a central step in the process of characterizing gene function and a necessary component of almost all publications describing individual genes or gene family members. However, throughout the literature, such studies lack consistency in genotype, tissues analyzed, and growth conditions applied, and, as a result, the body of information that is currently assembled is fragmented and difficult to compare between different studies. The development of a comprehensive platform for assaying gene expression that is available to the entire research community provides a major opportunity to assess whole biological systems in a single experiment. It also integrates detailed knowledge and information on individual genes into a unified framework that provides both context and resource to explore their contributions in a broader biological system. We have established a data set that describes the expression of 21,439 barley genes in 15 tissues sampled throughout the development of the barley cv. Morex grown under highly controlled conditions. Rather than attempting to address a specific biological question, our experiment was designed to provide a reference gene expression data set for barley researchers; a gene expression atlas and a comparative data set for those investigating genes or regulatory networks in other plant species. In this paper we describe the tissues sampled and their transcriptomes, and provide summary information on genes that are either specifically expressed in certain tissues or show correlated expression patterns across all 15 tissue samples. Using specific examples and an online tutorial, we describe how the data set can be interrogated for patterns and levels of barley gene expression and how the resulting information can be used to generate and/or test specific biological hypotheses.
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Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by Terminal Restriction Fragment Length Polymorphism (T-RFLP) and sequencing of 16S rRNA clones
(Amer Soc Microbiology, 2004) Conn, V.; Franco, C.; Australian Centre for Plant Functional Genomics (ACPFG)
The endophytic actinobacterial population in the roots of wheat grown in three different soils obtained from the southeast part of South Australia was investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of the amplified 16S rRNA genes. A new, validated approach was applied to the T-RFLP analysis in order to estimate, to the genus level, the actinobacterial population that was identified. Actinobacterium-biased primers were used together with three restriction enzymes to obtain terminal restriction fragments (TRFs). The TRFs were matched to bacterial genera by the T-RFLP Analysis Program, and the data were analyzed to validate and semiquantify the genera present within the plant roots. The highest diversity and level of endophytic colonization were found in the roots of wheat grown in a dark loam from Swedes Flat, and the lowest were found in water-repellent sand from Western Flat. This molecular approach detected a greater diversity of actinobacteria than did previous culture-dependent methods, with the predominant genera being Mycobacterium (21.02%) in Swedes Flat, Streptomyces (14.35%) in Red Loam, and Kitasatospora (15.02%) in Western Flat. This study indicates that the soil that supported a higher number of indigenous organisms resulted in wheat roots with higher actinobacterial diversity and levels of colonization within the plant tissue. Sequencing of 16S rRNA clones, obtained using the same actinobacterium-biased PCR primers that were used in the T-RFLP analysis, confirmed the presence of the actinobacterial diversity and identified a number of Mycobacterium and Streptomyces species.
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Boron tolerance in barley is mediated by efflux of boron from the roots
(Amer Soc Plant Physiologists, 2004) Hayes, J.; Reid, R.
Many plants are known to reduce the toxic effects of high soil boron (B) by reducing uptake of B, but no mechanism for limiting uptake has previously been identified. The B-tolerant cultivar of barley (Hordeum vulgare L.), Sahara, was shown to be able to maintain root B concentrations up to 50% lower than in the B-sensitive cultivar, Schooner. This translated into xylem concentrations that were approximately 64% lower and leaf concentrations 73% lower in the tolerant cultivar. In both cultivars, B accumulation was rapid and reached a steady-state concentration in roots within 3 h. In Schooner, this concentration was similar to the external medium, whereas in Sahara, the root concentration was maintained at a lower concentration. For this to occur, B must be actively extruded from the root in Sahara, and this is presumed to be the basis for B tolerance in barley. The extrusion mechanism was inhibited by sodium azide but not by treatment at low temperature. Several anion channel inhibitors were also effective in limiting extrusion, but it was not clear whether they acted directly or via metabolic inhibition. The ability of Sahara to maintain lower root B concentrations was constitutive and occurred across a wide range of B concentrations. This ability was lost at high pH, and both Schooner and Sahara then had similar root B concentrations. A predictive model that is consistent with the empirical results and explains the tolerance mechanism based on the presence of a borate anion efflux transporter in Sahara is presented.
