Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Jończyk, Maciej; Sobkowiak, Alicja; Trzcińska-Danielewicz, Joanna; Skoneczny, Marek; Solecka, Danuta; Fronk, Jan; Sowiński, Paweł

doi:10.1007/s11103-017-0651-3

Cited by 24 publications

(17 citation statements)

References 76 publications

(106 reference statements)

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“…Some salt stress-responsive genes, such as SOS1 , RD29A and DREB2A , exhibit a 24-h period of expression in Arabidopsis , suggesting that salt tolerance may also be affected by the circadian clock (Park et al, 2016a ). In some cases, other stress, such as cold and drought, modifies the transcription pattern of a major portion of genes showing diurnal oscillation (Wilkins et al, 2010 ; Jończyk et al, 2017 ). Resent evidence indicates that plants respond to salt stress more strongly during the day than at night and salt-induced expression of RD29A and SOS1 was much higher in the daytime than at night (Park et al, 2016b ).…”

Section: Discussionmentioning

confidence: 99%

OsRACK1A, encodes a circadian clock-regulated WD40 protein, negatively affect salt tolerance in rice

Zhang

Wang

Shen

et al. 2018

Rice

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The receptor for activated C kinase 1 (RACK1) is a WD40 type protein that is involved in multiple signaling pathways and is conserved from prokaryotes to eukaryotes. Here we report that rice RACK1A (OsRACK1A) is regulated by circadian clocks and plays an important role in the salt stress response. OsRACK1A was found to follow a rhythmic expression profile under circadian conditions at both the transcription and the translation levels, although the expression was arrhythmic under salt stress. Analysis of plant survival rates, fresh weight, proline content, malondialdehyde, and chlorophyll showed that suppression of OsRACK1A enhanced tolerance to salt stress. The ion concentration in both roots and leaves revealed that OsRACK1A-suppressed transgenic rice could maintain low Na+ and high K+ concentrations. Furthermore, OsRACK1A-suppressed transgenic rice accumulated significantly more abscisic acid (ABA) and more transcripts of ABA- and stress-inducible genes compared with the wild-type plants. Real-time quantitative polymerase chain reaction analysis revealed that many stress-related genes, including APETALA 2/Ethylene Responsive Factor (AP2/ERF) transcription factors, were upregulated in the OsRACK1A-suppressed transgenic rice line. We identified putative interactors of OsRACK1A, and found that OsRACK1A interacted with many salt stress-responsive proteins directly. These results suggest that OsRACK1A is regulated by circadian rhythm, and involved in the regulation of salt stress responses.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0232-3) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

OsRACK1A, encodes a circadian clock-regulated WD40 protein, negatively affect salt tolerance in rice

Zhang

Wang

Shen

et al. 2018

Rice

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“…Five studies reporting over 1,000 DEGs each, carried out on an aggregate of nine inbred lines, formed the core set of projects analysed here ( Fernandes et al, 2008 ; Sobkowiak et al, 2014 ; Jończyk et al, 2017 ; Lu et al, 2017 ; Waters et al, 2017 ; Table S1 ). Among them the reference study ( Sobkowiak et al, 2014 ) investigated two lines and found almost 8,000 genes changing expression in at least one line.…”

Section: A Search For Key Cold-affected Maize Genesmentioning

confidence: 99%

Maize Response to Low Temperatures at the Gene Expression Level: A Critical Survey of Transcriptomic Studies

et al. 2020

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Maize is a cold-sensitive plant whose physiological reactions to sub-optimal temperatures are well understood, but their molecular foundations are only beginning to be deciphered. In an attempt to identify key genes involved in these reactions, we surveyed several independent transcriptomic studies addressing the response of juvenile maize to moderate or severe cold. Among the tens of thousands of genes found to change expression upon cold treatment less than 500 were reported in more than one study, indicating an astonishing variability of the expression changes, likely depending on the experimental design and plant material used. Nearly all these “common” genes were specific to either moderate or to severe cold and formed distinct interaction networks, indicating fundamentally different responses. Moreover, down-regulation of gene expression dominated strongly in moderate cold and up-regulation prevailed in severe cold. Very few of these genes have ever been mentioned in the literature as cold-stress–related, indicating that most response pathways remain poorly known at the molecular level. We posit that the genes identified by the present analysis are attractive candidates for further functional studies and their arrangement in complex interaction networks indicates that a re-interpretation of the present state of knowledge on the maize cold-response is justified.

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“…Conversely, most non-genetic sources are due to macro-environmental fluctuations resulting from resource availability during crop lifetime (Shelford, 1931). Despite this unfolded division, the effect of the environment on shaping gene expression (e.g., Plessis et al, 2015;Jończyk et al, 2017;Liu et al, 2020) and fine-tuning epigenetic factors (Varotto et al, 2020;Vendramin et al, 2020) creates an indissoluble envirotype-phenotype covariance in the phenotypic records (Lynch and Walsh, 1998). Thus, for any genotype-phenotype association study across multiple environments (e.g., mapping quantitative trait loci, QLT; genomic association studies, GWAS), there is a strong non-genetic influence that can be better understood using envirotypingbased data, i.e., a foundation of multiple techniques to collect, process, and integrate environmental information in genetic and genomic studies, Costa-Neto et al (2020a).…”

Section: Introductionmentioning

confidence: 99%

EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture

Costa‐Neto

Galli

Fanelli

et al. 2020

Preprint

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Envirotyping is a core of techniques used to unfold the non-genetic drivers associated with the phenotypic adaptation of living organisms. Here we introduce the EnvRtype R package, a novel toolkit developed to interplay large-scale envirotyping data (enviromics) into quantitative genomics. To start an user-friendly envirotyping pipeline, this package offers: (1) remote sensing tools for collecting (get_weather and Extract_GIS functions) and processing ecophysiological variables (processWTH function) from raw-environmental data at single locations or worldwide level; (2) environmental characterization by typing environments and profiling descriptors of environmental quality (EnvTyping function), but also for gathering environmental covariables as quantitative descriptors for predictive purposes (W.matrix function); (3) identification of environmental similarity that can be used as an enviromic-based kernel (EnvKernel function) in whole-genome prediction (GP), aiming to increase ecophysiology knowledge in genomic-best unbiased predictions (GBLUP) and emulate reaction-norm effects (get_kernel function). We highlight literature mining concepts in fine-tuning envirotyping parameters for each plant species and target growing environment. We show that envirotyping for predictive breeding is not only collect raw data, but process it into a ecophysiology-smart way. Examples of use for creating global-scale envirotyping networks and the integration of reaction-norm modeling in GP is also outlined. We conclude that EnvRtype provides a cost-effective envirotyping pipeline capable to provide good-quality enviromic data for a diverse set of genomic-based studies, especially for increasing accuracy in GP across multiple environments.

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Global analysis of gene expression in maize leaves treated with low temperature. II. Combined effect of severe cold (8 °C) and circadian rhythm

Cited by 24 publications

References 76 publications

OsRACK1A, encodes a circadian clock-regulated WD40 protein, negatively affect salt tolerance in rice

OsRACK1A, encodes a circadian clock-regulated WD40 protein, negatively affect salt tolerance in rice

Maize Response to Low Temperatures at the Gene Expression Level: A Critical Survey of Transcriptomic Studies

EnvRtype: a software to interplay enviromics and quantitative genomics in agriculture

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