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Shamloo-Dashtpagerdi, R., Lindlöf, A. & Nouripour-Sisakht, J. (2023). Unraveling the regulatory role of MYC2 on ASMT gene expression in wheat: Implications for melatonin biosynthesis and drought tolerance. Physiologia Plantarum, 175(5), Article ID e14015.
Open this publication in new window or tab >>Unraveling the regulatory role of MYC2 on ASMT gene expression in wheat: Implications for melatonin biosynthesis and drought tolerance
2023 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 175, no 5, article id e14015Article in journal (Refereed) Published
Abstract [en]

Recognized for its multifaceted functions, melatonin is a hormone found in both animals and plants. In the plant kingdom, it plays diverse roles, regulating growth, development, and stress responses. Notably, melatonin demonstrates its significance by mitigating the effects of abiotic stresses like drought. However, understanding the precise regulatory mechanisms controlling melatonin biosynthesis genes, especially during monocots' response to stresses, requires further exploration. Seeking to understand the molecular basis of drought stress tolerance in wheat, we analyzed RNA-Seq libraries of wheat exposed to drought stress using bioinformatics methods. In light of our findings, we identified that the Myelocytomatosis oncogenes 2 (MYC2) transcription factor is a hub gene upstream of a main melatonin biosynthesis gene, N-acetylserotonin methyltransferase (ASMT), in the wheat drought response-gene network. Promoter analysis of the ASMT gene suggested that it might be a target gene of MYC2. We conducted a set of molecular and physiochemical assays along with robust machine learning approaches to elevate those findings further. MYC2 and ASMT were co-regulated under Jasmonate, drought, and a combination of them in the leaf tissues of wheat was detected. A meaningful correlation was observed among gene expression profiles, melatonin contents, photosynthetic activities, antioxidant enzyme activities, H2O2 levels, and plasma membrane damage. The results indicated an evident relationship between jasmonic acid and the melatonin biosynthesis pathway. Moreover, it seems that the MYC2-ASMT module might contribute to wheat drought tolerance by regulating melatonin contents. 

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
National Category
Bioinformatics and Systems Biology Genetics
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-23212 (URN)10.1111/ppl.14015 (DOI)001059267900001 ()2-s2.0-85169545506 (Scopus ID)
Note

© 2023 Scandinavian Plant Physiology Society.

Correspondence: Roohollah Shamloo-Dashtpagerdi, Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran. Email:shamloo.r@gmail.com

We acknowledge support from the department of Agriculture and Natural Resources, the Higher Education Center of Eghlid.

Available from: 2023-09-14 Created: 2023-09-14 Last updated: 2023-12-19Bibliographically approved
Shamloo-Dashtpagerdi, R., Aliakbari, M., Lindlöf, A. & Tahmasebi, S. (2022). A systems biology study unveils the association between a melatonin biosynthesis gene, O-methyl transferase 1 (OMT1) and wheat (Triticum aestivum L.) combined drought and salinity stress tolerance. Planta, 255(5), Article ID 99.
Open this publication in new window or tab >>A systems biology study unveils the association between a melatonin biosynthesis gene, O-methyl transferase 1 (OMT1) and wheat (Triticum aestivum L.) combined drought and salinity stress tolerance
2022 (English)In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 255, no 5, article id 99Article in journal (Refereed) Published
Abstract [en]

MAIN CONCLUSION: Enhanced levels of endogenous melatonin in the root of wheat, mainly through the OMT1 gene, augment the antioxidant system, reestablish redox homeostasis and are associated with combined stress tolerance. A systems biology approach, including a collection of computational analyses and experimental assays, led us to uncover some aspects of a poorly understood phenomenon, namely wheat (Triticum aestivum L.) combined drought and salinity stress tolerance. Accordingly, a cross-study comparison of stress experiments was performed via a meta-analysis of Expressed Sequence Tags (ESTs) data from wheat roots to uncover the overlapping gene network of drought and salinity stresses. Identified differentially expressed genes were functionally annotated by gene ontology enrichment analysis and gene network analysis. Among those genes, O-methyl transferase 1 (OMT1) was highlighted as a more important (hub) gene in the dual-stress response gene network. Afterwards, the potential roles of OMT1 in mediating physiochemical indicators of stress tolerance were investigated in two wheat genotypes differing in abiotic stress tolerance. Regression analysis and correspondence analysis (CA) confirmed that the expression profiles of the OMT1 gene and variations in melatonin content, antioxidant enzyme activities, proline accumulation, H2O2 and malondialdehyde (MDA) contents are significantly associated with combined stress tolerance. These results reveal that the OMT1 gene may contribute to wheat combined drought and salinity stress tolerance through augmenting the antioxidant system and re-establishing redox homeostasis, probably via the regulation of melatonin biosynthesis as a master regulator molecule. Our findings provide new insights into the roles of melatonin in wheat combined drought and salinity stress tolerance and suggest a novel plausible regulatory node through the OMT1 gene to improve multiple-stress tolerant crops.

