Comparative Transcriptome Profiling of Chilling Stress Responsiveness in Two Contrasting Rice Genotypes

Zhang, Ting; Zhao, Xiuqin; Wang, Wensheng; Pan, Ya-Jiao; Huang, Liying; Liu, Xiaoyue; Zong, Yuan; Zhu, Linghua; Yang, Daichang; Fu, Binying

doi:10.1371/journal.pone.0043274

Cited by 127 publications

(140 citation statements)

References 79 publications

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“…High gene expression prior to abiotic stress treatment might represent a constitutive tolerance mechanism (Zhang et al 2012b). In this work, OsWCOR413 gene expression was higher in the cold-tolerant than in the cold-sensitive genotype before cold treatment.…”

Section: Discussionmentioning

confidence: 52%

Identification and physiological characterization of two sister lines of indica rice (Oryza sativa L.) with contrasting levels of cold tolerance

et al. 2016

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Exposure to low temperature during germination and vegetative growth is a limiting factor to the establishment and development of rice seedlings. Higher cold tolerance of japonica than indica subspecies is well documented. However, reports of cold tolerance in indica genotypes are rare. We screened a large number of indica rice genotypes for cold tolerance during germination and initial vegetative growth. The indica genotypes IRGA 959-1-2-2F-4-1-4-A and IRGA 959-1-2-2F-4-1-4-D-1-CA-1, derived from the same cross, were characterized, respectively, as tolerant and sensitive to low temperature. Indexes of photosynthetic performance during light absorption were heavily affected by cold in both genotypes, but recovered after cold exposure only in the tolerant genotype. Activities of the antioxidant enzymes SOD and CAT (at the vegetative stage) and CAT and APX (at the germination stage) were higher in the tolerant than in the sensitive genotype. Expression of 20 genes previously related to cold response in rice was evaluated. Expression of OsLIP9 and OsWCOR413 were higher in the tolerant genotype upon or prior to cold exposure, respectively. The two sister lines show different molecular and physiological responses to low temperature stress. Further in-depth studies with these lines may help to identify new cold tolerance mechanisms in rice.Key words: abiotic stress, antioxidant enzymes, cold, gene expression, indica rice, JIP-test.Résumé : L'exposition à basse température pendant la germination et la croissance végétative est un facteur limitant à l'établissement et le développement des plantules de riz. La tolérance supérieure au froid observée en japonica par rapport à sous-espèces indica c'est bien documentée. Cependant, les rapports de la tolérance adéquate au froid dans les génotypes de indica sont encore rares. Cette étude a examiné plusieurs génotypes de indica en relation à leurs tolérances au froid pendant la germination et la croissance végétative initiale. Corresponding author: Janette P. Fett (email: jpfett@cbiot.ufrgs.br).*These authors contributed equally to this work.Abbreviations: ABS/RC, energy flux absorption per reaction center; APX, ascorbate peroxidase; CAT, catalase; DI 0 /RC, energy dissipation per reaction center; ET0/ABS, quantum yield of electron transport from QA − to the intersystem electron acceptors; ET0/CS, flow of electron transport per CS at t = 0; ET 0 /RC, electron transport flux per reaction center; ET 0 /TR 0 , probability that a trapped exciton moves an electron into the electron transport chain beyond QA − , at t = 0; H2O2, hydrogen peroxide; PIABS, performance index (potential) for energy conservation from photons absorbed by PSII to the reduction of intersystem electron acceptors; PIABS,total, performance index (potential) for energy conservation from photons absorbed by PSII to the reduction of PSI end acceptors; ROS, reactive oxygen species; SOD, superoxide dismutase; TBARS, thiobarbituric acid reactant substances; TR0/CS, flow of energy captured by CS at t = 0; TR0...

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Section: Discussionmentioning

confidence: 52%

Identification and physiological characterization of two sister lines of indica rice (Oryza sativa L.) with contrasting levels of cold tolerance

et al. 2016

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“…Identifying orthologous PSR TFs does not guarantee similar stress induction patterns, especially if there are overarching differences in the circadian regulation or simply differences in the timing of the expression data. Hierarchical clustering of microarray analysis under 2, 8, 24 and 48 h of cold, in chillingsensitive and chilling-tolerant rice genotypes, revealed differences in transcriptomic response between genotypes and also in the response of CBF1 duplicate genes, suggesting possible subfunctionalization of CBF1 [48].…”

Section: Abiotic Stress Time and Expanding Gene Familiesmentioning

confidence: 99%

“…Modeling gene expression changes in combination with cis-regulatory motif analysis can provide regulatory predictions [70,71]. GCNs generated using 815 Affymetrix rice arrays resulted in the identification of 15 gene modules with enrichment for stress-related biological processes as well as cis-regulatory elements including ABRE [48]. Several hub genes identified overlapped with known drought tolerant QTLs, resulting in a short list of candidate genes for further study [48].…”

Section: Current Opinion In Plant Biologymentioning

confidence: 99%

Transcriptional networks — crops, clocks, and abiotic stress

Gehan

Greenham

Mockler

et al. 2015

Current Opinion in Plant Biology

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Several factors affect the yield potential and geographical range of crops including the circadian clock, water availability, and seasonal temperature changes. In order to sustain and increase plant productivity on marginal land in the face of both biotic and abiotic stresses, we need to more efficiently generate stress-resistant crops through marker-assisted breeding, genetic modification, and new genome-editing technologies. To leverage these strategies for producing the next generation of crops, future transcriptomic data acquisition should be pursued with an appropriate temporal design and analyzed with a network-centric approach. The following review focuses on recent developments in abiotic stress transcriptional networks in economically important crops and will highlight the utility of correlation-based network analysis and applications.

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“…Various crops such as chickpea (Molina et al, 2011), rice (Mizuno et al, 2010;Zhang et al, 2012) 2014) have been subjected to high-throughput NGS for identification of abiotic stress-related genes. RNA-Seq is virtually changing the area of sequencing and transcriptome profiling (Wang et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

Kumar

Goswami

Sharma

et al. 2015

OMICS: A Journal of Integrative Biology

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Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22°-3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.

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Comparative Transcriptome Profiling of Chilling Stress Responsiveness in Two Contrasting Rice Genotypes

Cited by 127 publications

References 79 publications

Identification and physiological characterization of two sister lines of indica rice (Oryza sativa L.) with contrasting levels of cold tolerance

Identification and physiological characterization of two sister lines of indica rice (Oryza sativa L.) with contrasting levels of cold tolerance

Transcriptional networks — crops, clocks, and abiotic stress

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

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