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Guigard L, Jobert L, Busset N, Moulin L, Czernic P. Symbiotic compatibility between rice cultivars and arbuscular mycorrhizal fungi genotypes affects rice growth and mycorrhiza-induced resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1278990. [PMID: 37941658 PMCID: PMC10628536 DOI: 10.3389/fpls.2023.1278990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Introduction Arbuscular mycorrhizal fungi (AMF) belong to the Glomeromycota clade and can form root symbioses with 80% of Angiosperms, including crops species such as wheat, maize and rice. By increasing nutrient availability, uptake and soil anchoring of plants, AMF can improve plant's growth and tolerance to abiotic stresses. AMF can also reduce symptoms and pathogen load on infected plants, both locally and systemically, through a phenomenon called mycorrhiza induced resistance (MIR). There is scarce information on rice mycorrhization, despite the high potential of this symbiosis in a context of sustainable water management in rice production systems. Methods We studied the symbiotic compatibility (global mycorrhization & arbuscules intensity) and MIR phenotypes between six rice cultivars from two subspecies (indica: IR64 & Phka Rumduol; japonica: Nipponbare, Kitaake, Azucena & Zhonghua 11) and three AMF genotypes (Funneliformis mosseae FR140 (FM), Rhizophagus irregularis DAOM197198 (RIR) & R. intraradices FR121 (RIN)). The impact of mycorrhization on rice growth and defence response to Xanthomonas oryzae pv oryzae (Xoo) infection was recorded via both phenotypic indexes and rice marker gene expression studies. Results All three AMF genotypes colonise the roots of all rice varieties, with clear differences in efficiency depending on the combination under study (from 27% to 84% for Phka Rumduol-RIN and Nipponbare-RIR combinations, respectively). Mycorrhization significantly (α=0.05) induced negative to beneficial effects on rice growth (impact on dry weight ranging from -21% to 227% on Azucena-FM and Kitaake-RIN combinations, respectively), and neutral to beneficial effects on the extent of Xoo symptoms on leaves (except for Azucena-RIN combination which showed a 68% increase of chlorosis). R. irregularis DAOM197198 was the most compatible AMF partner of rice, with high root colonisation intensity (84% of Nipponbare's roots hyphal colonisation), beneficial effects on rice growth (dry weight +28% (IR64) to +178% (Kitaake)) and decrease of Xoo-induced symptoms (-6% (Nipponbare) to -27% (IR64)). Transcriptomic analyses by RT-qPCR on leaves of two rice cultivars contrasting in their association with AMF show two different patterns of response on several physiological marker genes. Discussion Overall, the symbiotic compatibility between rice cultivars and AMF demonstrates adequate colonization, effectively restricting the nutrient starvation response and mitigating symptoms of phytopathogenic infection.
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Affiliation(s)
| | | | | | | | - Pierre Czernic
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Eragam A, Mohapatra A, Shukla V, Kadumuri RV, George AP, Putta L, Akkareddy S, Chavali S, Vemireddy LR, Ramireddy E. Panicle transcriptome of high-yield mutant indica rice reveals physiological mechanisms and novel candidate regulatory genes for yield under reproductive stage drought stress. BMC PLANT BIOLOGY 2023; 23:493. [PMID: 37833626 PMCID: PMC10571340 DOI: 10.1186/s12870-023-04507-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Reproductive stage drought stress (RDS) is a major global threat to rice production. Due to climate change, water scarcity is becoming an increasingly common phenomenon in major rice-growing areas worldwide. Understanding RDS mechanisms will allow candidate gene identification to generate novel rice genotypes tolerant to RDS. RESULTS To generate novel rice genotypes that can sustain yield under RDS, we performed gamma-irradiation mediated mutation breeding in the drought stress susceptible mega rice variety, MTU1010. One of the mutant MM11 (MTU1010 derived mutant11) shows consistently increased performance in yield-related traits under field conditions consecutively for four generations. In addition, compared to MTU1010, the yield of MM11 is sustained in prolonged drought imposed during the reproductive stage under field and in pot culture conditions. A comparative emerged panicle transcriptome analysis of the MTU1010 and MM11 suggested metabolic adjustment, enhanced photosynthetic ability, and hormone interplay in regulating yield under drought responses during emerged panicle development. Regulatory network analysis revealed few putative significant transcription factor (TF)-target interactions involved in integrated signalling between panicle development, yield and drought stress. CONCLUSIONS A gamma-irradiate rice mutant MM11 was identified by mutation breeding, and it showed higher potential to sustain yield under reproductive stage drought stress in field and pot culture conditions. Further, a comparative panicle transcriptome revealed significant biological processes and molecular regulators involved in emerged panicle development, yield and drought stress integration. The study extends our understanding of the physiological mechanisms and candidate genes involved in sustaining yield under drought stress.
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Affiliation(s)
- Aparna Eragam
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Ankita Mohapatra
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Vishnu Shukla
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Rajashekar Varma Kadumuri
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Abin Panackal George
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Latha Putta
- Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Eswarayya Ramireddy
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.
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Shankar R, Dwivedi AK, Singh V, Jain M. Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance. PHYSIOLOGIA PLANTARUM 2023; 175:e13879. [PMID: 36805564 DOI: 10.1111/ppl.13879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.
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Affiliation(s)
- Rama Shankar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj Kumar Dwivedi
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Hu Z, He Z, Li Y, Wang Q, Yi P, Yang J, Yang C, Borovskii G, Cheng X, Hu R, Zhang W. Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco. FRONTIERS IN PLANT SCIENCE 2023; 13:1067076. [PMID: 36743571 PMCID: PMC9891310 DOI: 10.3389/fpls.2022.1067076] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/30/2022] [Indexed: 06/18/2023]
Abstract
Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.
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Affiliation(s)
- Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Zexue He
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Qing Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Pengfei Yi
- Hu'nan Tobacco Company Changde Company, Changde, Hunan, China
| | - Jiashuo Yang
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Chenkai Yang
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China
| | - Gennadii Borovskii
- Siberian Institute of Plant Physiology and Biochemistry Siberian Branch of Russian Academy of Sciences (SB RAS) Irkutsk, Lermontova, Russia
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Risheng Hu
- Hunan Tobacco Research Institute, Changsha, Hunan, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu, China
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Qiao K, Yao X, Zhou Z, Xiong J, Fang K, Lan J, Xu F, Deng X, Zhang D, Lin H. Mitochondrial alternative oxidase enhanced ABA-mediated drought tolerance in Solanum lycopersicum. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153892. [PMID: 36566671 DOI: 10.1016/j.jplph.2022.153892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The phytohormone abscisic acid (ABA) plays essential roles in modulating drought stress responses. Mitochondrial alternative oxidase (AOX) is critical for reactive oxygen species (ROS) scavenging in drought stress responses. However, whether ABA signal in concert with AOX to moderate drought stress response remains largely unclear. In our study, we uncover the positive role of AOX in ABA-mediated drought tolerance in tomato (Solanum lycopersicum). Here, we report that ABA participates in the regulation of alternative respiration, and the increased AOX was found to improve drought tolerance by reducing total ROS accumulation. We also found that transcription factor ABA response element-binding factor 1 (SlAREB1) can directly bind to the promoter of AOX1a to activate its transcription. Virus-induced gene silencing (VIGS) of SlAREB1 compromised the ABA-induced alternative respiratory pathway, disrupted redox homeostasis and decreased plant resistance to drought stress, while overexpression of AOX1a in TRV2-SlAREB1 plants partially rescued the severe drought phenotype. Taken together, our results indicated that AOX1a plays an essential role in ABA-mediated drought tolerance partially in a SlAREB1-dependent manner, providing new insights into how ABA modulates ROS levels to cope with drought stress by AOX.
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Affiliation(s)
- Kang Qiao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Xiuhong Yao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Zuxu Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Jiawei Xiong
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Ke Fang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Jiayi Lan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Fei Xu
- Life Science and Biotechnology, Wuhan Bioengineering Institute, Wuhan, China
| | - Xingguang Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China
| | - Dawei Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China.
| | - Honghui Lin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan, China.
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Li M, Liu Z, Liu C, Zhu F, Wang K, Wang Z, Li X, Lan X, Guan Q. Drought resistance of tobacco overexpressing the AfNAC1 gene of Amorpha fruticosa Linn. FRONTIERS IN PLANT SCIENCE 2022; 13:980171. [PMID: 36051295 PMCID: PMC9425102 DOI: 10.3389/fpls.2022.980171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Plants are often adversely affected by abiotic stresses such as drought, low temperature, and salinity during growth, and plant NAC-like transcription factors are involved in regulating growth and developmental processes in response to stresses such as drought and salinity. In this study, to investigate the function of AfNAC1, a co-expression network of AfNAC1 genes was constructed using gene expression data from the Chinese legume deciduous shrub, Amorpha fruticosa Linn. A 576 bp NAC transcription factor (AfNAC1 gene, MN180266) encoding 191 amino acids was isolated from Amorpha fruticosa seedlings by RT-PCR. qRT-PCR showed that the AfNAC1 gene was expressed in the roots, stems, leaves, and flowers of Amorpha fruticosa. However, drought stress significantly increased root expression, and the AfNAC1 protein was localized in the nucleus by green fluorescence detection. This study analyzed the drought resistance of overexpressing tobacco in depth. Under natural drought stress, the chlorophyll and antioxidant enzyme activities of overexpressing plants were significantly higher than those of wild-type (WT) plants, but the MDA content was lower than that of WT; after rehydration the Fv/Fm values of AfNAC1-overexpressing tobacco recovered faster than those of wild-type tobacco and rapidly reached the control levels; AfNAC1 may be involved in the regulation of the photosystem and indirectly in the regulation of the plant in response to drought stress.