Place, publisher, year, edition, pages
Springer Nature Switzerland AG, 2022
Keywords
Abiotic stress, Expressed sequence tags, Gene network, Melatonin, Meta-analysis
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-21072 (URN)10.1007/s00425-022-03885-4 (DOI)000778977800001 ()35386021 (PubMedID)2-s2.0-85127695780 (Scopus ID)
Note

© 2022 Springer Nature Switzerland AG. Part of Springer Nature.

Available from: 2022-04-21 Created: 2022-04-21 Last updated: 2022-10-11Bibliographically approved
Shamloo‐Dashtpagerdi, R., Lindlöf, A. & Tahmasebi, S. (2022). Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis. Physiologia Plantarum, 174(5), Article ID e13790.
Open this publication in new window or tab >>Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis
2022 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 174, no 5, article id e13790Article in journal (Refereed) Published
Abstract [en]

Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity-exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O-METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
physiological-responses, stress, accumulation, proline, targets
National Category
Biochemistry and Molecular Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-21978 (URN)10.1111/ppl.13790 (DOI)000864276800001 ()36169653 (PubMedID)2-s2.0-85140649007 (Scopus ID)
Note

This research was supported by Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran.

Available from: 2022-10-20 Created: 2022-10-20 Last updated: 2023-01-17Bibliographically approved
Lindlöf, A. (2022). The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies. Bioinformatics and Biology Insights, 16, 11779322211062722:1-11779322211062722:13
Open this publication in new window or tab >>The Vulnerability of the Developing Brain: Analysis of Highly Expressed Genes in Infant C57BL/6 Mouse Hippocampus in Relation to Phenotypic Annotation Derived From Mutational Studies
2022 (English)In: Bioinformatics and Biology Insights, E-ISSN 1177-9322, Vol. 16, p. 11779322211062722:1-11779322211062722:13Article in journal (Refereed) Published
Abstract [en]

The hippocampus has been shown to have a major role in learning and memory, but also to participate in the regulation of emotions. However, its specific role(s) in memory is still unclear. Hippocampal damage or dysfunction mainly results in memory issues, especially in the declarative memory but, in animal studies, has also shown to lead to hyperactivity and difficulty in inhibiting responses previously taught. The brain structure is affected in neuropathological disorders, such as Alzheimer’s, epilepsy, and schizophrenia, and also by depression and stress. The hippocampus structure is far from mature at birth and undergoes substantial development throughout infant and juvenile life. The aim of this study was to survey genes highly expressed throughout the postnatal period in mouse hippocampus and which have also been linked to an abnormal phenotype through mutational studies to achieve a greater understanding about hippocampal functions during postnatal development. Publicly available gene expression data from C57BL/6 mouse hippocampus was analyzed; from a total of 5 time points (at postnatal day 1, 10, 15, 21, and 30), 547 genes highly expressed in all of these time points were selected for analysis. Highly expressed genes are considered to be of potential biological importance and appear to be multifunctional, and hence any dysfunction in such a gene will most likely have a large impact on the development of abilities during the postnatal and juvenile period. Phenotypic annotation data downloaded from Mouse Genomic Informatics database were analyzed for these genes, and the results showed that many of them are important for proper embryo development and infant survival, proper growth, and increase in body size, as well as for voluntary movement functions, motor coordination, and balance. The results also indicated an association with seizures that have primarily been characterized by uncontrolled motor activity and the development of proper grooming abilities. The complete list of genes and their phenotypic annotation data have been compiled in a file for easy access.

