Isolation and characterization of cold responsive NAC gene from Lepidium latifolium

Aslam, Mohammad; Grover, Atul; Sinha, Vimlendu Bhushan; Fakher, Beenish; Pande, Veena; Yadav, Patade Vikas; Gupta, Sanjay Mohan; Anandhan, Sivalingam; Ahmed, Zakwan

doi:10.1007/s11033-012-1828-0

Cited by 31 publications

(12 citation statements)

References 42 publications

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“…Gene expression in response to abiotic stress has been known to be regulated in ABA-dependent and/or ABA-independent manner [39], [51]–[53]; thus, we also included ABA treatment into our study. A qRT-PCR assay was designed to measure the expression stability between control and stress- or ABA-treated samples of thirteen candidate reference genes obtained from published literature related to qRT-PCR expression profiling in soybean (Table 1, Dataset S1, Figure S1).…”

Section: Resultsmentioning

confidence: 99%

Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions

et al. 2012

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Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid) treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the Fbox/ABC, Fbox/60s gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. Fbox and 60s genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the ELF1b/IDE and Fbox/ELF1b are the most stably expressed gene pairs in roots and shoots, respectively, while 60s/Fbox is the best gene pair in both tissues. For studying cold stress in roots or shoots, IDE/60s and Fbox/Act27 are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, 60s/ELF1b, ELF1b/Fbox and 60s/ELF1b are the most suitable reference genes, respectively. The expression of ELF1b/60s, 60s/Fbox and 60s/Fbox genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, 60s was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.

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Section: Resultsmentioning

confidence: 99%

Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions

et al. 2012

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“…In the NAC transcription factor family, the transcripts of 9 and 5 members were up-regulated, while none was found down-regulated in both treated samples. Evidence that the WRKY and NAC transcription factor gene families may play important roles in the regulation of transcriptional reprogramming associated with cold stress responses is incremental [30–33]. The role of several WRKY genes, such as AtWRKY25, AtWRKY33, HvWRKY38, and GmWRKY21 [34–36], and several NAC genes, such as TaNAC2, SsNAC23, and OsNAC5 [30, 37, 38], in plant cold response has been established.…”

Section: Resultsmentioning

confidence: 99%

Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

et al. 2014

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BackgroundCompared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.ResultsUsing the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4°C-treated sample and -4°C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica.ConclusionsOur results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-326) contains supplementary material, which is available to authorized users.

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“…The ecotype of Lepidium latifolium from Ladakh is one such plant that is considered best among local wild edible plants of Ladakh [12]. Cold tolerance ability of this plant has recently been tapped using molecular techniques [10], [11], [24]. The present investigation is an attempt to evaluate its antioxidant and nutritional properties with an aim to utilize this information as guide and aid in its marketing efforts.…”

Section: Resultsmentioning

confidence: 99%

Evaluation of Nutritional and Antioxidant Status of Lepidium latifolium Linn.: A Novel Phytofood from Ladakh

et al. 2013

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Lepidium latifolium Linn. (perennial pepperweed) is one of the preferred phytofoods among cold arid region of Ladakh, India and its leaves contribute significantly to people's diet. This study was conducted to determine its nutritive value and antioxidant activity. Plant samples from three different locations were selected in the present study. Results showed that this plant is an excellent source of glucosinolates, notably sinigrin that is present in very high amount (∼70–90%). Its value ranged from 149 to 199 µg per g fresh weight. Fatty acid composition analysis showed that its leaves were abundant in unsaturated fatty acids, specifically linolenic acid (18∶3) whose percentage is about 50%. Higher glucose and crude protein along with higher nitrogen to sulfur ratio, supplements the nutritive value of this plant. Based on total phenol, flavanoids, free radical scavenging activity and DNA protective activity showed that this ecotype of perennial pepperweed contains high antioxidant properties. The percentage inhibition for O2 − scavenging activity ranged from 41.3% to 83.9%. Higher content of phenols (26.89 to 50.51 mg gallic acid equivalents per g dry weight) and flavanoids (38.66 to 76.00 mg quercetin equivalents per g dry weight) in leaves could be responsible for the free radical scavenging activity of this plant. Depending upon the location of the plants, variations were observed in different activities. Based on the systematic evaluation in this study, preparations of Lepidium latifolium from Ladakh can be promoted as substitute to dietary requirements.

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Isolation and characterization of cold responsive NAC gene from Lepidium latifolium

Cited by 31 publications

References 42 publications

Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions

Evaluation of Candidate Reference Genes for Normalization of Quantitative RT-PCR in Soybean Tissues under Various Abiotic Stress Conditions

Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica

Evaluation of Nutritional and Antioxidant Status of Lepidium latifolium Linn.: A Novel Phytofood from Ladakh

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