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Affiliation(s)
- Minghui Li
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Ziang Liu
- College of Forestry, Northeastern Forestry University, Harbin, China
| | - Chenxi Liu
- Agriculture and Rural Bureau, Suihua, China
| | - Fengjin Zhu
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Kai Wang
- College of Forestry, Northeastern Forestry University, Harbin, China
| | - Zhenyu Wang
- Key Laboratory of Molecular Design Breeding of Soybean, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - XiuFeng Li
- Key Laboratory of Molecular Design Breeding of Soybean, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xingguo Lan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Qingjie Guan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, China
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Melatonin Promotes SGT1-Involved Signals to Ameliorate Drought Stress Adaption in Rice. Int J Mol Sci 2022; 23:ijms23020599. [PMID: 35054782 PMCID: PMC8775989 DOI: 10.3390/ijms23020599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Drought has become one of the environmental threats to agriculture and food security. Applications of melatonin (MT) serve as an effective way to alleviate drought stress, but the underlying mechanism remains poorly understood. Here, we found that foliar spray of 100-µM MT greatly mitigated the severe drought stress-induced damages in rice seedlings, including improved survival rates, enhanced antioxidant system, and adjusted osmotic balance. However, mutation of the suppressor of the G2 allele of skp1 (OsSGT1) and ABSCISIC ACID INSENSITIVE 5 (OsABI5) abolished the effects of MT. Furthermore, the upregulated expression of OsABI5 was detected in wild type (WT) under drought stress, irrespective of MT treatment, whereas OsABI5 was significantly downregulated in sgt1 and sgt1abi5 mutants. In contrast, no change of the OsSGT1 expression level was detected in abi5. Moreover, mutation of OsSGT1 and OsABI5 significantly suppressed the expression of genes associated with the antioxidant system. These results suggested that the functions of OsSGT1 in the MT-mediated alleviation of drought stress were associated with the ABI5-mediated signals. Collectively, we demonstrated that OsSGT1 was involved in the drought response of rice and that melatonin promoted SGT1-involved signals to ameliorate drought stress adaption.
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Fernandes T, Melo F, Vieira MB, Lourenço TF, Pucciariello C, Saibo NJM, Abreu IA, Oliveira MM. Screening for Abiotic Stress Response in Rice. Methods Mol Biol 2022; 2494:161-194. [PMID: 35467207 DOI: 10.1007/978-1-0716-2297-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa L.) is the staple food for over half of the world population. However, most rice varieties are severely injured by abiotic stresses, with strong social and economic impacts. Understanding rice responses to stress may guide breeding for more tolerant varieties. However, the lack of consistency in the design of the stress experiments described in the literature limits comparative studies and output assessments. The use of identical setups is the only way to generate comparable data. This chapter comprises three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB NOVA to assess the response of rice plants to different abiotic stresses-high salinity, cold, drought, simulated drought, and submergence-and their recovery capacity when intended. All sections include a detailed description of the materials and methodology and useful notes gathered from our team experience. We use seedlings since rice plants at this stage show high sensitivity to abiotic stresses. For the salt, cold, and simulated drought (PEG, polyethylene glycol) stress assays, we grow rice seedlings in a hydroponic system, while for the drought assay, plants are grown in soil and subjected to water withholding. For submergence, we use water-filled Magenta boxes. All setups enable visual score determination and are suitable for sample collection during stress imposition and also recovery. The proposed methodologies are affordable and straightforward to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic levels.
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Affiliation(s)
- Telma Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Fredilson Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Maria Beatriz Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal.
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Singh A, Panwar R, Mittal P, Hassan MI, Singh IK. Plant cytochrome P450s: Role in stress tolerance and potential applications for human welfare. Int J Biol Macromol 2021; 184:874-886. [PMID: 34175340 DOI: 10.1016/j.ijbiomac.2021.06.125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 01/06/2023]
Abstract
Cytochrome P450s (CYPs) are a versatile group of enzymes and one of the largest families of proteins, controlling various physiological processes via biosynthetic and detoxification pathways. CYPs perform multiple roles through a critical irreversible enzymatic reaction in which an oxygen atom is inserted within hydrophobic molecules, converting them into the reactive and hydro soluble components. During evolution, plants have acquired significantly more number of CYPs and represent about 1% of the encoded genes . CYPs are highly conserved proteins involved in growth, development and tolerance against biotic and abiotic stresses. Furthermore, CYPs reinforce plants' molecular and chemical defense mechanisms by regulating the biosynthesis of secondary metabolites, enhancing reactive oxygen species (ROS) scavenging and controlling biosynthesis and homeostasis of phytohormones, including abscisic acid (ABA) and jasmonates. Thus, they are the critical targets of metabolic engineering for enhancing plant defense against environmental stresses. Additionally, CYPs are also used as biocatalysts in the fields of pharmacology and phytoremediation. Herein, we highlight the role of CYPs in plant stress tolerance and their applications for human welfare.
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Affiliation(s)
- Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India.
| | - Ruby Panwar
- Department of Botany, Hansraj College, University of Delhi, New Delhi 110007, India
| | - Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India.
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Aleem M, Raza MM, Haider MS, Atif RM, Ali Z, Bhat JA, Zhao T. Comprehensive RNA-seq analysis revealed molecular pathways and genes associated with drought tolerance in wild soybean (Glycine soja Sieb. and Zucc.). PHYSIOLOGIA PLANTARUM 2021; 172:707-732. [PMID: 32984966 DOI: 10.1111/ppl.13219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Drought stress at the germination stage is an important environmental stress limiting crop yield. Hence, our study investigated comparative root transcriptome profiles of four contrasting soybean genotypes viz., drought-tolerant (PI342618B/DTP and A214/DTL) and drought-sensitive (NN86-4/DSP and A195/DSL) under drought stress using RNA-Seq approach. A total of 4850 and 6272 differentially expressed genes (DEGs) were identified in tolerant (DTP and DTL) and sensitive (DSP and DSL) genotypes, respectively. Principle component analysis (PCA) and correlation analysis revealed higher correlation between DTP and DTL. Both gene ontology (GO) and MapMan analyses showed that the drought response was enriched in DEGs associated with water and auxin transport, cell wall/membrane, antioxidant activity, catalytic activity, secondary metabolism, signaling and transcription factor (TF) activities. Out of 981 DEGs screened from above terms, only 547 showed consistent opposite expression between contrasting genotypes. Twenty-eight DEGs of 547 were located on Chr.08 rich in QTLs and "Hotspot regions" associated with drought stress, and eight of them showed non-synonymous single nucleotide polymorphism. Hence, 10 genes (including above eight genes plus two hub genes) were predicated as possible candidates regulating drought tolerance, which needs further functional validation. Overall, the transcriptome profiling provided in-depth understanding about the genetic mechanism and candidate genes underlying drought tolerance in soybean.
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Affiliation(s)
- Muqadas Aleem
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad M Raza
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad S Haider
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Rana M Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Javaid A Bhat
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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11
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Wang X, Yang X, Feng Y, Dang P, Wang W, Graze R, Clevenger JP, Chu Y, Ozias-Akins P, Holbrook C, Chen C. Transcriptome Profile Reveals Drought-Induced Genes Preferentially Expressed in Response to Water Deficit in Cultivated Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:645291. [PMID: 33995444 PMCID: PMC8120000 DOI: 10.3389/fpls.2021.645291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/12/2021] [Indexed: 05/28/2023]
Abstract
Cultivated peanut (Arachis hypogaea) is one of the most widely grown food legumes in the world, being valued for its high protein and unsaturated oil contents. Drought stress is one of the major constraints that limit peanut production. This study's objective was to identify the drought-responsive genes preferentially expressed under drought stress in different peanut genotypes. To accomplish this, four genotypes (drought tolerant: C76-16 and 587; drought susceptible: Tifrunner and 506) subjected to drought stress in a rainout shelter experiment were examined. Transcriptome sequencing analysis identified that all four genotypes shared a total of 2,457 differentially expressed genes (DEGs). A total of 139 enriched gene ontology terms consisting of 86 biological processes and 53 molecular functions, with defense response, reproductive process, and signaling pathways, were significantly enriched in the common DEGs. In addition, 3,576 DEGs were identified only in drought-tolerant lines in which a total of 74 gene ontology terms were identified, including 55 biological processes and 19 molecular functions, mainly related to protein modification process, pollination, and metabolic process. These terms were also found in shared genes in four genotypes, indicating that tolerant lines adjusted more related genes to respond to drought. Forty-three significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified, and the most enriched pathways were those processes involved in metabolic pathways, biosynthesis of secondary metabolites, plant circadian rhythm, phenylpropanoid biosynthesis, and starch and sucrose metabolism. This research expands our current understanding of the mechanisms that facilitate peanut drought tolerance and shed light on breeding advanced peanut lines to combat drought stress.
