Sugarcane ESTs differentially expressed in immature and maturing internodal tissue

Carson, D.L.; Huckett, B. I.; Botha, Frederik C.

doi:10.1016/s0168-9452(01)00570-2

Cited by 50 publications

(24 citation statements)

References 27 publications

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“…The transcription factors DREB acts on dehydration-responsive cis-acting element (DRE) to trigger gene expression in an ABAindependent pathway YamaguchiShinozaki 2007, Agarwal andJha 2010). In sugarcane, gene expression profile studies detected genes related to sucrose accumulation, such as those expressed in maturing internodal tissues (Carson et al 2002), sugar transporter genes (Casu et al 2003, Rae et al 2005 and genes participating in signal transduction pathways during biotic and abiotic stresses (Papini-Terzi et al 2005, Rocha et al 2007.…”

Section: Introductionmentioning

confidence: 99%

Sugarcane genes differentially expressed during water deficit

et al. 2011

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To identify genes that are up and down-regulated by water deficit in sugarcane we used the macroarray methodology and the expression level of 3 575 independent sugarcane cDNAs was measured by hybridization with RNA extracted from plants submitted to mild, moderate and severe water deficit. We identified approximately 1 670 differentially expressed genes from which 62 % were up-regulated by different stress-conditions, whereas many repressed genes were exclusive for each time-point. Analysis of similarity showed that approximately 24 % of the differentially expressed genes shared homology with proteins involved in different processes such as signal transduction, hormone metabolism, photosynthesis, transcription and stress response. Transcripts with no known function accounted for approximately 39 % and those without similarity represented 36 % of the sequences. Five genes analyzed by RT-PCR confirmed the macroarray results.

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Section: Introductionmentioning

confidence: 99%

Sugarcane genes differentially expressed during water deficit

et al. 2011

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“…Recently, the SSH technique was used to identify five GSTs belonging to three different classes and a multidrug resistance-associated protein (MRP) that were induced by safener treatment in wheat (Theodoulou et al 2003). This technique had been successfully used to isolate differentially expressed genes in different plant systems, viz., potato (Birch et al 1999), Arabidopsis (Hinderhofer and Zentgraf 2001), Medicago sativa (Hays and Skinner 2001), rice (Chen et al 2002), wheat (Luo et al 2002), and sugarcane (Carson et al 2002;Watt 2003).…”

Section: Introductionmentioning

confidence: 99%

Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray

Rishi

Munir

Kapur

et al. 2004

Planta

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Safeners are the chemicals used to protect plants from detrimental effects of herbicides, but their mode of action at the molecular level is not well understood. As an initial step towards understanding the molecular mechanism of safener action in trees, homologous genes in hybrid poplar (Populus nigra x Populus maximowiczii) that were induced by a safener were identified. We here describe the identification of differentially expressed genes in Populus that are induced by Concep-III, a herbicide safener. Expressed sequence tags (ESTs) enriched for transcriptionally induced genes were isolated by suppressive subtractive hybridization (SSH). The SSH library cDNA inserts were used to construct a cDNA microarray for high-throughput validation of the up-regulated expression of safener-induced genes. Single-pass and partial sequences of 1,344 safener-induced ESTs were assembled into 418 singletons and 328 clusters, but the putative functions of almost 53% of the ESTs are not known. Genes encoding proteins involved in all three different phases of safener action, viz., oxidation, conjugation, and sequestration, were found in the SSH library. Almost 75% of genes that showed greater than 2-fold expression upon safener treatment were redundant in the SSH library. The expression pattern for selected genes was validated by reverse transcription-polymerase chain reaction. A few safener-induced genes that were not previously reported to be induced by safeners, but which may have a role in herbicide metabolism, were identified. The newly identified genes could have potential for application in genetic engineering of plants for herbicide detoxification and tolerance.

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“…The considerable level of variability observed in this and other arrayed transcript profiling studies (e.g. Hughes et al 2001;Mills et al 2001;Carson et al 2002) is not surprising, given that the signal intensity is dependent on parameters that are hard to standardize-including the amount of target DNA in each spot or colony and the degree of cross-hybridization between a cloned gene segment and other non-specific sequences present in the labelled probe. In view of the observed variability levels, we have chosen to focus on the clones for which (Z-M) ‡1.…”

Section: Discussionmentioning

confidence: 70%

Genes expressed in zoospores of Phytophthora nicotianae

2003

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The genus Phytophthora includes many highly destructive plant pathogens. In many Phytophthora species, pathogen dispersal and initiation of plant infection are achieved by motile, biflagellate zoospores that are chemotactically attracted to suitable infection sites. In order to study gene expression in zoospores, we have constructed a cDNA library using mRNA from zoospores of Phytophthora nicotianae. The library was arrayed and screened using probes derived from mycelium or zoospore mRNA. More than 400 clones representing genes preferentially expressed in zoospores were identified and sequenced from the 5' end of the insert. The expressed sequence tags (ESTs) generated were found to represent 240 genes. The ESTs were compared to sequences in GenBank and in the Phytophthora Genome Consortium database, and classified according to putative function based on homology to known proteins. To further characterize the identified genes, a colony array was created on replicate nylon filters and screened with probes derived from four Phytophthora developmental stages including zoospores, germinating cysts, vegetative mycelium and sporulating hyphae, and from inoculated and uninoculated tobacco seedlings. Data from sequence analysis and colony array screening were compiled into a local database, and searched to identify genes that are preferentially expressed in zoospores for future functional analysis.

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Sugarcane ESTs differentially expressed in immature and maturing internodal tissue

Cited by 50 publications

References 27 publications

Sugarcane genes differentially expressed during water deficit

Sugarcane genes differentially expressed during water deficit

Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray

Genes expressed in zoospores of Phytophthora nicotianae

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