Browsing by Subject "DROUGHT STRESS"

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  • Yang, Kun; Wen, Xiaopeng; Mudunuri, Suresh; Varma, G. P. Saradhi; Sablok, Gaurav (2019)
    Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at:
  • Sablok, Gaurav; Powell, Jonathan J.; Kazan, Kemal (2017)
    Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations. More recently, ribosome-associated mRNA profiling has emerged as an alternative and a robust way of identifying translating mRNAs, which are a set of mRNAs associated with ribosomes and more likely to contribute to proteome abundance. In this article, we briefly review recent studies that examined the processes affecting the abundance of translating mRNAs, their regulation during plant development and tolerance to stress conditions and plant factors affecting the selection of translating mRNA pools. This review also highlights recent findings revealing differential roles of alternatively spliced mRNAs and their translational control during stress adaptation. Overall, better understanding of processes involved in the regulation of translating mRNAs has obvious implications for improvement of stress tolerance in plants.
  • Mukrimin, Mukrimin; Kovalchuk, Andriy; Ghimire, Rajendra P.; Kivimaenpaa, Minna; Sun, Hui; Holopainen, Jarmo K.; Asiegbu, Fred O. (2019)
    Main conclusion Two terpene compounds and four genes were identified as potential biomarkers for further evaluation for Scots pine susceptibility or tolerance against Heterobasidion annosum. Scots pine (Pinus sylvestris) is one of the main sources of timber in the boreal zone of Eurasia. Commercial pine plantations are vulnerable to root and butt rot disease caused by the fungus Heterobasidion annosum. The pathogen affects host growth rate, causes higher mortality and decreases in timber quality, resulting in considerable economic losses to forest owners. Genetic and biochemical factors contributing to Scots pine tolerance against H. annosum infection are not well understood. We assessed the predictive values of a set of potential genetic and chemical markers in a field experiment. We determined the expression levels of 25 genes and the concentrations of 36 terpenoid compounds in needles of 16 Scots pine trees randomly selected from a natural population prior to artificial infection. Stems of the same trees were artificially inoculated with H. annosum, and the length of necrotic lesions was documented 5 months post inoculation. Higher expression level of four genes included in our analysis and encoding predicted alpha-pinene synthase (two genes), geranyl diphosphate synthase (GPPS), and metacaspase 5 (MC5), could be associated with trees exhibiting increased levels of necrotic lesion formation in response to fungal inoculation. In contrast, concentrations of two terpenoid compounds, beta-caryophyllene and alpha-humulene, showed significant negative correlations with the lesion size. Further studies with larger sample size will help to elucidate new biomarkers or clarify the potential of the evaluated markers for use in Scots pine disease resistance breeding programs.
  • Pavicic, M.; Wang, F.; Mouhu, K.; Himanen, K. (2019)
    Seed quality is an important factor for seedling vigour as well as adult plant resilience. The key quality attributes are related to physical characteristics, physiological performance, genetic background and health status of the seeds. Many ways to address seed quality attributes have been developed and recently many of them have featured automated high throughput methods. In our study, we addressed two of the seed quality attributes, namely physiological performance and genetic background by analysing germination rates in our mutant collection. These mutants represent ubiquitin E3 ligases that transcriptionally respond to abscisic acid (ABA). This plant hormone is an important regulator of germination and seedling establishment. To facilitate in vitro germination screens of large seed collections a high throughput image-based assay was developed. As a read out of the germination on ABA treatment the cotyledon emergence was detected with top view chlorophyll fluorescence camera. By applying the ABA treatment during germination, RING-type ubiquitin E3 ligase mutants were identified, showing either resistant or sensitive responses to ABA. In conclusion, a scalable high throughput screen for in vitro germination assay was established that allowed fast screening of tens of mutants in a hormone supplemented media.
  • Junttila, Samuli; Kaasalainen, Sanna; Vastaranta, Mikko; Hakala, Teemu; Nevalainen, Olli; Holopainen, Markus (2015)
    Global warming is posing a threat to the health and condition of forests as the amount and length of biotic and abiotic disturbances increase. Most methods for detecting disturbances and measuring forest health are based on multi- and hyperspectral imaging. We conducted a test with spruce and pine trees using a hyperspectral Lidar instrument in a laboratory to determine the capability of combined range and reflectance measurements to investigate forest health. A simple drought treatment was conducted by leaving the harvested trees outdoors without a water supply for 12 days. The results showed statistically significant variation in reflectance after the drought treatment for both species. However, the changes differed between the species, indicating that drought-induced alterations in spectral characteristics may be species-dependent. Based on our results, hyperspectral Lidar has the potential to detect drought in spruce and pine trees.
  • Grossiord, Charlotte; Sevanto, Sanna; Limousin, Jean-Marc; Meir, Patrick; Mencuccini, Maurizio; Pangle, Robert E.; Pockman, William T.; Salmon, Yann; Zweifel, Roman; McDowell, Nate G. (2018)
    Tree transpiration depends on biotic and abiotic factors that might change in the future, including precipitation and soil moisture status. Although short-term sap flux responses to soil moisture and evaporative demand have been the subject of attention before, the relative sensitivity of sap flux to these two factors under long-term changes in soil moisture conditions has rarely been determined experimentally. We tested how long-term artificial change in soil moisture affects the sensitivity of tree-level sap flux to daily atmospheric vapor pressure deficit (VPD) and soil moisture variations, and the generality of these effects across forest types and environments using four manipulative sites in mature forests. Exposure to relatively long-term (two to six years) soil moisture reduction decreases tree sap flux sensitivity to daily VPD and relative extractable water (REW) variations, leading to lower sap flux even under high soil moisture and optimal VPD. Inversely, trees subjected to long-term irrigation showed a significant increase in their sensitivity to daily VPD and REW, but only at the most water-limited site. The ratio between the relative change in soil moisture manipulation and the relative change in sap flux sensitivity to VPD and REW variations was similar across sites suggesting common adjustment mechanisms to long-term soil moisture status across environments for evergreen tree species. Overall, our results show that long-term changes in soil water availability, and subsequent adjustments to these novel conditions, could play a critical and increasingly important role in controlling forest water use in the future.