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Affiliation(s)
- Xu Wang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinlei Yang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
- State Key Laboratory of North China Crop Improvement and Regulation, Laboratory of Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Yucheng Feng
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Phat Dang
- United States Department of Agriculture–Agricultural Research Service National Peanut Research Laboratory, Dawson, GA, United States
| | - Wenwen Wang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Rita Graze
- Department of Biology, Auburn University, Auburn, AL, United States
| | - Josh P. Clevenger
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ye Chu
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, United States
| | - Corley Holbrook
- United States Department of Agriculture–Agricultural Research Service Crop Genetics and Breeding Research, Tifton, GA, United States
| | - Charles Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
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12
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Abstract
With the global climate anomalies and the destruction of ecological balance, the water shortage has become a serious ecological problem facing all mankind, and drought has become a key factor restricting the development of agricultural production. Therefore, it is essential to study the drought tolerance of crops. Based on previous studies, we reviewed the effects of drought stress on plant morphology and physiology, including the changes of external morphology and internal structure of root, stem, and leaf, the effects of drought stress on osmotic regulation substances, drought-induced proteins, and active oxygen metabolism of plants. In this paper, the main drought stress signals and signal transduction pathways in plants are described, and the functional genes and regulatory genes related to drought stress are listed, respectively. We summarize the above aspects to provide valuable background knowledge and theoretical basis for future agriculture, forestry breeding, and cultivation.
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13
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Sardans J, Peñuelas J. Potassium Control of Plant Functions: Ecological and Agricultural Implications. PLANTS (BASEL, SWITZERLAND) 2021; 10:419. [PMID: 33672415 PMCID: PMC7927068 DOI: 10.3390/plants10020419] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 02/06/2023]
Abstract
Potassium, mostly as a cation (K+), together with calcium (Ca2+) are the most abundant inorganic chemicals in plant cellular media, but they are rarely discussed. K+ is not a component of molecular or macromolecular plant structures, thus it is more difficult to link it to concrete metabolic pathways than nitrogen or phosphorus. Over the last two decades, many studies have reported on the role of K+ in several physiological functions, including controlling cellular growth and wood formation, xylem-phloem water content and movement, nutrient and metabolite transport, and stress responses. In this paper, we present an overview of contemporary findings associating K+ with various plant functions, emphasizing plant-mediated responses to environmental abiotic and biotic shifts and stresses by controlling transmembrane potentials and water, nutrient, and metabolite transport. These essential roles of K+ account for its high concentrations in the most active plant organs, such as leaves, and are consistent with the increasing number of ecological and agricultural studies that report K+ as a key element in the function and structure of terrestrial ecosystems, crop production, and global food security. We synthesized these roles from an integrated perspective, considering the metabolic and physiological functions of individual plants and their complex roles in terrestrial ecosystem functions and food security within the current context of ongoing global change. Thus, we provide a bridge between studies of K+ at the plant and ecological levels to ultimately claim that K+ should be considered at least at a level similar to N and P in terrestrial ecological studies.
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Affiliation(s)
- Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913 Bellaterra, Catalonia, Spain;
- CREAF, 08913 Cerdanyola del Vallès, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08913 Bellaterra, Catalonia, Spain;
- CREAF, 08913 Cerdanyola del Vallès, Catalonia, Spain
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14
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Ali MMAEH, Mansour E, Awaad HA. Drought Tolerance in Some Field Crops: State of the Art Review. MITIGATING ENVIRONMENTAL STRESSES FOR AGRICULTURAL SUSTAINABILITY IN EGYPT 2021:17-62. [DOI: 10.1007/978-3-030-64323-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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15
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Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR. Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1195-1214. [PMID: 32920943 DOI: 10.1111/tpj.14988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.
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Affiliation(s)
- Susan M Moenga
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Yunpeng Gai
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Laura M Perilla-Henao
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Douglas R Cook
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
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16
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Comparative Transcriptomics and Co-Expression Networks Reveal Tissue- and Genotype-Specific Responses of qDTYs to Reproductive-Stage Drought Stress in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11101124. [PMID: 32987927 PMCID: PMC7650634 DOI: 10.3390/genes11101124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. To dissect molecular mechanisms underlying drought-tolerant yield in rice, we applied differential expression and co-expression network approaches to transcriptomes from flag-leaf and emerging panicle tissues of a drought-tolerant yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Protein turnover and efficient reactive oxygen species scavenging were found to be the driving factors in both tissues. In the flag-leaf, the responses further included maintenance of photosynthesis and cell wall reorganization, while in the panicle biosynthesis of secondary metabolites was found to play additional roles. Hub genes of importance in differential drought responses included an expansin in the flag-leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. The approach highlights how the integration of differential expression and allelic variation can aid in the discovery of mechanism and putative causal contribution underlying quantitative trait loci for drought-tolerant yield.
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17
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Pandian BA, Sathishraj R, Djanaguiraman M, Prasad PV, Jugulam M. Role of Cytochrome P450 Enzymes in Plant Stress Response. Antioxidants (Basel) 2020; 9:antiox9050454. [PMID: 32466087 PMCID: PMC7278705 DOI: 10.3390/antiox9050454] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/20/2022] Open
Abstract
Cytochrome P450s (CYPs) are the largest enzyme family involved in NADPH- and/or O2-dependent hydroxylation reactions across all the domains of life. In plants and animals, CYPs play a central role in the detoxification of xenobiotics. In addition to this function, CYPs act as versatile catalysts and play a crucial role in the biosynthesis of secondary metabolites, antioxidants, and phytohormones in higher plants. The molecular and biochemical processes catalyzed by CYPs have been well characterized, however, the relationship between the biochemical process catalyzed by CYPs and its effect on several plant functions was not well established. The advent of next-generation sequencing opened new avenues to unravel the involvement of CYPs in several plant functions such as plant stress response. The expression of several CYP genes are regulated in response to environmental stresses, and they also play a prominent role in the crosstalk between abiotic and biotic stress responses. CYPs have an enormous potential to be used as a candidate for engineering crop species resilient to biotic and abiotic stresses. The objective of this review is to summarize the latest research on the role of CYPs in plant stress response.
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Affiliation(s)
- Balaji Aravindhan Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Rajendran Sathishraj
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Maduraimuthu Djanaguiraman
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
- Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India
| | - P.V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA; (B.A.P.); (R.S.); (M.D.); (P.V.V.P.)
- Correspondence: ; Tel.: +1-785-532-2755
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18
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Derakhshani B, Ayalew H, Mishina K, Tanaka T, Kawahara Y, Jafary H, Oono Y. Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat. PLANTS 2020; 9:plants9050596. [PMID: 32392904 PMCID: PMC7284651 DOI: 10.3390/plants9050596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/15/2020] [Accepted: 05/03/2020] [Indexed: 11/16/2022]
Abstract
Crop cultivars with larger root systems have an increased ability to absorb water and nutrients under conditions of water deficit. To unravel the molecular mechanism of water-stress tolerance in wheat, we performed RNA-seq analysis on the two genotypes, Colotana 296-52 (Colotana) and Tincurrin, contrasting the root growth under polyethylene-glycol-induced water-stress treatment. Out of a total of 35,047 differentially expressed genes, 3692 were specifically upregulated in drought-tolerant Colotana under water stress. Transcription factors, pyrroline-5-carboxylate reductase and late-embryogenesis-abundant proteins were among upregulated genes in Colotana. Variant calling between Colotana and Tincurrin detected 15,207 SNPs and Indels, which may affect protein function and mediate the contrasting root length phenotype. Finally, the expression patterns of five triads in response to water, high-salinity, heat, and cold stresses were analyzed using qRT-PCR to see if there were differences in homoeologous gene expression in response to those conditions. The five examined triads showed variation in the contribution of homoeologous genes to water, high-salinity, heat, and cold stresses in the two genotypes. The variation of homoeologous gene expression in response to environmental stresses may enable plants to better cope with stresses in their natural environments.
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Affiliation(s)
- Behnam Derakhshani
- Department of Agronomy & Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan 45371-38791, Iran;
- Breeding Material Development Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
| | - Habtamu Ayalew
- Small Grains Breeding Laboratory, Noble Research Institute LLC, Ardmore, OK 73401, USA;
| | - Kohei Mishina
- Plant Genome Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan;
| | - Tsuyoshi Tanaka
- Breeding Informatics Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan; (T.T.); (Y.K.)
- Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8518, Japan
| | - Yoshihiro Kawahara
- Breeding Informatics Research Unit, Institute of Crop Science, NARO, Tsukuba 305-8518, Japan; (T.T.); (Y.K.)
- Bioinformatics Team, Advanced Analysis Center, NARO, Tsukuba 305-8518, Japan
| | - Hossein Jafary
- Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran 19395-1454, Iran;
| | - Youko Oono
- Breeding Material Development Unit, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
- Correspondence: ; Tel.: +81-29-838-7443
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19
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Proteomic Responses to Drought Vary Widely Among Eight Diverse Genotypes of Rice ( Oryza sativa). Int J Mol Sci 2020; 21:ijms21010363. [PMID: 31935846 PMCID: PMC6982093 DOI: 10.3390/ijms21010363] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 01/01/2023] Open
Abstract
Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice (Oryza sativa L. ssp. japonica and indica) to drought stress at the late vegetative stage, and harvested leaves for label-free shotgun proteomics. Gene ontology analysis was used to identify common drought-responsive proteins in vegetative tissues, and leaf proteins that are unique to individual genotypes, suggesting diversity in the metabolic responses to drought. Eight proteins were found to be induced in response to drought stress in all eight genotypes. A total of 213 proteins were identified in a single genotype, 83 of which were increased in abundance in response to drought stress. In total, 10 of these 83 proteins were of a largely uncharacterized function, making them candidates for functional analysis and potential biomarkers for drought tolerance.
