Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomics Analyses of tobacco leaves and roots sample during water-deficit

ABSTRACT: Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblegen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons. The seeds were sown in sterile petri plates with modified half-strength MS agar medium. The seedlings were then aseptically transferred into sterile polycarbonate container with half-strength MS liquid medium. Seedlings were grown for 2 weeks in an incubator set at 25 oC with constant light and subjected to dehydration for 20min, 40min, 1hr, 2hrs, and 4hrs. We used a hydrophonics system for the trancriptome profiling of tobacco (cv Burley 21) root and leaves samples to study plant reponses during water- deficit or drought. Plants were grown in controlled growth chamber conditions and subjected to water deficit condition after 2 weeks.The plants were transferred to empty containers without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tissues and hence called 0-min dehydrated tissue. Similarly other time-points were processed( for instance, 20 min of dehydration, plants were dehydrated for 20 min after being taken out from the container and then harvested). Tissues for three biological replicates and 20 plants per biological replicates were collected for each time-point. RNA was isolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.

ORGANISM(S): Nicotiana tabacum

SUBMITTER: Roel Rabara

PROVIDER: E-GEOD-67434 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Arabidopsis thaliana plants that have experienced an initial exposure to dehydration stress (“trained plants”) have an increased ability to maintain leaf relative water content (RWC) during subsequent stresses than plants experiencing the stress for the first time and transcription of selected dehydration response genes is altered during successive exposures to dehydration stress. This physiological and transcriptional behavior of trained plants is consistent with a “memory “of an earlier stress. It is unknown whether such memory is present in other Angiosperm lineages and whether it is an evolutionarily conserved response to stress (see E-GEOD-48235). Here, we analyzed the behavior and transcriptomes of maize (Zea mays) plants experiencing multiple dehydration stresses and compare them with responses of the evolutionarily distant A. thaliana. We found structurally related genes in maize that displayed the same memory-type responses as in A. thaliana, providing evidence of the conservation of function and transcriptional memory in the evolution of plants’ dehydration stress response systems. Similar to A. thaliana, trained Z. mays plants retained higher RWC during dehydration stress than untrained plants, due in part to maintaining reduced stomatal conductance, despite full recovery of RWC, after the first stress. Divergent transcriptional memory responses were also expressed, suggesting diversification of function among stress memory genes. Some dehydration stress memory genes were also shared with other stress and hormone responding pathways, indicating complex and dynamic interactions between different plant signaling networks. The results provide new insight into how plants respond to multiple dehydration stresses and provide a platform for studies of the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants . For each condition (water, S1, and S3) the transcriptome was sequenced for two replicates. The watered condition is considered the control.

Project description:New shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. Because global climate change is expected to increase abiotic stress, such as dehydration, objectives of this study include examining the impact that dehydration stress has on molecular mechanisms associated with vegetative reproduction. Greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments, prior to decapitation of aerial tissue and rehydration of soil to induce new vegetative shoot growth. Compared to well-watered control plants, mild-dehydration accelerated new vegetative shoot growth but intermediate- and severe-dehydration treatments both delayed and reduced shoot growth, and 21-day dehydration treatment inhibited initiation of new vegetative shoots and was considered a lethal treatment. Overall, transcriptome profiles revealed that 2109 genes were differentially-expressed (P<0.05) in crown buds in response to the various dehydration treatments. Sub-network enrichment analyses identified central hubs of over-represented genes involved in processes such as hormone responses and signaling (e.g., ABA, auxin, ethylene, GA, and JA), response to abiotic stress (DREB1A/2A) and light (PIF3), phosphorylation (CLV1, MPK3/4/6, SOS2), gene silencing (miRNA156/172a), circadian regulation (CRY2, LHY, PHYA/B), and flowering (AGL8/20, AP2, FLC). Further, results from this and previous studies highlight HY5, MAF3, MYB-like/RVE1 and RD22 as molecular markers for endodormancy in crown buds of leafy spurge. Early response to dehydration also highlighted involvement of upstream ethylene and jasmonate signaling, whereas longer-term dehydration impacted ABA signaling. The identification of conserved ABRE- and MYC-consensus, cis-acting elements in the promoter of a leafy spurge gene similar to Arabidopsis MYB-like/RVE1 (AT5G17300) implicates a potential role for ABA signaling in its dehydration-induced expression. Response of these molecular mechanisms to dehydration-stress provides insights on the ability of invasive perennial weeds to adapt and survive under harsh environments, which provide new insights for addressing future management practices. Changes in transcript abundance for underground adventitious buds of leafy spurge which were exposed various levels of dehydration stress (Day-3, -7, -14, -16, -21) are analysed relative to controls (Day-0).

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Transcriptomics Analyses of tobacco leaves and roots sample during water-deficit

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