Australian Centre for Plant Functional Genomics publications
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Item Metadata only 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 qualityItem Metadata only Improving crop nitrogen use in dryland farming: interactions and potential trade-offs between water- and nutrient-use efficiency(John Wiley & Sons, 2013) Garnett, T.; Rebetzke, G.; Rengel, Z.Improved nitrogen-use efficiency and water-use efficiency (WUE) of dryland farming crops are important goals for cereal breeders. There have been considerable efforts to improve these traits separately, but now there is an increasing demand for crops with improvement in both of these traits. Analysis of ecological and crop-based experimental data has identified an apparent trade-off between N-use efficiency and WUE, suggesting that the two breeding goals are not compatible. This review summarises the physiology underlying these two traits and the genetic/breeding efforts underway to improve them. It then examines the observed interaction between N-use efficiency and WUE. Understanding the nature of this interaction provides scope to maximise yields in water-limiting environments whilst minimising N losses. Strategies focussing on genetic improvement to improve both traits concurrently are then discussed.Item Metadata only PCIT: an R package for weighted gene co-expression networks based on partial correlation and information theory approaches(Oxford University Press, 2010) Watson-Haigh, N.; Kadarmideen, H.; Reverter, A.Summary: We make the PCIT algorithm, used for detecting meaningful gene–gene associations in co-expression networks, available as an R package. Automatic detection of a suitable parallel environment is used such that scripts are portable between parallel and non-parallel environments with no modification of the script. Availability and implementation: Source code and binaries freely available (under GPL-3) for download via CRAN at http://cran.r-project.org/package=PCIT, implemented in R and supported on Linux and MS Windows.Item Open Access SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments(Oxford University Press, 2012) Ajawatanawong, P.; Atkinson, G.; Watson-Haigh, N.; MacKenzie, B.; Baldauf, S.Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.Item Metadata only Variation at range margins across multiple spatial scales: environmental temperature, population genetics and metabolomic phenotype(The Royal Society, 2009) Kunin, W.; Vergeer, P.; Kenta, T.; Davey, M.; Burke, T.; Woodward, F.; Quick, P.; Mannarelli, M.; Watson-Haigh, N.; Butlin, R.Range margins are spatially complex, with environmental, genetic and phenotypic variations occurring across a range of spatial scales. We examine variation in temperature, genes and metabolomic profiles within and between populations of the subalpine perennial plant Arabidopsis lyrata ssp. petraea from across its northwest European range. Our surveys cover a gradient of fragmentation from largely continuous populations in Iceland, through more fragmented Scandinavian populations, to increasingly widely scattered populations at the range margin in Scotland, Wales and Ireland. Temperature regimes vary substantially within some populations, but within-population variation represents a larger fraction of genetic and especially metabolomic variances. Both physical distance and temperature differences between sites are found to be associated with genetic profiles, but not metabolomic profiles, and no relationship was found between genetic and metabolomic population structures in any region. Genetic similarity between plants within populations is the highest in the fragmented populations at the range margin, but differentiation across space is the highest there as well, suggesting that regional patterns of genetic diversity may be scale dependent.Item Metadata only 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.Item Open Access Pre-conditioning the epigenetic response to high vapor pressure deficit increases the drought tolerance of Arabidopsis thaliana(Taylor & Francis, 2013) Tricker, P.; López, C.R.; Hadley, P.; Wagstaff, C.; Wilkinson, M.Epigenetic modification of the genome via cytosine methylation is a dynamic process that responds to changes in the growing environment. This modification can also be heritable. The combination of both properties means that there is the potential for the life experiences of the parental generation to modify the methylation profiles of their offspring and so potentially to "pre-condition" them to better accommodate abiotic conditions encountered by their parents. We recently identified high vapor pressure deficit (vpd)-induced DNA methylation at 2 gene loci in the stomatal development pathway and an associated reduction in leaf stomatal frequency. (1) Here, we test whether this epigenetic modification pre-conditioned parents and their offspring to the more severe water stress of periodic drought. We found that 3 generations of high vpd-grown plants were better able to withstand periodic drought stress over 2 generations. This resistance was not directly associated with de novo methylation of the target stomata genes, but was associated with the cmt3 mutant's inability to maintain asymmetric sequence context methylation. If our finding applies widely, it could have significant implications for evolutionary biology and breeding for stressful environments.Item Metadata only 