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20
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Sharma E, Jain M, Khurana JP. Differential quantitative regulation of specific gene groups and pathways under drought stress in rice. Genomics 2019; 111:1699-1712. [DOI: 10.1016/j.ygeno.2018.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 11/21/2018] [Indexed: 10/27/2022]
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21
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Buti M, Baldoni E, Formentin E, Milc J, Frugis G, Lo Schiavo F, Genga A, Francia E. A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice. Int J Mol Sci 2019; 20:E5662. [PMID: 31726733 PMCID: PMC6888222 DOI: 10.3390/ijms20225662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 12/16/2022] Open
Abstract
Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.
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Affiliation(s)
- Matteo Buti
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
- Present address: Department of Agriculture, Food, Environment and Forestry, University of Florence, 50144 Florence, Italy
| | - Elena Baldoni
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Elide Formentin
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Justyna Milc
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
| | - Giovanna Frugis
- CNR-IBBA, Rome Unit, via Salaria Km. 29,300, 00015 Monterotondo Scalo (Roma), Italy;
| | - Fiorella Lo Schiavo
- Department of Biology, University of Padova, 35131 Padova, Italy; (E.F.); (F.L.S.)
- Botanical Garden, University of Padova, 35123 Padova, Italy
| | - Annamaria Genga
- National Research Council (CNR), Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133 Milano, Italy;
| | - Enrico Francia
- Department of Life Sciences, Centre BIOGEST-SITEIA, University of Modena and Reggio Emilia, Via Amendola 2, 42124 Reggio Emilia, Italy; (M.B.); (J.M.); (E.F.)
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22
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Smita S, Katiyar A, Lenka SK, Dalal M, Kumar A, Mahtha SK, Yadav G, Chinnusamy V, Pandey DM, Bansal KC. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. Funct Integr Genomics 2019; 20:29-49. [PMID: 31286320 DOI: 10.1007/s10142-019-00697-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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Affiliation(s)
- Shuchi Smita
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amit Katiyar
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- ICMR-AIIMS Computational Genomics Center, Div. of I.S.R.M., Indian Council of Medical Research, Ansari Nagar, New Delhi, 110029, India
| | - Sangram Keshari Lenka
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India
| | - Monika Dalal
- ICAR-National Research Center on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Amish Kumar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Viswanathan Chinnusamy
- ICAR-Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kailash Chander Bansal
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India.
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India.
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23
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Debbarma J, Sarki YN, Saikia B, Boruah HPD, Singha DL, Chikkaputtaiah C. Ethylene Response Factor (ERF) Family Proteins in Abiotic Stresses and CRISPR-Cas9 Genome Editing of ERFs for Multiple Abiotic Stress Tolerance in Crop Plants: A Review. Mol Biotechnol 2019; 61:153-172. [PMID: 30600447 DOI: 10.1007/s12033-018-0144-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abiotic stresses such as extreme heat, cold, drought, and salt have brought alteration in plant growth and development, threatening crop yield and quality leading to global food insecurity. Many factors plays crucial role in regulating various plant growth and developmental processes during abiotic stresses. Ethylene response factors (ERFs) are AP2/ERF superfamily proteins belonging to the largest family of transcription factors known to participate during multiple abiotic stress tolerance such as salt, drought, heat, and cold with well-conserved DNA-binding domain. Several extensive studies were conducted on many ERF family proteins in plant species through over-expression and transgenics. However, studies on ERF family proteins with negative regulatory functions are very few. In this review article, we have summarized the mechanism and role of recently studied AP2/ERF-type transcription factors in different abiotic stress responses. We have comprehensively discussed the application of advanced ground-breaking genome engineering tool, CRISPR/Cas9, to edit specific ERFs. We have also highlighted our on-going and published R&D efforts on multiplex CRISPR/Cas9 genome editing of negative regulatory genes for multiple abiotic stress responses in plant and crop models. The overall aim of this review is to highlight the importance of CRISPR/Cas9 and ERFs in developing sustainable multiple abiotic stress tolerance in crop plants.
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Affiliation(s)
- Johni Debbarma
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-NEIST, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST, Jorhat, Assam, India
| | - Yogita N Sarki
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-NEIST, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST, Jorhat, Assam, India
| | - Banashree Saikia
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-NEIST, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST, Jorhat, Assam, India
| | - Hari Prasanna Deka Boruah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-NEIST, Jorhat, Assam, 785006, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST, Jorhat, Assam, India
| | - Dhanawantari L Singha
- Department of Agricultural Biotechnology, Assam Agriculture University, Jorhat, 785013, Assam, India.
| | - Channakeshavaiah Chikkaputtaiah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-NEIST, Jorhat, Assam, 785006, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-NEIST, Jorhat, Assam, India.
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24
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Lin YJ, Yu XZ, Zhang Q. Transcriptome analysis of Oryza sativa in responses to different concentrations of thiocyanate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:11696-11709. [PMID: 30806930 DOI: 10.1007/s11356-019-04544-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 02/13/2019] [Indexed: 05/21/2023]
Abstract
Effective concentrations of potassium thiocyanate (KSCN) to rice seedlings were experimentally determined using relative growth rate as a sensitive endpoint. Agilent 44-K rice microarray was used to profile the molecular responses of rice seedlings exposed to thiocyanate ion (SCN-) at three different effective concentrations (EC10, EC20, and EC50). A total of 18,498 known genes were collected from SCN-treated rice microarray analysis. Out of all, 1603, 1882, and 5085 differentially expressed genes (DEGs) were observed at EC10, EC20, and EC50 concentrations, respectively. More upregulated/downregulated DEGs were detected in shoots than in roots after SCN- exposure. Gene functions and pathway enrichment analysis of DEGs indicated that different effective concentrations of SCN- resulted in multiple enriched GO categories and KEGG pathways and outcomes were quite tissue-specific. Different regulations and adaptations of gene expression in molecular function (MF), biological process (BP), and cellular components (CC) were observed in rice tissues at different effective concentrations of SCN-, suggesting their different responsive and adaptive strategies. Information collected here presents a detailed description of SCN-induced alternations of gene expression in rice seedlings and provide valuable information for further searching specific genes participating in transportation, phytotoxic responses, and detoxification of SCN- in rice seedlings.
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Affiliation(s)
- Yu-Juan Lin
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
| | - Xiao-Zhang Yu
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China.
| | - Qing Zhang
- The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541004, People's Republic of China
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25
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Hu L, Xie Y, Fan S, Wang Z, Wang F, Zhang B, Li H, Song J, Kong L. Comparative analysis of root transcriptome profiles between drought-tolerant and susceptible wheat genotypes in response to water stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:276-293. [PMID: 29807601 DOI: 10.1016/j.plantsci.2018.03.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/13/2018] [Accepted: 03/20/2018] [Indexed: 05/13/2023]
Abstract
Water deficit is one of the major factors limiting crop productivity worldwide. Plant roots play a key role in uptaking water, perceiving and transducing of water deficit signals to shoot. Although the mechanisms of drought-tolerance have been reported recently, the transcriptional regulatory network of wheat root response to water stress has not been fully understood. In this study, drought-tolerant cultivar JM-262 and susceptible cultivar LM-2 are planted to characterize the root transcriptional changes and physiological responses to water deficit. A total of 8197 drought tolerance-associated differentially expressed genes (DEGs) are identified, these genes are mainly mapped to carbon metabolism, flavonoid biosynthesis, and phytohormone signal transduction. The number and expression level of DEGs involved in antioxidative and antiosmotic stresses are more enhanced in JM-262 under water stress. Furthermore, we find the DEGs related to root development are much more induced in JM-262 in phytohormone signal transduction and carbon metabolism pathway. In conclusion, JM-262 may alleviate the damage of drought by producing more osmoprotectants, ROS scavengers, biomass and energy. Interestingly, hormone signaling and cross-talk probably play an important role in promoting JM-262 greater root systems to take up more water, higher capabilities to induce more drought-related DEGs and higher resisitance to oxidative stresse.
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Affiliation(s)
- Ling Hu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yan Xie
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shoujin Fan
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fahong Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Bin Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jie Song
- College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Lingan Kong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
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26
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Li N, Liu H, Sun J, Zheng H, Wang J, Yang L, Zhao H, Zou D. Transcriptome analysis of two contrasting rice cultivars during alkaline stress. Sci Rep 2018; 8:9586. [PMID: 29941956 PMCID: PMC6018505 DOI: 10.1038/s41598-018-27940-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 06/13/2018] [Indexed: 12/26/2022] Open
Abstract
Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expressions of alkali-responsive genes in rice have not been previously investigated. In this study, the transcriptomic data between an alkaline-tolerant (WD20342) and an alkaline-sensitive (Caidao) rice cultivar were compared under alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis indicated the enrichment of IAR genes involved in various stimulus or stress responses. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.
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Affiliation(s)
- Ning Li
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hualong Liu
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jian Sun
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongliang Zheng
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Jingguo Wang
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Luomiao Yang
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Rice Research Institute, College of Agriculture, Northeast Agricultural University, Harbin, China.
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27
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Potassium: A Vital Regulator of Plant Responses and Tolerance to Abiotic Stresses. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8030031] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Among the plant nutrients, potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of the plant structure but it also has a regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, and enzyme activation. Several physiological processes depend on K, such as stomatal regulation and photosynthesis. In recent decades, K was found to provide abiotic stress tolerance. Under salt stress, K helps to maintain ion homeostasis and to regulate the osmotic balance. Under drought stress conditions, K regulates stomatal opening and helps plants adapt to water deficits. Many reports support the notion that K enhances antioxidant defense in plants and therefore protects them from oxidative stress under various environmental adversities. In addition, this element provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although considerable progress has been made in understanding K-induced abiotic stress tolerance in plants, the exact molecular mechanisms of these protections are still under investigation. In this review, we summarized the recent literature on the biological functions of K, its uptake, its translocation, and its role in plant abiotic stress tolerance.