Place, publisher, year, edition, pages
Sage Publications, 2022
Keywords
Hippocampus, postnatal development, infant, phenotypic annotation, mutational studies, mouse
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-20846 (URN)10.1177/11779322211062722 (DOI)000740693200001 ()35023907 (PubMedID)2-s2.0-85122386383 (Scopus ID)
Note

CC BY 4.0

The author(s) received no financial support for the research, authorship, and/or publication of this article.

Available from: 2022-01-10 Created: 2022-01-10 Last updated: 2023-04-26Bibliographically approved
Aliakbari, M., Cohen, S. P., Lindlöf, A. & Shamloo-Dashtpagerdi, R. (2021). Rubisco activase A (RcaA) is a central node in overlapping gene network of drought and salinity in Barley (Hordeum vulgare L.) and may contribute to combined stress tolerance. Plant physiology and biochemistry (Paris), 161, 248-258
Open this publication in new window or tab >>Rubisco activase A (RcaA) is a central node in overlapping gene network of drought and salinity in Barley (Hordeum vulgare L.) and may contribute to combined stress tolerance
2021 (English)In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 161, p. 248-258Article in journal (Refereed) Published
Abstract [en]

Co-occurrence of abiotic stresses, especially drought and salinity, is a natural phenomenon in field conditions and is worse for crop production than any single stress. Nowadays, rigorous methods of meta-analysis and systems biology have made it possible to perform cross-study comparisons of single stress experiments, which can uncover main overlapping mechanisms underlying tolerance to combined stress. In this study, a meta-analysis of RNA-Seq data was conducted to obtain the overlapping gene network of drought and salinity stresses in barley (Hordeum vulgare L.), which identified Rubisco activase A (RcaA) as a hub gene in the dual-stress response. Thereafter, a greenhouse experiment was carried out using two barley genotypes with different abiotic stress tolerance and evaluated several physiochemical properties as well as the expression profile and protein activity of RcaA. Finally, machine learning analysis was applied to uncover relationships among combined stress tolerance and evaluated properties. We identified 441 genes which were differentially expressed under both drought and salinity stress. Results revealed that the photosynthesis pathway and, in particular, the RcaA gene are major components of the dual-stress responsive transcriptome. Comparative physiochemical and molecular evaluations further confirmed that enhanced photosynthesis capability, mainly through regulation of RcaA expression and activity as well as accumulation of proline content, have a significant association with combined drought and salinity stress tolerance in barley. Overall, our results clarify the importance of RcaA in combined stress tolerance and may provide new insights for future investigations. 

Place, publisher, year, edition, pages
Elsevier, 2021
Keywords
Abiotic stress, Meta-Analysis, Photosynthesis, Physiological response, RNA-Sequencing, Systems biology
National Category
Agricultural Science Genetics Biochemistry and Molecular Biology Bioinformatics (Computational Biology)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-19530 (URN)10.1016/j.plaphy.2021.02.016 (DOI)000637955100024 ()33652257 (PubMedID)2-s2.0-85101639411 (Scopus ID)
Note