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Boron toxicity tolerance in barley arising from efflux transporter amplification
(Amer Assoc Advancement Science, 2007) Sutton, T.; Baumann, U.; Hayes, J.; Collins, N.; Shi, B.; Schnurbusch, T.; Hay, A.; Mayo, G.; Pallotta, M.; Tester, M.; Langridge, P.; Australian Centre for Plant Functional Genomics (ACPFG)
Both limiting and toxic soil concentrations of the essential micronutrient boron represent major limitations to crop production worldwide. We identified Bot1, a BOR1 ortholog, as the gene responsible for the superior boron-toxicity tolerance of the Algerian barley landrace Sahara 3771 (Sahara). Bot1 was located at the tolerance locus by high-resolution mapping. Compared to intolerant genotypes, Sahara contains about four times as many Bot1 gene copies, produces substantially more Bot1 transcript, and encodes a Bot1 protein with a higher capacity to provide tolerance in yeast. Bot1 transcript levels identified in barley tissues are consistent with a role in limiting the net entry of boron into the root and in the disposal of boron from leaves via hydathode guttation.
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Building gene co-expression networks using transcriptomics data for systems biology investigations: comparison of methods using microarray data
(Biomedical Informatics, 2012) Kadarmideen, H.; Watson-Haigh, N.
Gene co-expression networks (GCN), built using high-throughput gene expression data are fundamental aspects of systems biology. The main aims of this study were to compare two popular approaches to building and analysing GCN. We use real ovine microarray transcriptomics datasets representing four different treatments with Metyrapone, an inhibitor of cortisol biosynthesis. We conducted several microarray quality control checks before applying GCN methods to filtered datasets. Then we compared the outputs of two methods using connectivity as a criterion, as it measures how well a node (gene) is connected within a network. The two GCN construction methods used were, Weighted Gene Co-expression Network Analysis (WGCNA) and Partial Correlation and Information Theory (PCIT) methods. Nodes were ranked based on their connectivity measures in each of the four different networks created by WGCNA and PCIT and node ranks in two methods were compared to identify those nodes which are highly differentially ranked (HDR). A total of 1,017 HDR nodes were identified across one or more of four networks. We investigated HDR nodes by gene enrichment analyses in relation to their biological relevance to phenotypes. We observed that, in contrast to WGCNA method, PCIT algorithm removes many of the edges of the most highly interconnected nodes. Removal of edges of most highly connected nodes or hub genes will have consequences for downstream analyses and biological interpretations. In general, for large GCN construction (with > 20000 genes) access to large computer clusters, particularly those with larger amounts of shared memory is recommended.
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Cell wall modifications in maize pulvini in response to gravitational stress
(Amer Soc Plant Physiologists, 2011) Zhang, Q.; Pettolino, F.; Dhugga, K.; Rafalski, J.; Tingey, S.; Taylor, J.; Shirley, N.; Hayes, K.; Beatty, M.; Abrams, S.; Zaharia, L.; Burton, R.; Bacic, A.; Fincher, G.; Australian Centre for Plant Functional Genomics (ACPFG)
Changes in cell wall polysaccharides, transcript abundance, metabolite profiles, and hormone concentrations were monitored in the upper and lower regions of maize (Zea mays) pulvini in response to gravistimulation, during which maize plants placed in a horizontal position returned to the vertical orientation. Heteroxylan levels increased in the lower regions of the pulvini, together with lignin, but xyloglucans and heteromannan contents decreased. The degree of substitution of heteroxylan with arabinofuranosyl residues decreased in the lower pulvini, which exhibited increased mechanical strength as the plants returned to the vertical position. Few or no changes in noncellulosic wall polysaccharides could be detected on the upper side of the pulvinus, and crystalline cellulose content remained essentially constant in both the upper and lower pulvinus. Microarray analyses showed that spatial and temporal changes in transcript profiles were consistent with the changes in wall composition that were observed in the lower regions of the pulvinus. In addition, the microarray analyses indicated that metabolic pathways leading to the biosynthesis of phytohormones were differentially activated in the upper and lower regions of the pulvinus in response to gravistimulation. Metabolite profiles and measured hormone concentrations were consistent with the microarray data, insofar as auxin, physiologically active gibberellic acid, and metabolites potentially involved in lignin biosynthesis increased in the elongating cells of the lower pulvinus.
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Characterization of the wheat gene encoding a grain-specific lipid transfer protein TdPR61, and promoter activity in wheat, barley and rice
(Oxford Univ Press, 2012) Kovalchuk, N.; Gilson, J.; Bazanova, N.; Pyvovarenko, T.; Singh, R.; Shirley, N.; Ismagul, A.; Johnson, A.; Milligan, A.; Hrmova, M.; Langridge, P.; Lopato, S.; Australian Centre for Plant Functional Genomics (ACPFG)
The TaPR61 gene from bread wheat encodes a lipid transfer protein (LTP) with a hydrophobic signal peptide, predicted to direct the TaPR61 protein to the apoplast. Modelling of TaPR61 revealed the presence of an internal cavity which can accommodate at least two lipid molecules. The full-length gene, including the promoter sequence of a TaPR61 orthologue, was cloned from a BAC library of Triticum durum. Quantitative RT-PCR analysis revealed the presence of TaPR61 and TdPR61 mainly in grain. A transcriptional TdPR61 promoter-GUS fusion was stably transformed into wheat, barley, and rice. The strongest GUS expression in all three plants was found in the endosperm transfer cells, the embryo surrounding region (ESR), and in the embryo. The promoter is strong and has similar but not identical spatial patterns of activity in wheat, barley, and rice. These results suggest that the TdPR61 promoter will be a useful tool for improving grain quality by manipulating the quality and quantity of nutrient/lipid uptake to the endosperm and embryo. Mapping of regions important for the promoter function using transient expression assays in developing embryos resulted in the identification of two segments important for promoter activation in embryos. The putative cis-elements from the distal segment were used as bait in a yeast 1-hybrid (Y1H) screen of a cDNA library prepared from the liquid part of the wheat multinucleate syncytium. A transcription factor isolated in the screen is similar to BES1/BLZ1 from Arabidopsis, which is known to be a key transcriptional regulator of the brassinosteroid signalling pathway.
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Computing a consensus of multilabeled trees
(Society for Industrial and Applied Mathematics, 2012) Huber, K.; Moulton, V.; Spillner, A.; Suchecki, R.; 14th Meeting on Algorithm Engineering and Experiments 2012 (ALENEX12) (16 Jan 2012 - 16 Jan 2012 : Kyoto, Japan); Bader, D.A.; Mutzel, P.
In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential runtime in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance. Copyright © SIAM.
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Cytological investigations of the Arabidopsis thaliana elo1 mutant give new insights into leaf lateral growth and Elongator function
(Oxford Univ Press, 2007) Falcone, A.; Nelissen, H.; Fleury, D.; Van Lijsebettens, M.; Bitoni, M.; Australian Centre for Plant Functional Genomics (ACPFG)
Background and Aims: Leaf growth is a complex developmental process controlled by genetic and environmental factors and is determined by a proliferation, expansion and maturation phase. Mutational analysis in Arabidopsis thaliana showed that leaf size and shape is dependent on cell division and cell expansion activity. An investigation was made at the cytophysiological and ultrastructural level of the elo1 mutant of Arabidopsis thaliana, which is defective in one of the components of the histone acetyl transferase Elongator complex and displays a distinct ‘narrow leaves’ phenotype, owing to a reduced cell number and no transition between petiole and lamina. Relative expression levels of three sucrose metabolism/transport-related genes were also investigated. The aim was to determine the physiological basis of leaf morphology in this mutant, by investigating the modulatory role of sucrose. Methods: The elo1 mutant was taken as representative of all the elo mutations and investigated at cytophysiological level. A germination test and growth assays were performed on seedlings grown for 21 d at different sucrose concentrations. Leaf morphometric and ultrastructural features were also investigated by image analysis and electron microscopy, respectively. Finally, a quantitative PCR (qPCR) analysis was performed with three sucrose metabolism/transport-related genes that were investigated under different sucrose concentrations. Key Results elo1: plants at high sucrose concentrations exhibited an enhancement of germination and inhibition of leaf growth as compared with wild-type plants. qPCR experiments with three sucrose metabolism/transport-related genes showed an interaction between sucrose availability and the elo1 mutation. Furthermore, electron microscopy analysis provided the first ultrastructural description of an elo mutant, which showed a hypotonic vacuole, alterations in the size of grana and starch grains in the chloroplasts, and the massive presence of Golgi vesicles in the cytoplasm. Conclusions: Based on the results obtained it is proposed that mechanisms producing carbon assimilates or importing sucrose could be affected in elo1 plants and could account for the observed differences, implying a role for Elongator in the regulation of these processes.
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Dispersion and domestication shaped the genome of bread wheat
(Blackwell Publishing Ltd., 2013) Berkman, P.; Visendi, P.; Lee, H.; Stiller, J.; Manoli, S.; Lorenc, M.; Lai, K.; Batley, J.; Fleury, D.; Simkova, H.; Kubalakova, M.; Weining, S.; Dolezel, J.; Edwards, D.; Australian Centre for Plant Functional Genomics (ACPFG)
Despite the international significance of wheat, its large and complex genome hinders genome sequencing efforts. To assess the impact of selection on this genome, we have assembled genomic regions representing genes for chromosomes 7A, 7B and 7D. We demonstrate that the dispersion of wheat to new environments has shaped the modern wheat genome. Most genes are conserved between the three homoeologous chromosomes. We found differential gene loss that supports current theories on the evolution of wheat, with greater loss observed in the A and B genomes compared with the D. Analysis of intervarietal polymorphisms identified fewer polymorphisms in the D genome, supporting the hypothesis of early gene flow between the tetraploid and hexaploid. The enrichment for genes on the D genome that confer environmental adaptation may be associated with dispersion following wheat domestication. Our results demonstrate the value of applying next-generation sequencing technologies to assemble gene-rich regions of complex genomes and investigate polyploid genome evolution. We anticipate the genome-wide application of this reduced-complexity syntenic assembly approach will accelerate crop improvement efforts not only in wheat, but also in other polyploid crops of significance.
