Transcriptome analysis of rice-seedling roots under soil–salt stress using RNA-Seq method

Chandran, Anil Kumar Nalini; Kim, Jeong-Won; Yoo, Yo-Han; Park, Hye Lin; Kim, Yeon-Ju; Cho, Man-Ho; Jung, Ki‐Hong

doi:10.1007/s11816-019-00550-3

Cited by 43 publications

(27 citation statements)

References 56 publications

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“…Many of the upregulated genes also code for enzymes involved in secondary metabolism. While they are believed to be associated with biotic stresses, they are also expressed in response to abiotic stresses 16,17 , as shown in the transcriptome analysis by Chandran et al 58 for a japonica rice variety under salinity stress. Glycosylated flavonoids, hydroxycinnamic acids and chlorogenic acid are involved in antioxidative activity and induced in plants following endophyte colonization 59 .…”

Section: Differential Gene Expression In the Rice Variety Ir-64 On Comentioning

confidence: 97%

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Sampangi-Ramaiah¹,

Jagadheesh²,

Dey³

et al. 2020

Sci Rep

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Endophytes, both of bacterial and fungal origin, are ubiquitously present in all plants. While their origin and evolution are enigmatic, there is burgeoning literature on their role in promoting growth and stress responses in their hosts. We demonstrate that a salt-tolerant endophyte isolated from salt-adapted Pokkali rice, a Fusarium sp., colonizes the salt-sensitive rice variety IR-64, promotes its growth under salt stress and confers salinity stress tolerance to its host. Physiological parameters, such as assimilation rate and chlorophyll stability index were higher in the colonized plants. Comparative transcriptome analysis revealed 1348 up-regulated and 1078 down-regulated genes in plants colonized by the endophyte. Analysis of the regulated genes by MapMan and interaction network programs showed that they are involved in both abiotic and biotic stress tolerance, and code for proteins involved in signal perception (leucine-rich repeat proteins, receptor-like kinases) and transduction (ca 2+ and calmodulin-binding proteins), transcription factors, secondary metabolism and oxidative stress scavenging. For nine genes, the data were validated by qPCR analysis in both roots and shoots. Taken together, these results show that salt-adapted Pokkali rice varieties are powerful sources for the identification of novel endophytes, which can be used to confer salinity tolerance to agriculturally important, but salt-sensitive rice varieties. Salinity stress is one of the most devastating abiotic stresses that affect growth, development and productivity of major crops. A soil is termed saline if its osmotic pressure is approximately 0.2 M Pa with an electrical conductivity of 4 dS/m or more (equivalent to ~40 mM NaCl) 1,2. It is estimated that at least 50% of the arable land worldwide will be salt affected by the year 2050 and this is expected to further increase due to global climate change 3. Rice (Oryza sativa L.), a major staple food crop, is one of the most salt-sensitive cereals 4. In the Indo-Gangetic Basin in India, an estimated 45% loss in rice production was attributed to salinity stress alone 5,6. The responses of plants to salinity stress are often multi-faceted and complex. In the initial phase, salinity stress manifests itself as osmotic stress with reduction in water uptake by plants. This triggers a range of metabolic and molecular cascades such as inhibition of cell expansion, stomatal conductance, photosynthetic activity, abscisic acid (ABA)-mediated responses followed by stimulation of the SOD and peroxidase activities as well as accumulation of osmolytes like proline. The later phase of salinity stress leads to ionic stress, which is due to the

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Section: Differential Gene Expression In the Rice Variety Ir-64 On Comentioning

confidence: 97%

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

Sampangi-Ramaiah¹,

Jagadheesh²,

Dey³

et al. 2020

Sci Rep

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“…Dongjin) seeds were germinated on the Murashige Skoog medium for 14 days at 28 • C. Subsequently, the seedlings were washed with sterilized water to completely remove the agar and were air-dried for 0, 2, 6, and 12 h at 28 • C for drought stress treatment [25]. To simulate salinity stress, we exposed 14-day-old plants to 200 mM NaCl for 0, 2, 6, and 12 h at 28 • C [26]. In the last, we exposed 14-day-old plants to 4 • C ± 1 • C for 0, 2, 6, and 12 h for cold stress treatment.…”

Section: Plant Materials and Abiotic Stress Treatmentmentioning

confidence: 99%

An Abiotic Stress Responsive U-Box E3 Ubiquitin Ligase Is Involved in OsGI-Mediating Diurnal Rhythm Regulating Mechanism

Yoo

Jung

2020

Plants

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The plant U-box (PUB) protein is the E3 ligase that plays roles in the degradation or post-translational modification of target proteins. In rice, 77 U-box proteins were identified and divided into eight classes according to the domain configuration. We performed a phylogenomic analysis by integrating microarray expression data under abiotic stress to the phylogenetic tree context. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) expression analyses identified that eight, twelve, and eight PUB family genes are associated with responses to drought, salinity, and cold stress, respectively. In total, 16 genes showed increased expression in response to three abiotic stresses. Among them, the expression of OsPUB2 in class II and OsPUB33, OsPUB39, and OsPUB41 in class III increased in all three abiotic stresses, indicating their involvement in multiple abiotic stress regulation. In addition, we identified the circadian rhythmic expression for three out of 16 genes responding to abiotic stress through meta-microarray expression data analysis. Among them, OsPUB4 is predicted to be involved in the rice GIGANTEA (OsGI)-mediating diurnal rhythm regulating mechanism. In the last, we constructed predicted protein-protein interaction networks associated with OsPUB4 and OsGI. Our analysis provides essential information to improve environmental stress tolerance mediated by the PUB family members in rice.

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“…In recent years with the development of new high-throughput technologies such as RNA sequencing (RNA-seq) and data analysis methods, the functional characteristics of thousands of genes can be investigated systematically [12]. In rice, various RNA-seq studies have been conducted to explore the differentially expressed genes under salinity stress [13,14,15,16,17]. These datasets represent valuable genomic resources to perform meta-analysis to identify the core-conserved genes modulating salt responses in rice, regardless of the stress intensity, genotype, environment, etc.…”

Section: Introductionmentioning

confidence: 99%

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

Zhu

Xie

Wei

et al. 2019

Genes

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Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.

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Transcriptome analysis of rice-seedling roots under soil–salt stress using RNA-Seq method

Cited by 43 publications

References 56 publications

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

An endophyte from salt-adapted Pokkali rice confers salt-tolerance to a salt-sensitive rice variety and targets a unique pattern of genes in its new host

An Abiotic Stress Responsive U-Box E3 Ubiquitin Ligase Is Involved in OsGI-Mediating Diurnal Rhythm Regulating Mechanism

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice

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