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28
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Thirumalaikumar VP, Devkar V, Mehterov N, Ali S, Ozgur R, Turkan I, Mueller‐Roeber B, Balazadeh S. NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato. PLANT BIOTECHNOLOGY JOURNAL 2018; 16. [PMID: 28640975 PMCID: PMC5787828 DOI: 10.1111/pbi.12776] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Water deficit (drought stress) massively restricts plant growth and the yield of crops; reducing the deleterious effects of drought is therefore of high agricultural relevance. Drought triggers diverse cellular processes including the inhibition of photosynthesis, the accumulation of cell-damaging reactive oxygen species and gene expression reprogramming, besides others. Transcription factors (TF) are central regulators of transcriptional reprogramming and expression of many TF genes is affected by drought, including members of the NAC family. Here, we identify the NAC factor JUNGBRUNNEN1 (JUB1) as a regulator of drought tolerance in tomato (Solanum lycopersicum). Expression of tomato JUB1 (SlJUB1) is enhanced by various abiotic stresses, including drought. Inhibiting SlJUB1 by virus-induced gene silencing drastically lowers drought tolerance concomitant with an increase in ion leakage, an elevation of hydrogen peroxide (H2 O2 ) levels and a decrease in the expression of various drought-responsive genes. In contrast, overexpression of AtJUB1 from Arabidopsis thaliana increases drought tolerance in tomato, alongside with a higher relative leaf water content during drought and reduced H2 O2 levels. AtJUB1 was previously shown to stimulate expression of DREB2A, a TF involved in drought responses, and of the DELLA genes GAI and RGL1. We show here that SlJUB1 similarly controls the expression of the tomato orthologs SlDREB1, SlDREB2 and SlDELLA. Furthermore, AtJUB1 directly binds to the promoters of SlDREB1, SlDREB2 and SlDELLA in tomato. Our study highlights JUB1 as a transcriptional regulator of drought tolerance and suggests considerable conservation of the abiotic stress-related gene regulatory networks controlled by this NAC factor between Arabidopsis and tomato.
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Affiliation(s)
- Venkatesh P. Thirumalaikumar
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdam‐GolmGermany
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Vikas Devkar
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdam‐GolmGermany
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Nikolay Mehterov
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
- Present address:
Department of Medical BiologyMedical University of PlovdivBG ‐ 4000PlovdivBulgaria
| | - Shawkat Ali
- Division of Biological and Environmental Sciences and EngineeringCenter for Desert AgricultureKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Rengin Ozgur
- Department of BiologyFaculty of ScienceEge UniversityIzmirTurkey
| | - Ismail Turkan
- Department of BiologyFaculty of ScienceEge UniversityIzmirTurkey
| | - Bernd Mueller‐Roeber
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdam‐GolmGermany
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
| | - Salma Balazadeh
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdam‐GolmGermany
- Max Planck Institute of Molecular Plant PhysiologyPotsdam‐GolmGermany
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29
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Yashvardhini N, Bhattacharya S, Chaudhuri S, Sengupta DN. Molecular characterization of the 14-3-3 gene family in rice and its expression studies under abiotic stress. PLANTA 2018; 247:229-253. [PMID: 28956163 DOI: 10.1007/s00425-017-2779-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/16/2017] [Indexed: 05/17/2023]
Abstract
14-3-3 isoforms were relatively less conserved at the C-terminal region across plant groups. Both Os 14-3-3f and Os 14-3-3g were inducible with differential gene expression levels under different abiotic stress and developmental stages in sensitive and tolerant indica rice cultivars as confirmed both at transcript and protein level. Plant 14-3-3s has been well characterized to function in several signaling pathways, biotic as well as abiotic stress and nutrient metabolism. We attempted comprehensive analysis of 14-3-3 genes in different plant lineages such as green algae (Chlamydomonas reinhardtii), moss (Physcomitrella patens) and lycophyte (Selaginella moellendorffii), dicot Arabidopsis thaliana and monocot Oryza sativa sub sp. japonica at the gene and protein level. Sequence alignment results revealed that 14-3-3 isoforms were evolutionarily conserved across all taxa with variable C-terminal end. Phylogenetic analysis indicated that the majority of 14-3-3 isoforms in rice belong to the non-epsilon group that clustered separately from the dicot group. Segmental duplication event played a significant role in the expansion of both, Arabidopsis and rice, 14-3-3 isoforms as revealed by synteny studies. In silico gene expression using Massive Parallel Signature Sequencing and microarray analysis revealed that 14-3-3 isoforms have variable expression in different tissue types and under different abiotic stress regime in Arabidopsis and japonica rice. Both, semi-quantitative and qPCR results, confirmed that Os14-3-3f and Os14-3-3g were inducible under abiotic stress in lamina and roots of indica rice and relatively higher under salinity and cold stress in Nonabokra, under dehydration stress in N-22 and under exogenous ABA in IR-29 usually after 3-6 h of treatment. Both, 14-3-3f and 14-3-3g, were highly expressed in flag leaves, stems and panicles and mature roots. These results were further confirmed by immunoblot analysis of rice cultivars using Os14-3-3f antibody generated from recombinant Os14-3-3f protein. The results provide the first comprehensive report of Os14-3-3 gene expression in indica rice cultivars which differ in tolerance to abiotic stress that might be useful for further research.
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Affiliation(s)
- Niti Yashvardhini
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal, 700009, India
| | - Saurav Bhattacharya
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal, 700009, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute, Centenary Campus, P1/12, C.I.T. Scheme VII(M), Kolkata, West Bengal, 700054, India
| | - Dibyendu Narayan Sengupta
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal, 700009, India.
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30
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Islam A, Leung S, Nikmatullah A, Dijkwel PP, McManus MT. Kunitz Proteinase Inhibitors Limit Water Stress Responses in White Clover ( Trifolium repens L.) Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1683. [PMID: 29046678 PMCID: PMC5632647 DOI: 10.3389/fpls.2017.01683] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/13/2017] [Indexed: 05/22/2023]
Abstract
The response of plants to water deficiency or drought is a complex process, the perception of which is triggered at the molecular level before any visible morphological responses are detected. It was found that different groups of plant proteinase inhibitors (PIs) are induced and play an active role during abiotic stress conditions such as drought. Our previous work with the white clover (Trifolium repens L.) Kunitz Proteinase Inhibitor (Tr-KPI) gene family showed that Tr-KPIs are differentially regulated to ontogenetic and biotic stress associated cues and that, at least some members of this gene family may be required to maintain cellular homeostasis. Altered cellular homeostasis may also affect abiotic stress responses and therefore, we aimed to understand if distinct Tr-PKI members function during drought stress. First, the expression level of three Tr-KPI genes, Tr-KPI1, Tr-KPI2, and Tr-KPI5, was measured in two cultivars and one white clover ecotype with differing capacity to tolerate drought. The expression of Tr-KPI1 and Tr-KPI5 increased in response to water deficiency and this was exaggerated when the plants were treated with a previous period of water deficiency. In contrast, proline accumulation and increased expression of Tr-NCED1, a gene encoding a protein involved in ABA biosynthesis, was delayed in plants that experienced a previous drought period. RNAi knock-down of Tr-KPI1 and Tr-KPI5 resulted in increased proline accumulation in leaf tissue of plants grown under both well-watered and water-deficit conditions. In addition, increased expression of genes involved in ethylene biosynthesis was found. The data suggests that Tr-KPIs, particularly Tr-KPI5, have an explicit function during water limitation. The results also imply that the Tr-KPI family has different in planta proteinase targets and that the functions of this protein family are not solely restricted to one of storage proteins or in response to biotic stress.
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Affiliation(s)
| | | | | | - Paul P. Dijkwel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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31
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Xu Y, Burgess P, Huang B. Transcriptional regulation of hormone-synthesis and signaling pathways by overexpressing cytokinin-synthesis contributes to improved drought tolerance in creeping bentgrass. PHYSIOLOGIA PLANTARUM 2017; 161:235-256. [PMID: 28543596 DOI: 10.1111/ppl.12588] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 05/20/2023]
Abstract
The objective of this study was to investigate transcriptomic changes and molecular factors regulated by cytokinins that may contribute to improved drought tolerance in creeping bentgrass (Agrostis stolonifera) overexpressing adenine isopentenyltransferase (ipt). Wild-type (WT) and ipt-transgenic plants were maintained well irrigated or exposed to 21 days of drought stress in growth chambers. Transcriptomic analysis conducted by RNA-seq revealed 661 and 648 upregulated and 764 and 862 downregulated drought-responsive genes (DRGs) in the WT and ipt-transgenic plants, respectively, under drought stress using adjusted P-value of 0.001 and log2 fold change. Gene ontology (GO) term classification showed that a greater number of DRGs were found in ipt-transgenic plants than in WT plants pertaining to biological functions including metabolic process, cellular process, cell structure and growth, macromolecular complex, and binding and catalytic activity, whereas fewer DRGs were found in ipt-transgenic plants than in WT plants pertaining to response to stimulus and antioxidant activity. Furthermore, plant hormone signal transduction pathway analysis revealed three downregulated transcripts [type B - Arabidopsis response regulators (B-ARR), ABA-responsive element binding factor (ABF) and pyrabactin resistance/like (PYR/PYL)] and two upregulated transcripts (BIN2 and JAZ) that were significantly differentiated between ipt-transgenic and WT plants under drought stress, which are particularly interesting for further investigation of molecular mechanisms of hormone-regulation of drought tolerance.