Open Access
Endo-(1,4)-β-Glucanase gene families in the grasses: temporal and spatial Co-transcription of orthologous genes
(BioMed Central Ltd., 2012) Buchanan, M.; Burton, R.; Dhugga, K.; Rafalski, A.; Tingey, S.; Shirley, N.; Fincher, G.; Australian Centre for Plant Functional Genomics (ACPFG)
BACKGROUND Endo-(1,4)-β-glucanase (cellulase) glycosyl hydrolase GH9 enzymes have been implicated in several aspects of cell wall metabolism in higher plants, including cellulose biosynthesis and degradation, modification of other wall polysaccharides that contain contiguous (1,4)-β-glucosyl residues, and wall loosening during cell elongation. RESULTS The endo-(1,4)-β-glucanase gene families from barley (Hordeum vulgare), maize (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa) and Brachypodium (Brachypodium distachyon) range in size from 23 to 29 members. Phylogenetic analyses show variations in clade structure between the grasses and Arabidopsis, and indicate differential gene loss and gain during evolution. Map positions and comparative studies of gene structures allow orthologous genes in the five species to be identified and synteny between the grasses is found to be high. It is also possible to differentiate between homoeologues resulting from ancient polyploidizations of the maize genome. Transcript analyses using microarray, massively parallel signature sequencing and quantitative PCR data for barley, rice and maize indicate that certain members of the endo-(1,4)-β-glucanase gene family are transcribed across a wide range of tissues, while others are specifically transcribed in particular tissues. There are strong correlations between transcript levels of several members of the endo-(1,4)-β-glucanase family and the data suggest that evolutionary conservation of transcription exists between orthologues across the grass family. There are also strong correlations between certain members of the endo-(1,4)-β-glucanase family and other genes known to be involved in cell wall loosening and cell expansion, such as expansins and xyloglucan endotransglycosylases. CONCLUSIONS The identification of these groups of genes will now allow us to test hypotheses regarding their functions and joint participation in wall synthesis, re-modelling and degradation, together with their potential role in lignocellulose conversion during biofuel production from grasses and cereal crop residues.
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Endophytic Actinobacteria Induce Defense Pathways in Arabidopsis thaliana
(Amer Phytopathological Soc, 2008) Conn, V.; Walker, A.; Franco, C.; Australian Centre for Plant Functional Genomics (ACPFG)
Endophytic actinobacteria, isolated from healthy wheat tissue, which are capable of suppressing a number wheat fungal pathogens both in vitro and in planta, were investigated for the ability to activate key genes in the systemic acquired resistance (SAR) or the jasmonate/ethylene (JA/ET) pathways in Arabidopsis thaliana. Inoculation of A. thaliana (Col-0) with selected endophytic strains induced a low level of SAR and JA/ET gene expression, measured using quantitative polymerase chain reaction. Upon pathogen challenge, endophyte-treated plants demonstrated a higher abundance of defense gene expression compared with the non-endophyte- treated controls. Resistance to the bacterial pathogen Erwinia carotovora subsp. carotovora required the JA/ET pathway. On the other hand, resistance to the fungal pathogen Fusarium oxysporum involved primarily the SAR pathway. The endophytic actinobacteria appear to be able to “prime” both the SAR and JA/ET pathways, upregulating genes in either pathway depending on the infecting pathogen. Culture filtrates of the endophytic actinobacteria were investigated for the ability to also activate defense pathways. The culture filtrate of Micromonospora sp. strain EN43 grown in a minimal medium resulted in the induction of the SAR pathway; however, when grown in a complex medium, the JA/ET pathway was activated. Further analysis using Streptomyces sp. strain EN27 and defense-compromised mutants of A. thaliana indicated that resistance to E. carotovora subsp. carotovora occurred via an NPR1-independent pathway and required salicylic acid whereas the JA/ET signaling molecules were not essential. In contrast, resistance to F. oxysporum mediated by Streptomyces sp. strain EN27 occurred via an NPR1-dependent pathway but also required salicylic acid and was JA/ET independent.
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Expression of phytase in plants as a method of modifying plant productivity
(2001) Richardson, A.; Hayes, J.; Simpson, R.; Australian Centre for Plant Functional Genomics (ACPFG); Australian Centre for Plant Functional Genomics (ACPFG)
The present invention provides a method of modifying plant productivity comprising expressing in a plant cell, tissue or organ one or more genes capable of facilitating a plant's ability to utilise soil phosphorus, and, in particular, a phytase gene, wherein said phytase gene expresses a phytase polypeptide in secretable form. More particularly, the present invention provides a method of increasing plant productivity comprising expressing in the root of a plant an isolated nucleic acid molecule encoding a phytase polypeptide for a time and under conditions sufficient for said phytase to be secreted from the root. In a preferred embodiment of the invention the chemistry of the soil around the root is modified by the application of an organic acid. The invention also provides novel phytase-encoding genes; genetic constructs which are useful for performing the inventive method; and transgenic plants produced therewith having improved productivity compared to their otherwise isogenic counterparts.