  • Lunden, Karl; Danielsson, Marie; Durling, Mikael Brandstrom; Ihrmark, Katarina; Gorriz, Miguel Nemesio; Stenlid, Jan; Asiegbu, Frederick O.; Elfstrand, Malin (2015)
    Heterobasidion annosum sensu lato is a serious pathogen causing root and stem rot to conifers in the northern hemisphere and rendering the timber defective for sawing and pulping. In this study we applied next-generation sequencing to i) identify transcriptional responses unique to Heterobasidion-inoculated Norway spruce and ii) investigate the H. annosum transcripts to identify putative virulence factors. To address these objectives we wounded or inoculated 30-year-old Norway spruce clones with H. annosumand 454-sequenced the transcriptome of the interaction at 0, 5 and 15 days post inoculation. The 491860 high-quality reads were de novo assembled and the relative expression was analysed. Overall, very few H. annosum transcripts were represented in our dataset. Three delta-12 fatty acid desaturase transcripts and one Clavaminate synthase-like transcript, both associated with virulence in other pathosystems, were found among the significantly induced transcripts. The analysis of the Norway spruce transcriptional responses produced a handful of differentially expressed transcripts. Most of these transcripts originated from genes known to respond to H. annosum. However, three genes that had not previously been reported to respond to H. annosum showed specific induction to inoculation: an oxophytodienoic acid-reductase (OPR), a beta-glucosidaseand a germin-like protein (GLP2) gene. Even in a small data set like ours, five novel highly expressed Norway spruce transcripts without significant alignment to any previously annotated protein in Genbank but present in the P. abies (v1.0) gene catalogue were identified. Their expression pattern suggests a role in defence. Therefore a more complete survey of the transcriptional responses in the interactions between Norway spruce and its major pathogen H. annosumwould probably provide a better understanding of gymnosperm defence than accumulated until now.
  • Pour-Aboughadareh, Alireza; Omidi, Mansoor; Naghavi, Mohammad Reza; Etminan, Alireza; Mehrabi, Ali Ashraf; Poczai, Peter (2020)
    Previous studies have revealed that some wild wheat accessions respond well to water deficit treatments and have a good potential in terms of photosynthetic parameters, root system architecture, and several physiological properties. However, the biochemical responses and molecular mechanisms of antioxidant-encoding genes remain to be elucidated. Herein, we investigated the most tolerant accessions fromA. crassa,Ae. tauschii, andAe. cylindricapreviously identified from a core collection in previous studies, along with a control variety of bread wheat (T. aestivumcv. Sirvan) through measuring the shoot fresh and dry biomasses; the activities of antioxidant enzymes (including ascorbate peroxidase (APX), catalase (CAT), guaiacol peroxidase (GPX), and peroxidase (POD)); and the relative expression ofCAT, superoxide dismutase (MnSOD), andGPXandAPXgenes under control and water deficit conditions. Water deficit stress caused a significant decrease in the shoot biomasses but resulted in an increase in the activity of all antioxidant enzymes and relative expression of antioxidant enzyme-encoding genes. Principal component analysis showed a strong association between the shoot dry biomass and the activity of CAT, POD, and APX, as well asMnSODgene expression. Thus, these traits can be used as biomarkers to screen the tolerant plant material in the early growth stage. Taken together, our findings exposed the fact thatAe. tauschiiandAe. crassarespond better to water deficit stress thanAe. cylindricaand a control variety. Furthermore, these accessions can be subjected to further molecular investigation.
  • Dianatmanesh, Marziye; Kazemeini, Seyed A.; Bahrani, Mohammad J.; Shakeri, Ehsan; Alinia, Mozhgan; Amjad, Syeda F.; Mansoora, Nida; Poczai, Peter; Lalarukh, Irfana; Abbas, Mohamed H. H.; Abdelhafez, Ahmed A.; Hamed, Mahdy H. (2022)
    Incorporation of crop residues into agricultural system has become a worldwide efficient practice for enhancing crop production. The main objectives of this experiment was to investigate the major role of incorporating wheat (Triticum aestivum L.) residues and nitrogen (N) fertilizers rates under different water requirements (WR) on growth, seed yield and yield components of common bean (Phaseolus vulgaris L.). The results showed that seed yield under 80% WR in retained crop residue plots was & SIM;11% higher than WR treatment with no residue incorporation. Seed yield was not significantly different between residue retention and removal treatments in 2016, whereas it was higher (12% and 17%) under residue retained plots compared to removed ones in subsequent years. Seed yields responded to N up to 170 and 225 kg ha(-1) in removed and retained residue treatments, respectively in 2017 and 2018. Annual increment of seed yield in residue retained plots (36%) was 2.11 times higher than the residue removed ones (17%). There was higher soil N content in 50% residue retention with 225 kg N ha(-1) under both water deficit treatments in all years. The highest soil organic carbon (SOC) was achieved with normal irrigation in retained residue plots with 225 kg N ha(-1) in all years. Overall, wheat residue incorporation into the soil and N-supply substantially contributed to counteracting yield declines of common bean under water deficit conditions.& nbsp;(c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (