Identification of novel stress-responsive biomarkers from gene expression datasets in tomato roots

Published by CSIRO Publishing. This is the Author Accepted Manuscript. This article may be used for personal use only.Abiotic stresses such as heat, drought or salinity have been widely studied individually. Nevertheless, in the nature and in the field, plants and crops are commonly exposed to a different combination of stresses, which often result in a synergistic response mediated by the activation of several molecular pathways that cannot be inferred from the response to each individual stress. By screening microarray data obtained from different plant species and under different stresses, we identified several conserved stress-responsive genes whose expression was differentially regulated in tomato (Solanum lycopersicum L.) roots in response to one or several stresses. We validated 10 of these genes as reliable biomarkers whose expression levels are related to different signalling pathways involved in adaptive stress responses. In addition, the genes identified in this work could be used as general salt-stress biomarkers to rapidly evaluate the response of salt-tolerant cultivars and wild species for which sufficient genetic information is not yet available

Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence.

Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation

EDISA: extracting biclusters from multiple time-series of gene expression profiles

<p>Abstract</p> <p>Background</p> <p>Cells dynamically adapt their gene expression patterns in response to various stimuli. This response is orchestrated into a number of gene expression modules consisting of co-regulated genes. A growing pool of publicly available microarray datasets allows the identification of modules by monitoring expression changes over time. These time-series datasets can be searched for gene expression modules by one of the many clustering methods published to date. For an integrative analysis, several time-series datasets can be joined into a three-dimensional <it>gene-condition-time </it>dataset, to which standard clustering or biclustering methods are, however, not applicable. We thus devise a probabilistic clustering algorithm for <it>gene-condition-time </it>datasets.</p> <p>Results</p> <p>In this work, we present the EDISA (Extended Dimension Iterative Signature Algorithm), a novel probabilistic clustering approach for 3D <it>gene-condition-time </it>datasets. Based on mathematical definitions of gene expression modules, the EDISA samples initial modules from the dataset which are then refined by removing genes and conditions until they comply with the module definition. A subsequent extension step ensures gene and condition maximality. We applied the algorithm to a synthetic dataset and were able to successfully recover the implanted modules over a range of background noise intensities. Analysis of microarray datasets has lead us to define three biologically relevant module types: 1) We found modules with independent response profiles to be the most prevalent ones. These modules comprise genes which are co-regulated under several conditions, yet with a different response pattern under each condition. 2) Coherent modules with similar responses under all conditions occurred frequently, too, and were often contained within these modules. 3) A third module type, which covers a response specific to a single condition was also detected, but rarely. All of these modules are essentially different types of biclusters.</p> <p>Conclusion</p> <p>We successfully applied the EDISA to different 3D datasets. While previous studies were mostly aimed at detecting coherent modules only, our results show that coherent responses are often part of a more general module type with independent response profiles under different conditions. Our approach thus allows for a more comprehensive view of the gene expression response. After subsequent analysis of the resulting modules, the EDISA helped to shed light on the global organization of transcriptional control. An implementation of the algorithm is available at http://www-ra.informatik.uni-tuebingen.de/software/IAGEN/.</p

Applications of Molecular Biology and Genomics to Genetic Enhancement of Crop Tolerance to Abiotic Stress : a Discussion Document

The discussions on abiotic stress genomics were initiated at TAC 80 in March 2000 at ICARDA, Aleppo, Syria. Under the agenda item Trends in Science: Implications for CGIAR, TAC discussed the opportunities offered by the new sciences in improving the relevance, quality and impact of research in the CGIAR. In the area of biological sciences, TAC considered that the advances in molecular biology had important long-term implications for CGIAR’s work on genetic enhancement and how that work could be organized in the future. This paper contains three reports: 1. The report by Mike Gale dated August 2002 where he states that it is an appropriate time to tackle abiotic stress head-on, given the motivation already in place, the experience of the ARIs in technology and model systems, the knowledge among the NARS plant breeders on stressed agricultural environments, and the CGIAR Centres’ comparative advantage over mandate crops along with their links to the developing world as well as to industry.2. The report entitled "Status of Breeding for Telerance of Abiotic Stresses and Prospects for Use of Molecular Techniques" by John Bennett dated March 2001. He states that the CGIAR Centers have a comparative advantage in many aspects of abiotic stress research because of their germplasm collections, their new capacity for genetic and molecular dissection of complex traits, and their ability to conduct multidisciplinary plant improvement programs in target environments. The combined resources of the CGIAR for this work are immense but are underutilized. Investment by the CGIAR in the new tools for gene discovery will produce breakthroughs in our understanding of abiotic stress tolerance that will benefit all the mandated crops.3. The report by Hirofumi Uchimiya dated September 2001 entitled "Genetic Engineering for Abiotic Stress Tolerance in Plants"

Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily

The completion of the grape genome sequencing project has paved the way for novel gene discovery and functional analysis. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD(P)(+)-dependent enzymes that catalyze the irreversible oxidation of a wide range of endogenous and exogenous aromatic and aliphatic aldehydes. Although ALDHs have been systematically investigated in several plant species including Arabidopsis and rice, our knowledge concerning the ALDH genes, their evolutionary relationship and expression patterns in grape has been limited.A total of 23 ALDH genes were identified in the grape genome and grouped into ten families according to the unified nomenclature system developed by the ALDH Gene Nomenclature Committee (AGNC). Members within the same grape ALDH families possess nearly identical exon-intron structures. Evolutionary analysis indicates that both segmental and tandem duplication events have contributed significantly to the expansion of grape ALDH genes. Phylogenetic analysis of ALDH protein sequences from seven plant species indicates that grape ALDHs are more closely related to those of Arabidopsis. In addition, synteny analysis between grape and Arabidopsis shows that homologs of a number of grape ALDHs are found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the speciation of the grape and Arabidopsis. Microarray gene expression analysis revealed large number of grape ALDH genes responsive to drought or salt stress. Furthermore, we found a number of ALDH genes showed significantly changed expressions in responses to infection with different pathogens and during grape berry development, suggesting novel roles of ALDH genes in plant-pathogen interactions and berry development.The genome-wide identification, evolutionary and expression analysis of grape ALDH genes should facilitate research in this gene family and provide new insights regarding their evolution history and functional roles in plant stress tolerance

Stressztoleranciát biztosító gének azonosítása a halofita Lepidium crassifolium-ból

Extreme environmental conditions limit plant growth and impose abiotic stress to plants. Land degradation, including desertification, drought and salinity affects around one third of the global land surface (Jarraud 2005). Adaptation of plants to suboptimal conditions requires extensive physiological and molecular reprogramming, leading to major changes in metabolic, proteomic and transcript profiles. Research on model organisms such as Arabidopsis thaliana and application of system biology approaches has identified a number of genes and regulatory hubs which control the networks linking stress perception and metabolic or developmental responses (Ahuja et al. 2010). However, study of a stress sensitive model has limitations in understanding tolerance to harsh environments. Extremophile plants, such as xerophytes and halophytes can grow in arid regions or on saline soils, which are otherwise lethal to nonadapted species. Halophytes represent 1% of all plant species; can optimally thrive in the presence of 50–250mM NaCl, whilst some withstand salt concentrations up to 600mM NaCl (Flowers and Colmer 2008). While the physiology of halophytes has been extensively studied, molecular regulation of the extremophile character still remains to be understood. Eutrema salsugineum (previously called Thellungiella salsuginea) is a salt tolerant relative of Arabidopsis, which has been used in a number of comparative studies to reveal the genetic and molecular basis of halophytism (Amtmann 2009). Natural genetic variability of extremophiles is an attractive genetic resource to improve tolerance of crops to adverse environments (Nevo and Chen 2010). Transfer of tolerance traits to other species is however usually hampered by incompatibility. Transformation of genomic or cDNA libraries can facilitate random gene transfer between different species. Examples include a cDNA library of E. salsugineum, expressed in Arabidopsis, leading to the identification of several Eutrema genes which improved salt tolerance (Du et al. 2008). A binary bacterial artificial chromosome library was used to transfer large genomic fragments of E. salsugineum to Arabidopsis and screen for salt tolerance (Wang et al. 2010). Here, we describe the novel version of the Conditional cDNA Overexpressing System (COS), which was developed to randomly transfer and express cDNA clones in Arabidopsis under the control of a chemically inducible promoter system (Papdi et al. 2008; Rigó et al. 2012). The cDNA library was derived from the less-known halophyte of the Brassicaceae family Lepidium crassifolium, which naturally grows on salty-sodic soils in Central Europe and Asia. Random transfer and overexpression of L. crassifolium cDNA in Arabidopsis could facilitate the identification of novel tolerance genes. Here, we demonstrate that regulated expression of several L. crassifolium cDNA could enhance salt, osmotic or oxidative stress tolerance of Arabidopsis. The COS system is therefore suitable for interspecific gene transfer and can be employed to identify valuable genes from less-known wild species

A strategy for the identification of new abiotic stress determinants in arabidopsis using web-based data mining and reverse genetics

Since the sequencing of the Arabidopsis thaliana genome in 2000, plant researchers have faced the complex challenge of assigning function to thousands of genes. Functional discovery by in silico prediction or homology search resolved a significant number of genes, but only a minor part has been experimentally validated. Arabidopsis entry into the post-genomic era signified a massive increase in high-throughput approaches to functional discovery, which have since become available through publicly-available web-based resources. The present work focuses on an easy and straightforward strategy that couples data-mining to reverse genetics principles, to allow for the identification of new abiotic stress determinant genes. The strategy explores systematic microarray-based transcriptomics experiments, involving Arabidopsis abiotic stress responses. An overview of the most significant resources and databases for functional discovery in Arabidopsis is presented. The successful application of the outlined strategy is illustrated by the identification of a new abiotic stress determinant gene, HRR, which displays a heat stress-related phenotype after a loss-of-function reverse genetics approach.No competing financial interests exist. The present work was supported by Foundation for Science and Technology (POCTI/AGR/45462/2002). H. Azevedo (SFRH/BPD/17198/2004), J. Correia (SFRH/BD/16663/2004), J. Oliveira (SFRH/BD/38379/2007), S. Laranjeira (SFRH/BD/29778/2006), C. Barbeta (SFRH/BD/12081/2003) and V. Amorim-Silva (SFRH/BD/29778/2006) were supported by Foundation for Science and Technology

Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70–84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress