High-quality reference genes for quantifying the transcriptional responses of Oryza sativa L. (ssp. indica and japonica) to abiotic stress conditions

Maksup, Sarunyaporn; Supaibulwatana, Kanyaratt; Selvaraj, Gopalan

doi:10.1007/s11434-013-5726-1

Cited by 32 publications

(34 citation statements)

References 48 publications

(63 reference statements)

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“…After electrophoresis on a 1% agarose gel and staining with EtBr, the band intensities were quantified using ImageJ (http://imagej.nih.gov/ij/). The relative transcript level of each gene was normalized for the amplification of the rice eukaryotic elongation factor 1‐α ( eELF1‐α ; Os03g08060) and expressed protein ( EP ; Os05g08980) (Maksup et al ). Results were obtained from at least three technical replicates.…”

Section: Methodsmentioning

confidence: 99%

Rice calcium‐dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose‐phosphate synthase and is required for a proper cold stress response

Almadanim

Alexandre

Rosa

et al. 2017

Plant Cell & Environment

107

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Calcium-dependent protein kinases (CDPKs) are involved in plant tolerance mechanisms to abiotic stresses. Although CDPKs are recognized as key messengers in signal transduction, the specific role of most members of this family remains unknown. Here we test the hypothesis that OsCPK17 plays a role in rice cold stress response by analyzing OsCPK17 knockout, silencing, and overexpressing rice lines under low temperature. Altered OsCPK17 gene expression compromises cold tolerance performance, without affecting the expression of key cold stress-inducible genes. A comparative phosphoproteomic approach led to the identification of six potential in vivo OsCPK17 targets, which are associated with sugar and nitrogen metabolism, and with osmotic regulation. To test direct interaction, in vitro kinase assays were performed, showing that the sucrose phosphate synthase OsSPS4, and the aquaporin OsPIP2;1/OsPIP2;6 are phosphorylated by OsCPK17 in a calcium-dependent manner. Altogether, our data indicates that OsCPK17 is required for a proper cold stress response in rice, likely affecting the activity of membrane channels and sugar metabolism.Rice production is severely affected by different abiotic stresses, including cold. Cold perception is mediated by calcium signals that activate kinases to elicit the adequate cellular response. In this work, we show the involvement of the rice calciumdependent protein kinase 17 (OsCPK17) in such a process. We show that altered OsCPK17 gene expression in transgenic lines affects cold tolerance performance, This article is protected by copyright. All rights reserved.and that OsCPK17 targets proteins are associated with osmotic regulation, and sugar and nitrogen metabolism.

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Section: Methodsmentioning

confidence: 99%

Rice calcium‐dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose‐phosphate synthase and is required for a proper cold stress response

Almadanim

Alexandre

Rosa

et al. 2017

Plant Cell & Environment

107

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“…and OsCDPK7 genes exhibit different functional involvement in mediating salinity tolerant mechanisms under salinity stress (Ahmadi et al,2011;Gupta and Huang, 2014;Kumar et al,2013;Ismail et al, 2007;Chen et al, 2007;Xiong and Yang, 2003;Saijo et al,2000;Maksup et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…Triosephosphate isomerise (housekeeping gene) Maksup et al, 2013 time to salinity, in order to make inferences regarding the differential expression of genes over the tested time period under salinity stress.…”

Section: Oscdpk7mentioning

confidence: 99%

Comparative Analysis of Salinity Responsive Candidate Gene Expression in Selected Sri Lankan Rice Varieties

et al. 2015

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Studying of expression dynamics of salt responsive candidate genes under different genetic background of rice is important to develop resilient salt tolerant rice varieties. The present study was focused to assess the comparative expression of salinity responsive genes which are involved in Na + /K + homeostasis (OsNHX1), signal transduction pathway (OsMAPK5, OsCDPK7) and synthesis of osmoprotectant (OsTPS1). Comparative expression of selected genes were assessed in At354 (improved), Godawee (traditional) and Kuruwi Perunel (traditional), salinity tolerant varieties and Suwandel, a salinity susceptible traditional variety. The assessment was done before salinization (at 0 h) and after salinization at 24 h and 72 h using semi-quantitative Reverse Transcriptase PCR (RT-PCR). RT-PCR products were analysed using 1.5% agarose gel electrophoresis. Resulted gel profiles were assessed and relative level of gene expression was measured based on the intensity of the PCR product in terms of average pixel values. Relative level of gene expression in four varieties was plotted against the exposure time to salinity. Accordingly, marked variation in expression pattern of the selected genes was detected in four varieties over the tested in Godawee and Suwandel compared to At354 and Kuruwi Perunel. At 24 h, all four genes were up-XT regulated in At354 and Godawee while they were down-regulated in Suwandel. In Kuruwi Perunel, OsNHX1, OsMAPK5 and OsCDPK7 genes were up-regulated at 24 h while OsTPS1 was up-regulated at 72 h. At 72 h, continuous expression of all genes was observed in Kuruwi Perunel and Godawee, whereas expression was comparatively down-regulated in At354 approximately to the same level under non-stress condition. It could be suggested that At354 might have been adapted to the stress relatively earlier compared to Godawee and Kuruwi Perunel, where expressions of genes were less pronounced. Further experiments with various time period of salinity exposure should be carried out to make detailed inference regarding the expression dynamics in tested rice varieties.

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“…Statistic analysis of reference gene stability under drought stressFor the analysis of reference genes under drought stress, 27 publications within 26 plant species were collected in Table S2(Bin et al 2012;Borges et al 2012;Carvalho et al 2010;Chandna et al 2012;Chang et al 2012;Cruz et al 2009;Dombrowski and Martin 2009;Dong et al 2012;Garg et al 2010;Goulao et al 2012;Hong et al 2008;Janska et al 2013;Kumar et al 2013;Kundu et al 2013;Le et al 2012; Lee et al 2010a, b;Maksup et al 2013;Park et al 2012;Qi et al 2010;Reddy et al 2013;Schmidt and Delaney 2010;Shi et al 2012;Wan et al 2010;Wei et al 2013;Zhang et al 2013;Zhu et al 2013).…”

mentioning

confidence: 99%

Systematic assessment of reference genes for RT-qPCR across plant species under salt stress and drought stress

Xiao

et al. 2015

Acta Physiol Plant

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Suitable reference gene (RGs) is the prerequisite for accurate normalization of real-time quantitative PCR (RT-qPCR) data. However, previous results are diverse in various researches that focused on selecting stable RGs. This study aims at systematically assessing various RGs in plants under salt stress or drought stress by collection of geNorm rankings of genes, data transformation and statistic analysis. Although none of the analyzed genes can guarantee universally stable expressions in plant species under salt stress or drought stress, we found that 18S (18S ribosomal RNA) was generally the least stable gene under salt and drought stress. This gene should not be used as the RG in RT-qPCR. On the contrary, it is least risk to use EF1 for salt stress and TIP41 for drought treatment experiments. We compared the effects of salt and drought stresses on 7 frequently used RGs through paired-samples T test. The expression of Ubiquitin gene under drought stress is much more unstable than that under salt stress. The tested genes belonging to multigene family and having different stability could be one reason of variations in the published studies, which was supported by the analysis of expression profile of Salicornia europaea transcriptome. This is the first systematic assessment quantifying global stability of RGs across plant species under salt stress and drought stress, which will improve our understanding of RGs and facilitate the future work on RGs selection.

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High-quality reference genes for quantifying the transcriptional responses of Oryza sativa L. (ssp. indica and japonica) to abiotic stress conditions

Cited by 32 publications

References 48 publications

Rice calcium‐dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose‐phosphate synthase and is required for a proper cold stress response

Rice calcium‐dependent protein kinase OsCPK17 targets plasma membrane intrinsic protein and sucrose‐phosphate synthase and is required for a proper cold stress response

Comparative Analysis of Salinity Responsive Candidate Gene Expression in Selected Sri Lankan Rice Varieties

Systematic assessment of reference genes for RT-qPCR across plant species under salt stress and drought stress

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