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Affiliation(s)
- Yi Xu
- Rutgers University, Department of Plant Biology, New Brunswick, NJ 08901, USA
| | - Patrick Burgess
- Rutgers University, Department of Plant Biology, New Brunswick, NJ 08901, USA
| | - Bingru Huang
- Rutgers University, Department of Plant Biology, New Brunswick, NJ 08901, USA
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32
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Chae S, Kim JS, Jun KM, Lee SB, Kim MS, Nahm BH, Kim YK. Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq. Mol Cells 2017; 40:714-730. [PMID: 29047256 PMCID: PMC5682249 DOI: 10.14348/molcells.2017.2297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 08/21/2017] [Accepted: 08/24/2017] [Indexed: 11/30/2022] Open
Abstract
Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.
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Affiliation(s)
- Songhwa Chae
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Joung Sug Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
| | - Kyong Mi Jun
- GreenGene Biotech Inc., 116, Yongin 17058,
Korea
| | - Sang-Bok Lee
- Central Area Crop Breeding Research Division, National Institute of Crop Science, Chuncheon 24219,
Korea
| | | | - Baek Hie Nahm
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
- GreenGene Biotech Inc., 116, Yongin 17058,
Korea
| | - Yeon-Ki Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin 17058,
Korea
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33
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Tang S, Li L, Wang Y, Chen Q, Zhang W, Jia G, Zhi H, Zhao B, Diao X. Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses). Sci Rep 2017; 7:10009. [PMID: 28855520 PMCID: PMC5577110 DOI: 10.1038/s41598-017-08854-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023] Open
Abstract
Understanding drought-tolerance mechanisms and identifying genetic dominance are important for crop improvement. Setaria italica, which is extremely drought-tolerant, has been regarded as a model plant for studying stress biology. Moreover, different genotypes of S. italica have evolved various drought-tolerance/avoidance mechanisms that should be elucidated. Physiological and transcriptomic comparisons between drought-tolerant S. italica cultivar 'Yugu1' and drought-sensitive 'An04' were conducted. 'An04' had higher yields and more efficient photosystem activities than 'Yugu1' under well-watered conditions, and this was accompanied by positive brassinosteroid regulatory actions. However, 'An04's growth advantage was severely repressed by drought, while 'Yugu1' maintained normal growth under a water deficiency. High-throughput sequencing suggested that the S. italica transcriptome was severely remodelled by genotype × environment interactions. Expression profiles of genes related to phytohormone metabolism and signalling, transcription factors, detoxification, and other stress-related proteins were characterised, revealing genotype-dependent and -independent drought responses in different S. italica genotypes. Combining our data with drought-tolerance-related QTLs, we identified 20 candidate genes that contributed to germination and early seedling' drought tolerance in S. italica. Our analysis provides a comprehensive picture of how different S. italica genotypes respond to drought, and may be used for the genetic improvement of drought tolerance in Poaceae crops.
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Affiliation(s)
- Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, People's Republic of China
| | - Lin Li
- College of Life Science, Hebei Normal University, 050012, Shijiazhuang, People's Republic of China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences, 050030, Shijiazhuang, People's Republic of China
| | - Qiannan Chen
- College of Life Science, Hebei Normal University, 050012, Shijiazhuang, People's Republic of China
| | - Wenying Zhang
- Institute of Dryland Agriculture, Hebei Academy of Agricultural and Forestry Sciences, 050000, Hengshui, People's Republic of China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, People's Republic of China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, People's Republic of China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, 050012, Shijiazhuang, People's Republic of China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, People's Republic of China.
- College of Life Science, Hebei Normal University, 050012, Shijiazhuang, People's Republic of China.
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34
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Greenham K, Guadagno CR, Gehan MA, Mockler TC, Weinig C, Ewers BE, McClung CR. Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa. eLife 2017; 6:e29655. [PMID: 28826479 PMCID: PMC5628015 DOI: 10.7554/elife.29655] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/11/2017] [Indexed: 11/13/2022] Open
Abstract
The dynamics of local climates make development of agricultural strategies challenging. Yield improvement has progressed slowly, especially in drought-prone regions where annual crop production suffers from episodic aridity. Underlying drought responses are circadian and diel control of gene expression that regulate daily variations in metabolic and physiological pathways. To identify transcriptomic changes that occur in the crop Brassica rapa during initial perception of drought, we applied a co-expression network approach to associate rhythmic gene expression changes with physiological responses. Coupled analysis of transcriptome and physiological parameters over a two-day time course in control and drought-stressed plants provided temporal resolution necessary for correlation of network modules with dynamic changes in stomatal conductance, photosynthetic rate, and photosystem II efficiency. This approach enabled the identification of drought-responsive genes based on their differential rhythmic expression profiles in well-watered versus droughted networks and provided new insights into the dynamic physiological changes that occur during drought.
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Affiliation(s)
- Kathleen Greenham
- Department of Biological SciencesDartmouth CollegeHanoverUnited States
| | | | - Malia A Gehan
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Todd C Mockler
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Cynthia Weinig
- Department of BotanyUniversity of WyomingLaramieUnited States
- Department of Molecular BiologyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
| | - Brent E Ewers
- Department of BotanyUniversity of WyomingLaramieUnited States
- Program in EcologyUniversity of WyomingLaramieUnited States
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Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice ( Oryza rufipogon). Biosci Rep 2017; 37:BSR20160509. [PMID: 28424372 PMCID: PMC6434088 DOI: 10.1042/bsr20160509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 04/05/2017] [Accepted: 04/19/2017] [Indexed: 11/17/2022] Open
Abstract
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice (Oryza rufipogon, DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought-stress response. The results indicated that 11231 transcripts were differentially expressed in the leaves (4040 up-regulated and 7191 down-regulated) and 7025 transcripts were differentially expressed in the roots (3097 up-regulated and 3928 down-regulated). Among these differentially expressed genes (DEGs), the detection of many transcriptional factors and functional genes demonstrated that multiple regulatory pathways were involved in drought resistance. Meanwhile, the DEGs were also annotated with gene ontology (GO) terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway mapping, respectively. A set of the most interesting candidate genes was then identified by combining the DEGs with previously identified drought-resistant quantitative trait loci (QTL). The present work provides abundant genomic information for functional dissection of the drought resistance of DXWR, and findings will further help the current understanding of the biological regulatory mechanisms of drought resistance in plants and facilitate the breeding of new drought-resistant rice cultivars.
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Ahn H, Jung I, Shin SJ, Park J, Rhee S, Kim JK, Jung W, Kwon HB, Kim S. Transcriptional Network Analysis Reveals Drought Resistance Mechanisms of AP2/ERF Transgenic Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1044. [PMID: 28663756 PMCID: PMC5471331 DOI: 10.3389/fpls.2017.01044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/30/2017] [Indexed: 05/18/2023]
Abstract
This study was designed to investigate at the molecular level how a transgenic version of rice "Nipponbare" obtained a drought-resistant phenotype. Using multi-omics sequencing data, we compared wild-type rice (WT) and a transgenic version (erf71) that had obtained a drought-resistant phenotype by overexpressing OsERF71, a member of the AP2/ERF transcription factor (TF) family. A comprehensive bioinformatics analysis pipeline, including TF networks and a cascade tree, was developed for the analysis of multi-omics data. The results of the analysis showed that the presence of OsERF71 at the source of the network controlled global gene expression levels in a specific manner to make erf71 survive longer than WT. Our analysis of the time-series transcriptome data suggests that erf71 diverted more energy to survival-critical mechanisms related to translation, oxidative response, and DNA replication, while further suppressing energy-consuming mechanisms, such as photosynthesis. To support this hypothesis further, we measured the net photosynthesis level under physiological conditions, which confirmed the further suppression of photosynthesis in erf71. In summary, our work presents a comprehensive snapshot of transcriptional modification in transgenic rice and shows how this induced the plants to acquire a drought-resistant phenotype.
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Affiliation(s)
- Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Inuk Jung
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
| | - Seon-Ju Shin
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Jinwoo Park
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Sungmin Rhee
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National UniversitySeoul, South Korea
| | - Woosuk Jung
- Department of Applied Bioscience, Konkuk UniversitySeoul, South Korea
| | - Hawk-Bin Kwon
- Department of Biomedical Sciences, Sunmoon UniversityAsan, South Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National UniversitySeoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National UniversitySeoul, South Korea
- Bioinformatics Institute, Seoul National UniversitySeoul, South Korea
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Mustikarini ED, Ardiarini NR, Basuki N, Kuswanto K. The improvement of early maturity red rice mutant trait for drought tolerance. INTERNATIONAL JOURNAL OF PLANT BIOLOGY 2017. [DOI: 10.4081/pb.2016.6345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Accession of red rice does not have the traits of early maturity, drought tolerance and high yield. Mutation is needed to obtain the desired genetic resources. Gamma-ray irradiation is the right method because it was proved capable of producing hundreds of new varieties, which are better than the previous. This study aimed to identify the improvement of early maturity and drought tolerance of red rice mutant to gamma ray irradiation results. The research materials are M4, M5 and M6 strain, which are derived from the Bangka’s accession local red rice (Celak Madu, Ruten Puren and radix). The three accession seed have been treated with gamma-ray irradiation doses of 150, 200 and 250 Gray. The results showed gamma ray irradiation dose of 150 Gray and 200 Gray to red rice accession can form a mutant with the character of harvesting time less than 115 days after planting and was more drought tolerant than the previous. M6-GR150- 1-9-13 strain was selected as a candidate for early maturity, drought tolerant and high yield mutant.