© 2021 Elsevier Masson SAS

Available from: 2021-03-11 Created: 2021-03-11 Last updated: 2021-05-17Bibliographically approved
Keane, S., Améen, S., Lindlöf, A. & Ejeskär, K. (2020). Low DLG2 gene expression, a link between 11q-deleted and MYCN-amplified neuroblastoma, causes forced cell cycle progression, and predicts poor patient survival. Cell Communication and Signaling, 18(1), Article ID 65.
Open this publication in new window or tab >>Low DLG2 gene expression, a link between 11q-deleted and MYCN-amplified neuroblastoma, causes forced cell cycle progression, and predicts poor patient survival
2020 (English)In: Cell Communication and Signaling, E-ISSN 1478-811X, Vol. 18, no 1, article id 65Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: Neuroblastoma (NB) is a childhood neural crest tumor. There are two groups of aggressive NBs, one with MYCN amplification, and another with 11q chromosomal deletion; these chromosomal aberrations are generally mutually exclusive. The DLG2 gene resides in the 11q-deleted region, thus makes it an interesting NB candidate tumor suppressor gene. METHODS: We evaluated the association of DLG2 gene expression in NB with patient outcomes, stage and MYCN status, using online microarray data combining independent NB patient data sets. Functional studies were also conducted using NB cell models and the fruit fly. RESULTS: Using the array data we concluded that higher DLG2 expression was positively correlated to patient survival. We could also see that expression of DLG2 was inversely correlated with MYCN status and tumor stage. Cell proliferation was lowered in both 11q-normal and 11q-deleted NB cells after DLG2 over expression, and increased in 11q-normal NB cells after DLG2 silencing. Higher level of DLG2 increased the percentage of cells in the G2/M phase and decreased the percentage of cells in the G1 phase. We detected increased protein levels of Cyclin A and Cyclin B in fruit fly models either over expressing dMyc or with RNAi-silenced dmDLG, indicating that both events resulted in enhanced cell cycling. Induced MYCN expression in NB cells lowered DLG2 gene expression, which was confirmed in the fly; when dMyc was over expressed, the dmDLG protein level was lowered, indicating a link between Myc over expression and low dmDLG level. CONCLUSION: We conclude that low DLG2 expression level forces cell cycle progression, and that it predicts poor NB patient survival. The low DLG2 expression level could be caused by either MYCN-amplification or 11q-deletion. Video Abstract.

Place, publisher, year, edition, pages
BioMed Central (BMC), 2020
Keywords
11q, DLG2, MAGUK, MYCN, Neuroblastoma
National Category
Medical Genetics Cancer and Oncology
Research subject
Translational Medicine TRIM; Bioinformatics
Identifiers
urn:nbn:se:his:diva-18430 (URN)10.1186/s12964-020-00553-6 (DOI)000615918700002 ()32312269 (PubMedID)2-s2.0-85083811841 (Scopus ID)
Note

CC BY 4.0

Available from: 2020-05-07 Created: 2020-05-07 Last updated: 2023-10-23Bibliographically approved
Shamloo-Dashtpagerdi, R., Lindlöf, A., Aliakbari, M. & Pirasteh-Anosheh, H. (2020). Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes. Physiologia Plantarum, 170(1), 46-59
Open this publication in new window or tab >>Plausible association between drought stress tolerance of barley (Hordeum vulgare L.) and programmed cell death via MC1 and TSN1 genes
2020 (English)In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 170, no 1, p. 46-59Article in journal (Refereed) Published
Abstract [en]

Studying the drought-responsive transcriptome is of high interest as it can serve as a blueprint for stress adaptation strategies. Despite extensive studies in this area, there are still many details to be uncovered, such as the importance of each gene involved in the stress response as well as the relationship between these genes and the physiochemical processes governing stress tolerance. This study was designed to address such important details and to gain insights into molecular responses of barley (Hordeum vulgare L.) to drought stress. To that, we combined RNA-seq data analysis with field and greenhouse drought experiments in a systems biology approach. RNA-sequence analysis identified a total of 665 differentially expressed genes (DEGs) belonging to diverse functional categories. A gene network was derived from the DEGs, which comprised of a total of 131 nodes and 257 edges. Gene network topology analysis highlighted two programmed cell death (PCD) modulating genes, MC1 (metacaspase 1) and TSN1 (Tudor-SN 1), as important (hub) genes in the predicted network. Based on the field trial, a drought-tolerant and a drought-susceptible barley genotype was identified from eight tested cultivars. Identified genotypes exhibited different physiochemical characteristics, including proline content, chlorophyll concentration, percentage of electrolyte leakage and malondialdehyde content as well as expression profiles of MC1 and TSN1 genes. Machine learning and correspondence analysis revealed a significant relationship between drought tolerance and measured characteristics in the context of PCD. Our study provides new insights which bridge barley drought tolerance to PCD through MC1 and TSN1 pathway.