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Extracellular secretion of Aspergillus phytase from Arabidopsis roots enables plants to obtain phosphorus from phytate
(Blackwell Publishing Ltd, 2001) Richardson, A.; Hadobas, P.; Hayes, J.; Australian Centre for Plant Functional Genomics (ACPFG)
Phosphorus (P) deficiency in soil is a major constraint for agricultural production worldwide. Despite this, most soils contain significant amounts of total soil P that occurs in inorganic and organic fractions and accumulates with phosphorus fertilization. A major component of soil organic phosphorus occurs as phytate. We show that when grown in agar under sterile conditions, Arabidopsis thaliana plants are able to obtain phosphorus from a range of organic phosphorus substrates that would be expected to occur in soil, but have only limited ability to obtain phosphorus directly from phytate. In wild-type plants, phytase constituted less than 0.8% of the total acid phosphomonoesterase activity of root extracts and was not detectable as an extracellular enzyme. By comparison, the growth and phosphorus nutrition of Arabidopsis plants supplied with phytate was improved significantly when the phytase gene (phyA) from Aspergillus niger was introduced. The Aspergillus phytase was only effective when secreted as an extracellular enzyme by inclusion of the signal peptide sequence from the carrot extensin (ex) gene. A 20-fold increase in total root phytase activity in transgenic lines expressing ex::phyA resulted in improved phosphorus nutrition, such that the growth and phosphorus content of the plants was equivalent to control plants supplied with inorganic phosphate. These results show that extracellular phytase activity of plant roots is a significant factor in the utilization of phosphorus from phytate and indicate that opportunity exists for using gene technology to improve the ability of plants to utilize accumulated forms of soil organic phosphorus.
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Functional genomics of seed development in cereals
(Springer, 2013) Li, M.; Lopato, S.; Kovalchuk, N.; Langridge, P.; Gupta, P.; Varshney, R.
Seeds are the product of sexual reproduction in flowering plants. The seeds of cereals are the main source of staple food, animal feed and the raw material of food and fiber-based industries worldwide (Olsen 2001). More recently, cereal seeds have also been used as a source of starch for the production of biofuels, although this use has become controversial (Fischer et al. 2009). New strategies for raising grain production have become a high international priority to help feed a growing world population in a scenario where resources are limiting and climate variability is increasing (Tester and Langridge 2010). Abiotic and biotic stresses such as drought, frost/cold, salt, micronutrient-deficiency, heavy metal toxicity and damage caused by microbes and pests can lead to dramatic yield loss and have a great impact on seed quality
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Genetic and molecular characterization of the maize rp3 rust resistance locus
(Genetics, 2002) Webb, C.; Richter, T.; Collins, N.; Nicolas, M.; Trick,, H.; Pryor, A.; Hulbert, S.
In maize, the Rp3 gene confers resistance to common rust caused by Puccinia sorghi. Flanking marker analysis of rust-susceptible rp3 variants suggested that most of them arose via unequal crossing over, indicating that rp3 is a complex locus like rp1. The PIC13 probe identifies a nucleotide binding site-leucine-rich repeat (NBS-LRR) gene family that maps to the complex. Rp3 variants show losses of PIC13 family members relative to the resistant parents when probed with PIC13, indicating that the Rp3 gene is a member of this family. Gel blots and sequence analysis suggest that at least 9 family members are at the locus in most Rp3-carrying lines and that at least 5 of these are transcribed in the Rp3-A haplotype. The coding regions of 14 family members, isolated from three different Rp3-carrying haplotypes, had DNA sequence identities from 93 to 99%. Partial sequencing of clones of a BAC contig spanning the rp3 locus in the maize inbred line B73 identified five different PIC13 paralogues in a region of ~140 kb.

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