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Transcriptomic basis for drought-resistance in Brassica napus L. Sci Rep 2017; 7:40532. [PMID: 28091614 PMCID: PMC5238399 DOI: 10.1038/srep40532] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/07/2016] [Indexed: 01/06/2023] Open
Abstract
Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.
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Chen Q, Li M, Zhang Z, Tie W, Chen X, Jin L, Zhai N, Zheng Q, Zhang J, Wang R, Xu G, Zhang H, Liu P, Zhou H. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco. BMC Genomics 2017; 18:62. [PMID: 28068898 PMCID: PMC5223433 DOI: 10.1186/s12864-016-3372-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 12/02/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). RESULTS In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants. CONCLUSIONS This study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.
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Affiliation(s)
- Qiansi Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Meng Li
- Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410000, China
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410000, China
| | - Zhongchun Zhang
- School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Xia Chen
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Lifeng Jin
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Niu Zhai
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Qingxia Zheng
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Jianfeng Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Ran Wang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Guoyun Xu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Hui Zhang
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China
| | - Pingping Liu
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Huina Zhou
- Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
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Glaubitz U, Li X, Schaedel S, Erban A, Sulpice R, Kopka J, Hincha DK, Zuther E. Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles. PLANT, CELL & ENVIRONMENT 2017; 40:121-137. [PMID: 27761892 DOI: 10.1111/pce.12850] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/12/2016] [Accepted: 10/15/2016] [Indexed: 05/05/2023]
Abstract
Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars.
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Affiliation(s)
- Ulrike Glaubitz
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Xia Li
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian District, Beijing, 100081, China
| | - Sandra Schaedel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- ICRC Weyer GmbH, Bölschestraße 35, D-12587, Berlin, Germany
| | - Alexander Erban
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Ronan Sulpice
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
- Plant Systems Biology Research Lab, Plant and AgriBiosciences Research Centre, Botany and Plant Science, National University of Galway, Galway, Ireland
| | - Joachim Kopka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476, Potsdam, Germany
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Almeida DM, Gregorio GB, Oliveira MM, Saibo NJM. Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype. PLANT MOLECULAR BIOLOGY 2017; 93:61-77. [PMID: 27766460 DOI: 10.1007/s11103-016-0547-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 09/24/2016] [Indexed: 05/03/2023]
Abstract
This manuscript reports the identification and characterization of five transcription factors binding to the promoter of OsNHX1 in a salt stress tolerant rice genotype (Hasawi). Although NHX1 encoding genes are known to be highly regulated at the transcription level by different abiotic stresses, namely salt and drought stress, until now only one transcription factor (TF) binding to its promoter has been reported. In order to unveil the TFs regulating NHX1 gene expression, which is known to be highly induced under salt stress, we have used a Y1H system to screen a salt induced rice cDNA expression library from Hasawi. This approach allowed us to identify five TFs belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and three NIN-like (OsNIN-like2, OsNIN-like3 and OsNIN-like4) binding to the OsNHX1 gene promoter. We have also shown that these TFs act either as transcriptional activators (OsPCF2, OsNIN-like4) or repressors (OsCPP5, OsNIN-like2) and their encoding genes are differentially regulated by salt and PEG-induced drought stress in two rice genotypes, Nipponbare (salt-sensitive) and Hasawi (salt-tolerant). The transactivation activity of OsNIN-like3 was not possible to determine. Increased soil salinity has a direct impact on the reduction of plant growth and crop yield and it is therefore fundamental to understand the molecular mechanisms underlying gene expression regulation under adverse environmental conditions. OsNHX1 is the most abundant K+-Na+/H+ antiporter localized in the tonoplast and its gene expression is induced by salt, drought and ABA. To investigate how OsNHX1 is transcriptionally regulated in response to salt stress in a salt-tolerant rice genotype (Hasawi), a salt-stress-induced cDNA expression library was constructed and subsequently screened using the yeast one-hybrid system and the OsNHX1 promoter as bait. Five transcription factors (TFs) belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and three NIN-like (OsNIN-like2, OsNIN-like3 and OsNIN-like4) were identified as binding to OsNHX1 promoter. Transactivation activity assays performed in Arabidopsis and rice protoplasts showed that OsPCF2 and OsNIN-like4 are activators of the OsNHX1 gene expression, while OsCPP5 and OsNIN-like2 act as repressors. The transactivation activity of OsNIN-like3 needs to be further investigated. Gene expression studies showed that OsNHX1 transcript level is highly induced by salt and PEG-induced drought stress in both shoots and roots in both Nipponbare and Hasawi rice genotypes. Nevertheless, OsNHX1 seems to play a particular role in shoots in response to drought. Most of the TFs binding to OsNHX1 promoter showed a modest transcriptional regulation under stress conditions, however, in response to most of the conditions studied, the OsPCF2 was induced earlier than OsNHX1, indicating that OsPCF2 may activate OsNHX1 gene expression. In addition, although the OsNHX1 response to salt and PEG-induced drought stress in either shoots or roots was quite similar in both rice genotypes, the expression of OsPCF2 in roots under salt stress and the OsNIN-like4 in roots subjected to PEG was mainly up-regulated in Hasawi, indicating that these TFs may be associated with the salt and drought stress tolerance observed for this genotype.
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Affiliation(s)
- Diego M Almeida
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Av. da República, 2780-157, Oeiras, Portugal
| | - Glenn B Gregorio
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- East-West Seed Company (EWS), Km. 54 Cagayan Valley Road, San Rafael, 3008, Bulacan, Philippines
| | - M Margarida Oliveira
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Av. da República, 2780-157, Oeiras, Portugal
| | - Nelson J M Saibo
- Genomics of Plant Stress Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológica, Av. da República, 2780-157, Oeiras, Portugal.
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Chandran AKN, Lee GS, Yoo YH, Yoon UH, Ahn BO, Yun DW, Kim JH, Choi HK, An G, Kim TH, Jung KH. Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response. RICE (NEW YORK, N.Y.) 2016; 9:17. [PMID: 27076183 PMCID: PMC4830809 DOI: 10.1186/s12284-016-0089-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 03/04/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice is one of the most important food crops for humans. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. The completed, map-based sequence of the rice genome has significantly accelerated the functional characterization of rice genes, but progress remains limited in assigning functions to all predicted non-transposable element (non-TE) genes, estimated to number 37,000-41,000. RESULTS The International Rice Functional Genomics Consortium (IRFGC) has generated a huge number of gene-indexed mutants by using mutagens such as T-DNA, Tos17 and Ds/dSpm. These mutants have been identified by 246,566 flanking sequence tags (FSTs) and cover 65 % (25,275 of 38,869) of the non-TE genes in rice, while the mutation ratio of TE genes is 25.7 %. In addition, almost 80 % of highly expressed non-TE genes have insertion mutations, indicating that highly expressed genes in rice chromosomes are more likely to have mutations by mutagens such as T-DNA, Ds, dSpm and Tos17. The functions of around 2.5 % of rice genes have been characterized, and studies have mainly focused on transcriptional and post-transcriptional regulation. Slow progress in characterizing the function of rice genes is mainly due to a lack of clues to guide functional studies or functional redundancy. These limitations can be partially solved by a well-categorized functional classification of FST genes. To create this classification, we used the diverse overviews installed in the MapMan toolkit. Gene Ontology (GO) assignment to FST genes supplemented the limitation of MapMan overviews. CONCLUSION The functions of 863 of 1,022 known genes can be evaluated by current FST lines, indicating that FST genes are useful resources for functional genomic studies. We assigned 16,169 out of 29,624 FST genes to 34 MapMan classes, including major three categories such as DNA, RNA and protein. To demonstrate the MapMan application on FST genes, transcriptome analysis was done from a rice mutant of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene with FST. Mapping of 756 down-regulated genes in dxr mutants and their annotation in terms of various MapMan overviews revealed candidate genes downstream of DXR-mediating light signaling pathway in diverse functional classes such as the methyl-D-erythritol 4-phosphatepathway (MEP) pathway overview, photosynthesis, secondary metabolism and regulatory overview. This report provides a useful guide for systematic phenomics and further applications to enhance the key agronomic traits of rice.
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Affiliation(s)
- Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Gang-Seob Lee
- Molecular Breeding Division, National Academy of Agricultural Science, RDA, Jeonju, 560-500, Republic of Koreas
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea
| | - Ung-Han Yoon
- Genomics Division, National Academy of Agricultural Science, RDA, Jeonju, 560-500, Republic of Korea
| | - Byung-Ohg Ahn
- R&D Coordination Division, Research Policy Bureau, RDA, Jeonju, 560-500, Republic of Korea
| | - Doh-Won Yun
- Planning & Coordination Division, National Academy of Agricultural Science, RDA, Jeonju, 560-500, Republic of Korea
| | - Jin-Hyun Kim
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - GynHeung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
| | - Tae-Ho Kim
- Genomics Division, National Academy of Agricultural Science, RDA, Jeonju, 560-500, Republic of Korea.
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Republic of Korea.
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Baldoni E, Bagnaresi P, Locatelli F, Mattana M, Genga A. Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress. RICE (NEW YORK, N.Y.) 2016; 9:25. [PMID: 27216147 PMCID: PMC4877341 DOI: 10.1186/s12284-016-0098-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/14/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes. RESULTS The physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes. CONCLUSIONS Our results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response.
