Genome-wide identification and analysis of early heat stress responsive genes in rice

Jung, Kyungsook; Ko, Hyunjung; Nguyen, Minh; Kim, Sung-Ryul; Ronald, Pamela C.; An, Gynheung

doi:10.1007/s12374-012-0271-z

Cited by 47 publications

(25 citation statements)

References 40 publications

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“…The arrival of Next-Generation Sequencing (NGS) technologies could overcome the limitations and allow investigators to simultaneously measure the changes and regulation at a genome-wide level under certain biological conditions for non-model plants for which the background genomic information is not available [39], [58]–[59]. In recent years,the newly developed NGS-based RNA-seq technique has been widely used for de novo transcriptome sequencing assembly, discovery of novel genes and investigation of gene expression in many non-model plants such as rice [60], peanuts [61], purple sweet potato [62], medicinal plant Polygonum cuspidatum [63] and floral plant Dendrocalamus latiflorus [64].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

et al. 2013

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Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

et al. 2013

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“…To overcome the challenges presented by climate change, it is important to understand how crops perceive and respond to high temperatures (Jung et al 2012). Heat is a serious problem in many areas in the world (Wahid et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci Associated with Heat Tolerance in Rice (Oryza sativa L.)

Buu

Ha²,

Tam³

et al. 2014

Plant Breed. Biotech.

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“…HSR requires a complex network of distinct and interconnected pathways involved in maintenance of protein homeostasis, reduction of cellular damages, and readjustment of metabolic activities. Genes encoding for heat shock proteins (Hsps), such as molecular chaperones, are the best studied HS-induced genes, but a plethora of other genes are upregulated to contribute to HSR as shown by transcriptome analysis in several plant species (Finka et al, 2011;Jung et al, 2012;Liu and Charng, 2013;Sarkar et al, 2014;Fragkostefanakis et al, 2015b). The rapid and strong transcriptional activation of the majority of genes is controlled by the activity of the heat stress transcription factors (Hsfs).…”

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confidence: 99%

HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues

et al. 2016

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Genome-wide identification and analysis of early heat stress responsive genes in rice

Cited by 47 publications

References 40 publications

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Quantitative Trait Loci Associated with Heat Tolerance in Rice (Oryza sativa L.)

HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues

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