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.Item Restricted Metrics on multilabeled trees: interrelationships and diameter bounds(IEEE, 2011) Huber, K.; Spillner, A.; Suchecki, R.; Moulton, V.Multilabeled trees or MUL-trees, for short, are trees whose leaves are labeled by elements of some nonempty finite set X such that more than one leaf may be labeled by the same element of X. This class of trees includes phylogenetic trees and tree shapes. MUL-trees arise naturally in, for example, biogeography and gene evolution studies and also in the area of phylogenetic network reconstruction. In this paper, we introduce novel metrics which may be used to compare MUL-trees, most of which generalize well-known metrics on phylogenetic trees and tree shapes. These metrics can be used, for example, to better understand the space of MUL-trees or to help visualize collections of MUL-trees. In addition, we describe some relationships between the MUL-tree metrics that we present and also give some novel diameter bounds for these metrics. We conclude by briefly discussing some open problems as well as pointing out how MUL-tree metrics may be used to define metrics on the space of phylogenetic networks.Item Metadata only 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.Item Open Access Soil quality and constraints in global rice production(Elsevier Science, 2014) Haefele, S.; Nelson, A.; Hijmans, R.We assessed soil quality in global rice production areas with the Fertility Capability Soil Classification (FCC) system adjusted to match the harmonized world soil database, established by the Food and Agriculture Organization and the International Institute for Applied Systems Analysis. We computed the distribution of 20 soil constraints, and used these to categorize soils as 'good', 'poor', 'very poor', or 'problem soil' for rice production. These data were then combined with data of global rice distribution to determine soil quality in the main rice production systems around the world. Most rice is grown in Asia (143.4. million. ha), followed by Africa (10.5. million. ha) and the Americas (7.2. million. ha). Globally, one-third of the total rice area is grown on very poor soils, which includes 25.6. million. ha of irrigated rice land, 18.5. million. ha in rainfed lowlands, and 7.5. million. ha of upland rice. At least 8.3. million. ha of rice is grown on problem soils, including saline, alkaline/sodic, acid-sulfate, and organic soils. Asia has the largest percentage of rice on good soils (47%) whereas rice production on good soils is much less common in the Americas (28%) and accounts for only 18% in Africa. The most common soil chemical problems in rice fields are very low inherent nutrient status (35.8. million. ha), very low pH (27.1. million. ha), and high P fixation (8.1. million. ha); widespread soil physical problems especially severe in rainfed environments are very shallow soils and low water-holding capacity. The results of the analysis can be used to better target crop improvement research, plant breeding, and the dissemination of stress-specific tolerant varieties and soil management technologies. © 2014 Elsevier B.V.Item Metadata only 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.Item Metadata only Nitrogen use efficiency in selected rice (Oryza sativa L.) genotypes under different water regimes and nitrogen levels(Elsevier Science, 2008) Haefele, S.; Jabbar, S.; Siopongco, J.; Tirol-Padre, A.; Amarante, S.; Sta Cruz, P.; Cosico, W.Water and nutrient availability are two major constraints in most rice-based rainfed shallow lowland systems of Asia. Both stresses interact and contribute to the low productivity and widespread poverty in this environment. The objective of this study was to improve the understanding of interaction between the two factors and to identify varietal characteristics beneficial for productivity in a water- and nutrient-limited rice environment. For this purpose, we screened 19 rice genotypes adapted to different rice environments under two water and two nutrient treatments during the wet season of 2004 and 2005 in southern Luzon, Philippines. Across all genotypes tested and in comparison with the irrigated control, rainfed conditions reduced grain yield of the treatment without N application by 69% in 2004 and by 59% in 2005. The mean nitrogen fertilizer response was highest in the dryer season of 2004 and the rainfed treatment, indicating that water stress had no effect on fertilizer response. Nitrogen application reduced the relative yield loss to 49% of the irrigated treatment in 2004 and to 52% of the irrigated treatment in 2005. Internal efficiency of N (IEN) and recovery efficiency of applied N (REN) were significantly different between genotypes, but were not affected by water availability (REN) or by water and nutrient availability (IEN). In contrast, grain yield and total N uptake were affected by cultivar, N and water availability. Therefore, germplasm for rainfed environments should be screened under conditions of limited and good nitrogen and water supplies. The four best cultivars, CT6510-24-1-2, IR55423-01, IR72, and IR57514-PMI5-B-1-2, performed well across all treatments and both years. Except for IR72, they were all characterized by medium height, medium duration, high early vigor, and a moderate level of drought tolerance. This combination of characteristics seems to enable the optimal use of limited water and nutrient resources occurring in many shallow rainfed lowlands. We also concluded that moderate drought stress does not necessarily affect the response to moderate N rates, provided that drought does not induce high spikelet sterility and that fertilizer N is properly managed.Item Open Access The impact of biochar application on soil properties and plant growth of pot grown lettuce (Lactuca sativa) and cabbage (Brassica chinensis)(MDPI, 2013) Carter, S.; Shackley, S.; Sohi, S.; Suy, T.; Haefele, S.The effect of rice-husk char (potentially biochar) application on the growth of transplanted lettuce (Lactuca sativa) and Chinese cabbage (Brassica chinensis) was assessed in a pot experiment over a three crop (lettuce-cabbage-lettuce) cycle in Cambodia. The biochar was the by-product of a rice-husk gasification unit and consisted of 28.7% carbon (C) by mass. Biochar application rates to potting medium of 25, 50 and 150 g kg−1 were used with and without locally available fertilizers (a mixture of compost, liquid compost and lake sediment). The rice-husk biochar used was slightly alkaline (pH 7.79), increased the pH of the soil, and contained elevated levels of some trace metals and exchangeable cations (K, Ca and Mg) in comparison to the soil. The biochar treatments were found to increase the final biomass, root biomass, plant height and number of leaves in all the cropping cycles in comparison to no biochar treatments. The greatest biomass increase due to biochar additions (903%) was found in the soils without fertilization, rather than fertilized soils (483% with the same biochar application as in the “without fertilization” case). Over the cropping cycles the impact was reduced; a 363% increase in biomass was observed in the third lettuce cycle.Item Open Access Impact of rice nursery nutrient management, seeding density and seedling age on yield and yield attributes(Scientific Research Publishing, 2013) Adhikari, B.; Mehera, B.; Haefele, S.To help farmers in the mid hills of Nepal improve their crop management and rice yields, we conducted a study testing different nursery management options and their effect on grain yield and yield components under rainfed conditions. The experiment was conducted in a farmer’s field during the cropping season 2009 and 2010 at Sundarbazar, Lamjung, Nepal, using a 3-factor factorial RCB design with 3 replications. The three management factors tested were 1) fertilizer management in the nursery, 2) seeding density, and 3) seedling age at transplanting, using the rainfed lowland rice vari-ety Radha-4. There were eight treatment combinations, consisting of two levels of fertilization (0 and 20:20:0:13 kg NPKS ha⁻¹ at 15 DAS), two levels of seeding density (607 and 303 g·m⁻²) and two seedling ages (20 and 40 days old). Two years’ results showed that top-dressed fertilizer in the nursery had no consistent effect on grain yield. However, lower seeding density (303 g·m⁻²) resulted in taller plants, more productive tillers m⁻², less sterility and higher grain yield. In addition, older seedlings (40 days) produced taller plants, more productive tillers, more filled grains, and a higher grain and straw yield. The interaction analysis between both factors indicated that 40 days old seedling with a low seeding density produced the highest grain yield, both in the drought season 2009 and the high-yielding season 2010. The economic analysis confirmed that the treatment with low seeding density and 40 days old seedlings produced by far the highest net returns and B:C ratio in both seasons, independent of the fertilizer treatment. The combination of these two management components is therefore economically viable and profitable, and can be recommended to farm-ers. However, the results need to be confirmed for other varieties used by farmers in the region.Item Open Access Response of salt-tolerant rice varieties to biocompost application in sodic soil of Eastern Uttar Pradesh(Scientific Research Publishing, 2014) Khan, A.H.; Singh, A.K.; Mubeen,; Singh, S.; Zaidi, N.W.; Singh, U.S.; Haefele, S.M.Sodic soils have immense productivity potential, if managed through proper technology interventions. Biocom-post is prepared by composting pressmud (a sugar industry byproduct) received from cane juice filtration and spent wash received from distilleries through microbial aerobic decomposition and can be used to reclaim sodic soils. Field experiments were conducted during the wet season of 2011 and 2012 to study the effect of incorpora-tion of biocompost in sodic soil with four treatments: T1—Control, T2—Biocompost at 2 t ha⁻¹, T3—Biocompost at 4 t ha⁻¹ and T4—Biocompost at 6 t ha⁻¹. The two promising salt tolerant rice varieties preferred by farmers, Narendra usar 3 and NDR 359 were used as test crops, which can produce yields ranging between 2 - 4 t ha⁻¹ in soil having a pH range of 9.2 to 10.5. Among the different doses of biocompost tested, application of biocompost at 6 t ha⁻¹ registered highest yields, enabled by a higher biomass, ear bearing tiller (EBT), and grain fertility in both varieties. Narendra usar 3 was more responsive to treatments even at lower doses of biocompost than NDR 359, but NDR 359 yielded slightly higher than Narendra usar 3 in all treatments. Soil health was also improved evidently on better fertility and low soil pH and EC at harvest. Thus, biocompost can be considered as a com-mercially viable, environmentally acceptable and practically enforceable option for improving