Place, publisher, year, edition, pages
John Wiley & Sons, 2020
National Category
Genetics
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-18411 (URN)10.1111/ppl.13102 (DOI)000526701900001 ()32246464 (PubMedID)2-s2.0-85083302349 (Scopus ID)
Available from: 2020-04-30 Created: 2020-04-30 Last updated: 2022-05-10Bibliographically approved
Shamloo-Dashtpagerdia, R., Lindlöf, A., Niazi, A. & Pirasteh-Anosheh, H. (2019). LOS2 gene plays a potential role in barley (Hordeum vulgare L.) salinity tolerance as a hub gene. Molecular breeding, 39(8), Article ID 119.
Open this publication in new window or tab >>LOS2 gene plays a potential role in barley (Hordeum vulgare L.) salinity tolerance as a hub gene
2019 (English)In: Molecular breeding, ISSN 1380-3743, E-ISSN 1572-9788, Vol. 39, no 8, article id 119Article in journal (Refereed) Published
Abstract [en]

Understanding how plants respond to salinity stress is essential for developing tolerant genotypes, to keep human food secure since it is threaten by climate changes and increasing population worldwide. Barley (Hordeum vulgare) is a crop that possesses various salinity tolerance mechanisms that remain to be explored. In this study, data from an RNA-Seq experiment in barley was analyzed to identify changes in genome activities as well as differentially expressed genes (DEGs) in response to salinity stress. A gene network was predicted among identified DEGs and was subjected to network topology analysis, which resulted in the prediction of a hub gene, namely low expression of osmotically responsive gene 2 (LOS2). LOS2 and its two hierarchical downstream genes, salt-tolerant zinc finger (ZAT10) and ascorbate peroxidase 1 (APX1), were used in a genome-wide association (GWA) survey to confirm their importance. A field experiment was conducted to recognize susceptible and tolerant genotypes among 10 different barley genotypes based on the principle component analysis (PCA) of stress-related indices. In a separate salinity experiment, two of the genotypes were assessed to assign their physiological and biochemical responses as well as to identify expression profiles of LOS2, ZAT10, and APX1. From the results, the activity of the barley genome was significantly altered toward response to stress. In total, 5692 DEGs were identified and the gene network derived from these genes contained 131 nodes and 257 edges. The identified genotypes clearly showed the difference in water status, osmolyte accumulation, cell membrane damages, and ion homeostasis as well as in expression profiles for studied genes during salinity stress. Our results suggest that LOS2 along with the ZAT10 and APX1 genes may serve as an important part of barley salinity stress tolerance pathways. To our knowledge, this is the first report on the role(s) of LOS2 in barley salinity stress tolerance in a gene network system.

Place, publisher, year, edition, pages
Springer, 2019
Keywords
RNA-Seq analysis, Gene network, Principle component analysis, QTL, Genome-wide association
National Category
Genetics
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-17576 (URN)10.1007/s11032-019-1026-z (DOI)000478951500002 ()2-s2.0-85070233673 (Scopus ID)
Available from: 2019-08-23 Created: 2019-08-23 Last updated: 2020-05-27Bibliographically approved
Shamloo-Dashtpagerdi, R., Razi, H., Aliakbari, M., Lindlöf, A., Ebrahimi, M. & Ebrahimie, E. (2015). A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis: Application to Arabidopsis. Journal of Theoretical Biology, 364, 364-376
Open this publication in new window or tab >>A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: Application to Arabidopsis: Application to Arabidopsis
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2015 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, Vol. 364, p. 364-376Article in journal (Refereed) Published
Abstract [en]

Cis regulatory elements (CREs), located within promoter regions, play a significant role in the blueprint for transcriptional regulation of genes. There is a growing interest to study the combinatorial nature of CREs including presence or absence of CREs, the number of occurrences of each CRE, as well as of their order and location relative to their target genes. Comparative promoter analysis has been shown to be a reliable strategy to test the significance of each component of promoter architecture. However, it remains unclear what level of difference in the number of occurrences of each CRE is of statistical significance in order to explain different expression patterns of two genes. In this study, we present a novel statistical approach for pairwise comparison of promoters of Arabidopsis genes in the context of number of occurrences of each CRE within the promoters. First, using the sample of 1000 Arabidopsis promoters, the results of the goodness of fit test and non-parametric analysis revealed that the number of occurrences of CREs in a promoter sequence is Poisson distributed. As a promoter sequence contained functional and non-functional CREs, we addressed the issue of the statistical distribution of functional CREs by analyzing the ChIP-seq datasets. The results showed that the number of occurrences of functional CREs over the genomic regions was determined as being Poisson distributed. In accordance with the obtained distribution of CREs occurrences, we suggested the Audic and Claverie (AC) test to compare two promoters based on the number of occurrences for the CREs. Superiority of the AC test over Chi-square (2 2) and Fisher’s exact tests was also shown, as the AC test was able to detect a higher number of significant CREs. The two case studies on the Arabidopsis genes were performed in order to biologically verify the pairwise test for promoter comparison. Consequently, a number of CREs with significantly different occurrences was identified between the promoters. The results of the pairwise comparative analysis together with the expression data for the studied genes revealed the biological significance of the identified CREs. 

