Novel insights into the genomics of rice root adaptive development

Rebouillat, Julia; Brasileiro, Amc; Diévart, Anne; Gantet, Pascal; Breitler, Jean‐Christophe; Johnson, Alexander; Courtois, B.; Ahmadi, Nourollah; Raı̈ssac, Marcel De; Luquet, Delphine; Conte, Mariana; This, Dominique; Pati, P.; Le, Quang Hien; Meynard, Donaldo; Verdeil, Jean‐Luc; Guiderdoni, Emmanuel

doi:10.1142/9789812708816_0009

Cited by 6 publications

(6 citation statements)

References 51 publications

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“…Roots are considered a primary site for stress signal perception, where a signaling mechanism cascade initiates gene expression in response to drought stress. These transcriptional changes can result in successful adaptations, protecting plants against environmental stress [ 31 ]. The differentially expressed ESTs identified in our study provide a list of gene regulated in response to terminal drought stress in root tissue of chickpea.…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

et al. 2011

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BackgroundChickpea (Cicer arietinum L.) is an important grain-legume crop that is mainly grown in rainfed areas, where terminal drought is a major constraint to its productivity. We generated expressed sequence tags (ESTs) by suppression subtraction hybridization (SSH) to identify differentially expressed genes in drought-tolerant and -susceptible genotypes in chickpea.ResultsEST libraries were generated by SSH from root and shoot tissues of IC4958 (drought tolerant) and ICC 1882 (drought resistant) exposed to terminal drought conditions by the dry down method. SSH libraries were also constructed by using 2 sets of bulks prepared from the RNA of root tissues from selected recombinant inbred lines (RILs) (10 each) for the extreme high and low root biomass phenotype. A total of 3062 unigenes (638 contigs and 2424 singletons), 51.4% of which were novel in chickpea, were derived by cluster assembly and sequence alignment of 5949 ESTs. Only 2185 (71%) unigenes showed significant BLASTX similarity (<1E-06) in the NCBI non-redundant (nr) database. Gene ontology functional classification terms (BLASTX results and GO term), were retrieved for 2006 (92.0%) sequences, and 656 sequences were further annotated with 812 Enzyme Commission (EC) codes and were mapped to 108 different KEGG pathways. In addition, expression status of 830 unigenes in response to terminal drought stress was evaluated using macro-array (dot blots). The expression of few selected genes was validated by northern blotting and quantitative real-time PCR assay.ConclusionOur study compares not only genes that are up- and down-regulated in a drought-tolerant genotype under terminal drought stress and a drought susceptible genotype but also between the bulks of the selected RILs exhibiting extreme phenotypes. More than 50% of the genes identified have been shown to be associated with drought stress in chickpea for the first time. This study not only serves as resource for marker discovery, but can provide a better insight into the selection of candidate genes (both up- and downregulated) associated with drought tolerance. These results can be used to identify suitable targets for manipulating the drought-tolerance trait in chickpea.

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Section: Resultsmentioning

confidence: 99%

Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

et al. 2011

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“…When subjected to various abiotic stresses from soil, such as drought and heavy metals, roots are the first site for sensing stress signals and initiating signaling cascades at the molecular level in response to adverse environments. Through these responses, plants can regulate gene expression of regulatory and functional proteins to enhance stress tolerance 9 . Plant response to drought stress has become highly important in current plant biology research because drought stress can lead to a complex process that involves morphological, physiological, and biochemical changes 10 – 13 .…”

Section: Introductionmentioning

confidence: 99%

Identification of differentially accumulated proteins involved in regulating independent and combined osmosis and cadmium stress response in Brachypodium seedling roots

Chen

Zhu

et al. 2018

Sci Rep

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In this study, we aimed to identify differentially accumulated proteins (DAPs) involved in PEG mock osmotic stress, cadmium (Cd2+) stress, and their combined stress responses in Brachypodium distachyon seedling roots. The results showed that combined PEG and Cd2+ stresses had more significant effects on Brachypodium seedling root growth, physiological traits, and ultrastructures when compared with each individual stress. Totally, 106 DAPs were identified that are responsive to individual and combined stresses in roots. These DAPs were mainly involved in energy metabolism, detoxification and stress defense and protein metabolism. Principal component analysis revealed that DAPs from Cd2+ and combined stress treatments were grouped closer than those from osmotic stress treatment, indicating that Cd2+ and combined stresses had more severe influences on the root proteome than osmotic stress alone. Protein–protein interaction analyses highlighted a 14-3-3 centered sub-network that synergistically responded to osmotic and Cd2+ stresses and their combined stresses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 14 key DAP genes revealed that most genes showed consistency between transcriptional and translational expression patterns. A putative pathway of proteome metabolic changes in Brachypodium seedling roots under different stresses was proposed, which revealed a complicated synergetic responsive network of plant roots to adverse environments.

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“…Roots are supposed to be the primary site for sensing drought stress to initiate signaling cascade at molecular level in responses to drought. Plants can successfully adopt a tolerance mechanism against environmental stress by regulating gene expression through transcriptional changes in regulatory and functional proteins (Périn et al, 2007 ). In a study, Kawasaki et al ( 2001 ) observed that gene expression profiling of rice under salt stress may result in up and downregulation of ~10% of the transcripts.…”

Section: Introductionmentioning

confidence: 99%

Elucidation of Complex Nature of PEG Induced Drought-Stress Response in Rice Root Using Comparative Proteomics Approach

et al. 2016

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Along with many adaptive strategies, dynamic changes in protein abundance seem to be the common strategy to cope up with abiotic stresses which can be best explored through proteomics. Understanding of drought response is the key to decipher regulatory mechanism of better adaptation. Rice (Oryza sativa L.) proteome represents a phenomenal source of proteins that govern traits of agronomic importance, such as drought tolerance. In this study, a comparison of root cytoplasmic proteome was done for a drought tolerant rice (Heena) cultivar in PEG induced drought conditions. A total of 510 protein spots were observed by PDQuest analysis and 125 differentially regulated spots were subjected for MALDI-TOF MS-MS analysis out of which 102 protein spots identified which further led to identification of 78 proteins with a significant score. These 78 differentially expressed proteins appeared to be involved in different biological pathways. The largest percentage of identified proteins was involved in bioenergy and metabolism (29%) and mainly consists of malate dehydrogenase, succinyl-CoA, putative acetyl-CoA synthetase, and pyruvate dehydrogenase etc. This was followed by proteins related to cell defense and rescue (22%) such as monodehydroascorbate reductase and stress-induced protein sti1, then by protein biogenesis and storage class (21%) e.g. putative thiamine biosynthesis protein, putative beta-alanine synthase, and cysteine synthase. Further, cell signaling (9%) proteins like actin and prolyl endopeptidase, and proteins with miscellaneous function (19%) like Sgt1 and some hypothetical proteins were also represented a large contribution toward drought regulatory mechanism in rice. We propose that protein biogenesis, cell defense, and superior homeostasis may render better drought-adaptation. These findings might expedite the functional determination of the drought-responsive proteins and their prioritization as potential molecular targets for perfect adaptation.

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Novel insights into the genomics of rice root adaptive development

Cited by 6 publications

References 51 publications

Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

Comparative analysis of expressed sequence tags (ESTs) between drought-tolerant and -susceptible genotypes of chickpea under terminal drought stress

Identification of differentially accumulated proteins involved in regulating independent and combined osmosis and cadmium stress response in Brachypodium seedling roots

Elucidation of Complex Nature of PEG Induced Drought-Stress Response in Rice Root Using Comparative Proteomics Approach

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