the crop produc-tivity and soil fertility status.Item Metadata only Optimization of TaDREB3 gene expression in transgenic barley using cold-inducible promoters(Blackwell Publishing Ltd., 2013) Kovalchuk, N.; Jia, W.; Aini, O.; Morran, S.; Pyvovarenko, T.; Fletcher, S.; Bazanova, N.; Harris, J.; Beck-Oldach, K.; Shavrukov, Y.; Langridge, P.; Lopato, S.; Australian Centre for Plant Functional Genomics (ACPFG)Constitutive over-expression of the TaDREB3 gene in barley improved frost tolerance of transgenic plants at the vegetative stage of plant development, but leads to stunted phenotypes and 3- to 6-week delays in flowering compared to control plants. In this work, two cold-inducible promoters with contrasting properties, the WRKY71 gene promoter from rice and the Cor39 gene promoter from durum wheat, were applied to optimize expression of TaDREB3. The aim of the work was to increase plant frost tolerance and to decrease or prevent negative developmental phenotypes observed during constitutive expression of TaDREB3. The OsWRKY71 and TdCor39 promoters had low-to-moderate basal activity and were activated by cold treatment in leaves, stems and developing spikes of transgenic barley and rice. Expression of the TaDREB3 gene, driven by either of the tested promoters, led to a significant improvement in frost tolerance. The presence of the functional TaDREB3 protein in transgenic plants was confirmed by the detection of strong up-regulation of cold-responsive target genes. The OsWRKY71 promoter-driven TaDREB3 provides stronger activation of the same target genes than the TdCor39 promoter. Analysis of the development of transgenic plants in the absence of stress revealed small or no differences in plant characteristics and grain yield compared with wild-type plants. The WRKY71-TaDREB3 promoter-transgene combination appears to be a promising tool for the enhancement of cold and frost tolerance in crop plants but field evaluation will be needed to confirm that negative development phenotypes have been controlled.Item Metadata only Genetic variation in the root growth response of barley genotypes to salinity stress(C S I R O Publishing, 2013) Shelden, M.; Roessner, U.; Sharp, R.; Tester, M.; Bacic, A.; Australian Centre for Plant Functional Genomics (ACPFG)We aimed to identify genetic variation in root growth in the cereal crop barley (Hordeum vulgare L.) in response to the early phase of salinity stress. Seminal root elongation was examined at various concentrations of salinity in seedlings of eight barley genotypes consisting of a landrace, wild barley and cultivars. Salinity inhibited seminal root elongation in all genotypes, with considerable variation observed between genotypes. Relative root elongation rates were 60–90% and 30–70% of the control rates at 100 and 150 mM NaCl, respectively. The screen identified the wild barley genotype CPI71284–48 as the most tolerant, maintaining root elongation and biomass in response to salinity. Root elongation was most significantly inhibited in the landrace Sahara. Root and shoot Na+ concentrations increased and K+ concentrations decreased in all genotypes in response to salinity. However, the root and shoot ion concentrations did not correlate with root elongation rates, suggesting that the Na+ and K+ concentrations were not directly influencing root growth, at least during the early phase of salt stress. The identification of genetic diversity in root growth responses to salt stress in barley provides important information for future genetic, physiological and biochemical characterisation of mechanisms of salinity tolerance.Item Metadata only 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.Item Metadata only Salt stress or salt shock: which genes are we studying?(Oxford Univ Press, 2013) Shavrukov, Y.; Australian Centre for Plant Functional Genomics (ACPFG)Depending on the method of NaCl application, whether gradual or in a single step, plants may experience either salt stress or salt shock, respectively. The first phase of salt stress is osmotic stress. However, in the event of salt shock, plants suffer osmotic shock, leading to cell plasmolysis and leakage of osmolytes, phenomena that do not occur with osmotic stress. Patterns of gene expression are different in response to salt stress and salt shock. Salt stress initiates relatively smooth changes in gene expression in response to osmotic stress and a more pronounced change in expression of significant numbers of genes related to the ionic phase of salt stress. There is a considerable time delay between changes in expression of genes related to the osmotic and ionic phases of salt stress. In contrast, osmotic shock results in strong, rapid changes in the expression of genes with osmotic function, and fewer changes in ionic-responsive genes that occur earlier. There are very few studies in which the effects of salt stress and salt shock are described in parallel experiments. However, the patterns of changes in gene expression observed in these studies are consistently as described above, despite the use of diverse plant species. It is concluded that gene expression profiles are very different depending the method of salt application. Imposition of salt stress by gradual exposure to NaCl rather than salt shock with a single application of a high concentration of NaCl is recommended for genetic and molecular studies, because this more closely reflects natural incidences of salinity.