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Affiliation(s)
- Elena Baldoni
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy.
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy.
| | - Paolo Bagnaresi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy
| | - Monica Mattana
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133, Milan, Italy.
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Wang W, Qin Q, Sun F, Wang Y, Xu D, Li Z, Fu B. Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:1675. [PMID: 27877189 PMCID: PMC5099141 DOI: 10.3389/fpls.2016.01675] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/24/2016] [Indexed: 05/26/2023]
Abstract
Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions. The introgression of donor genomic DNA induced genome-wide DNA methylation changes in DK151 plants. A total of 1190 differentially methylated regions (DMRs) were detected between the two genotypes under normal growth conditions, and the DMR-associated genes in DK151 plants were mainly related to stress response, programmed cell death, and nutrient reservoir activity, which are implicated to constitutive drought stress tolerance. A comparison of the DNA methylation changes in the two genotypes under drought conditions indicated that DK151 plants have a more stable methylome, with only 92 drought-induced DMRs, than IR64 plants with 506 DMRs. Gene ontology analyses of the DMR-associated genes in drought-stressed plants revealed that changes to the DNA methylation status of genotype-specific genes are associated with the epigenetic regulation of drought stress responses. Transcriptome analysis further helped to identify a set of 12 and 23 DMR-associated genes that were differentially expressed in DK151 and IR64, respectively, under drought stress compared with respective controls. Correlation analysis indicated that DNA methylation has various effects on gene expression, implying that it affects gene expression directly or indirectly through diverse regulatory pathways. Our results indicate that drought-induced alterations to DNA methylation may influence an epigenetic mechanism that regulates the expression of unique genes responsible for drought stress tolerance.
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Affiliation(s)
- Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qiao Qin
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fan Sun
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yinxiao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
| | - Dandan Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- College of Agronomy, Anhui Agricultural UniversityHefei, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesBeijing, China
- Shenzhen Institute for Innovative Breeding, Chinese Academy of Agricultural SciencesShenzhen, China
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45
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Comparative transcriptome profiling of chilling tolerant rice chromosome segment substitution line in response to early chilling stress. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0471-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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46
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Viger M, Smith HK, Cohen D, Dewoody J, Trewin H, Steenackers M, Bastien C, Taylor G. Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.). TREE PHYSIOLOGY 2016; 36:909-28. [PMID: 27174702 PMCID: PMC4969554 DOI: 10.1093/treephys/tpw017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/14/2016] [Indexed: 05/17/2023]
Abstract
Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. 'North eastern' genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ(13)C. In contrast, 'southern' genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1-3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.
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Affiliation(s)
- Maud Viger
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - Hazel K Smith
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - David Cohen
- UMR Ecologie et Ecophysiologie Forestières, INRA NANCY-Lorraine, 54280 Champenoux, France UMR Ecologie et Ecophysiologie Forestière, Université de Lorraine, BP 239, F-54506 Vandoeuvre, France
| | - Jennifer Dewoody
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK Present address: USDA Forest Service, National Forest Genetics Lab, 2480 Carson Road, Placerville, CA 95667, USA
| | - Harriet Trewin
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - Marijke Steenackers
- Ministry of the Flemish Community, Research Institute for Nature and Forest (INBO), Geraardsbergen B-9500, Belgium
| | - Catherine Bastien
- INRA, Unité de Recherche Amélioration Génétique et Physiologie Forestières, 2163 avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans Cedex 2, France
| | - Gail Taylor
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
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47
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Wang Y, Li L, Tang S, Liu J, Zhang H, Zhi H, Jia G, Diao X. Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genet 2016; 17:57. [PMID: 27068810 PMCID: PMC4828802 DOI: 10.1186/s12863-016-0364-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/01/2016] [Indexed: 12/03/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs that play important regulatory roles in the development and stress response in plants. Results In this study, we applied Illumina sequencing to systematically investigate the drought-responsive miRNAs derived from S. italica inbred An04-4783 seedlings grown under control and drought conditions. Degradome sequencing was applied to confirm the targets of these miRNAs at a global level. A total of 81 known miRNAs belonging to 28 families were identified, among which 14 miRNAs were upregulated and four were downregulated in response to drought. In addition, 72 potential novel miRNAs were identified, three of which were differentially expressed under drought conditions. Degradome sequencing analysis showed that 56 and 26 genes were identified as targets of known and novel miRNAs, respectively. Conclusions Our analysis revealed post-transcriptional remodeling of cell development, transcription factors, ABA signaling, and cellar homeostasis in S.italica in response to drought. This preliminary characterization provided useful information for further studies on the regulatory networks of drought-responsive miRNAs in foxtail millet. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0364-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongqiang Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China.,Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China
| | - Lin Li
- College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Jianguang Liu
- Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China
| | - Hanshuang Zhang
- Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Xianmin Diao
- College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China. .,Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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48
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Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci Rep 2016; 6:23719. [PMID: 27029818 PMCID: PMC4814823 DOI: 10.1038/srep23719] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 01/18/2023] Open
Abstract
Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.
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Almeida DM, Almadanim MC, Lourenço T, Abreu IA, Saibo NJM, Oliveira MM. Screening for Abiotic Stress Tolerance in Rice: Salt, Cold, and Drought. Methods Mol Biol 2016; 1398:155-82. [PMID: 26867623 DOI: 10.1007/978-1-4939-3356-3_14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rice (Oryza sativa) is the primary source of food for more than half of the world population. Most rice varieties are severely injured by abiotic stresses, with strong social and economic impact. Understanding rice responses to stress may help breeding for more tolerant varieties. However, papers dealing with stress experiments often describe very different experimental designs, thus making comparisons difficult. The use of identical setups is the only way to generate comparable data. This chapter is organized into three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB to assess the response of rice plants to three different abiotic stresses--high salinity, cold stress, and drought. All sections include a detailed description of the materials and methodology, as well as useful notes gathered from the GPlantS team's experience. We use rice seedlings as plants at this stage show high sensitivity to abiotic stresses. For the salt and cold stress assays we use hydroponic cultures, while for the drought assay plants are grown in soil and subjected to water withholding. All setups enable visual score determination and are suitable for sample collection along the imposition of stress. The proposed methodologies are simple and affordable to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic level.
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Affiliation(s)
- Diego M Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal
- IBET, Apartado 12, 2781-901, Oeiras, Portugal
| | - M Cecília Almadanim
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal
- IBET, Apartado 12, 2781-901, Oeiras, Portugal
| | - Tiago Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal
- IBET, Apartado 12, 2781-901, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal
- IBET, Apartado 12, 2781-901, Oeiras, Portugal
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal
- IBET, Apartado 12, 2781-901, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Av. da República, 2780-157, Oeiras, Portugal.
- IBET, Apartado 12, 2781-901, Oeiras, Portugal.
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50
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Fu Y, Poli M, Sablok G, Wang B, Liang Y, La Porta N, Velikova V, Loreto F, Li M, Varotto C. Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:54. [PMID: 26958077 PMCID: PMC4782572 DOI: 10.1186/s13068-016-0471-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 02/22/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND Arundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available. RESULTS We obtained by Illumina-based RNA-seq the whole root and shoot transcriptomes of young A. donax plants subjected to osmotic/water stress with 10 and 20 % polyethylene glycol (PEG; 3 biological replicates/organ/condition corresponding to 18 RNA-Seq libraries), and identified a total of 3034 differentially expressed genes. Blast-based mining of stress-related genes indicated the higher responsivity of roots compared to shoots at the early stages of water stress especially under the milder PEG treatment, with a majority of genes responsive to salt, oxidative, and dehydration stress. Analysis of gene ontology terms underlined the qualitatively different responses between root and shoot tissues. Among the most significantly enriched metabolic pathways identified using a Fisher's exact test with FDR correction, a crucial role was played in both shoots and roots by genes involved in the signaling cascade of abscisic acid. We further identified relatively large organ-specific differences in the patterns of drought-related transcription factor AP2-EREBP, AUX/IAA, MYB, bZIP, C2H2, and GRAS families, which may underlie the transcriptional reprogramming differences between organs. Through comparative analyses with major Poaceae species based on Blast, we finally identified a set of 53 orthologs that can be considered as a core of evolutionary conserved genes important to mediate water stress responses in the family. CONCLUSIONS This study provides the first characterization of A. donax transcriptome in response to water stress, thus shedding novel light at the molecular level on the mechanisms of stress response and adaptation in this emerging bioenergy species. The inventory of early-responsive genes to water stress identified could constitute useful markers of the physiological status of A. donax and be a basis for the improvement of its productivity under water limitation. The full water-stressed A. donax transcriptome is available for Blast-based homology searches through a dedicated web server (http://ecogenomics.fmach.it/arundo/).
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Affiliation(s)
- Yuan Fu
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, Italy
| | - Michele Poli
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Dipartimento di Scienze Agrarie, Università di Bologna, Bologna, Italy
| | - Gaurav Sablok
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Bo Wang
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Centro di Biologia Integrata (CIBIO), University of Trento, Trento, Italy
| | - Yanchun Liang
- />College of Computer Science and Technology, Jilin University, Changchun, China
| | - Nicola La Porta
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />MOUNTFOR Project Centre, European Forest Institute, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Violeta Velikova
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
- />Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Francesco Loreto
- />The National Research Council of Italy (CNR), Department of Biology, Agriculture and Food Sciences, Rome, Italy
| | - Mingai Li
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
| | - Claudio Varotto
- />Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Trento Italy
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