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
CREs occurrence, Motif enrichment, Transcriptional regulation
National Category
Bioinformatics and Systems Biology
Research subject
Natural sciences; Bioinformatics
Identifiers
urn:nbn:se:his:diva-10113 (URN)10.1016/j.jtbi.2014.09.038 (DOI)000347022500037 ()25303887 (PubMedID)2-s2.0-84908323856 (Scopus ID)
Note

This publication was based on a collaboration between researchers at University of Skövde and Shiraz University, Iran.

Available from: 2014-10-23 Created: 2014-10-23 Last updated: 2020-05-27Bibliographically approved
Lindlöf, A., Chawade, A., Sikora, P. & Olsson, O. (2015). Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms. PLOS ONE, 10(5), Article ID e0125385.
Open this publication in new window or tab >>Comparative Transcriptomics of Sijung and Jumli Marshi Rice during Early Chilling Stress Imply Multiple Protective Mechanisms
2015 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 5, article id e0125385Article in journal (Refereed) Published
Abstract [en]

Introduction

Low temperature is one of the major environmental factors that adversely affect plant growth and yield. Many cereal crops from tropical regions, such as rice, are chilling sensitive and, therefore, are affected already at <10°C. Interestingly, it has been demonstrated that chilling susceptibility varies greatly among rice varieties, which indicates differences in the underlying molecular responses. Understanding these differences is vital for continued development of rational breeding and transgenic strategies for more tolerant varieties. Thus, in this study, we conducted a comparative global gene expression profiling analysis of the chilling tolerant varieties Sijung and Jumli Marshi (spp. Japonica) during early chilling stress (<24 h, 10°C).

Methods and Results

Global gene expression experiments were conducted with Agilent Rice Gene Expression Microarray 4x44K. The analysed results showed that there was a relatively low (percentage or number) overlap in differentially expressed genes in the two varieties and that substantially more genes were up-regulated in Jumli Marshi than in Sijung but the number of down-regulated genes were higher in Sijung. In broad GO annotation terms, the activated response pathways in Sijung and Jumli Marshi were coherent, as a majority of the genes belonged to the catalytic, transcription regulator or transporter activity categories. However, a more detailed analysis revealed essential differences. For example, in Sijung, activation of calcium and phosphorylation signaling pathways, as well as of lipid transporters and exocytosis-related proteins take place very early in the stress response. Such responses can be coupled to processes aimed at strengthening the cell wall and plasma membrane against disruption. On the contrary, in Jumli Marshi, sugar production, detoxification, ROS scavenging, protection of chloroplast translation, and plausibly the activation of the jasmonic acid pathway were the very first response activities. These can instead be coupled to detoxification processes.

Conclusions

Based on the results inferred from this study, we conclude that different, but overlapping, strategies are undertaken by the two varieties to cope with the chilling stress; in Sijung the initial molecular responses seem to be mainly targeted at strengthening the cell wall and plasma membrane, whereas in Jumli Marshi the protection of chloroplast translation and detoxification is prioritized.

Place, publisher, year, edition, pages
Public Library of Science, 2015
Keywords
cold stress, rice, Oryza sativa, microarray, data analysis, systems biology, bioinformatics
National Category
Bioinformatics and Systems Biology
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-10985 (URN)10.1371/journal.pone.0125385 (DOI)000354545600015 ()25973918 (PubMedID)2-s2.0-84929353184 (Scopus ID)
Note

CC BY 4.0

Available from: 2015-06-02 Created: 2015-06-02 Last updated: 2022-05-06Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-1837-429X

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