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Yin Z, Zhao Q, Lv X, Zhang X, Wu Y. Circular RNA ath-circ032768, a competing endogenous RNA, response the drought stress by targeting miR472-RPS5 module. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:544-559. [PMID: 38588338 DOI: 10.1111/plb.13645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024]
Abstract
CircRNAs (circular RNAs) reduce the abundance of miRNAs through ceRNA (competing endogenous RNA), to regulate many physiological processes and stress responses in plants. However, the role of circRNA in drought stress is poorly understood. Through ring identification and sequencing verification of ath-circ032768, bioinformatics analysis predicted the interaction of ath-circ032768-miR472-RPS5, and further obtained transgenic plants overexpressing ath-circ032768 and silencing STTM-miR472. The change in drought stress was analysed using biochemical and molecular biological methods. Sequencing and biological analysis confirmed that ath-circ032768, miR472 and RPS5 were responsive to drought stress, and changes in gene expression were consistent with the prediction of ceRNA. The silencing vectors ath-circ032768 and STTM-miR472 were constructed using molecular biology techniques, and stable transgenic plants with drought tolerance obtained. Further physiological and biochemical studies showed that ath-circ032768 could bind to miR472, and that miR472 could bind to the RPS5 gene, resulting in decreased expression of RPS5. Hence, ath-circ032768 can competitively inhibit degradation of RPS5 by miR472 through ceRNA. This process is accompanied by increased expression of DREB2A, RD29A and RD29B genes. Through the ath-circ032768-miR472-RPS5 pathway, the RPS5 stress resistance protein interacts with DREB2A protein to enhance expression of downstream drought resistance genes, RD29A and RD29B, and participate in the regulation mechanism of plant drought resistance, thereby improving drought tolerance of plants.
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Affiliation(s)
- Z Yin
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Q Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Lv
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - X Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
| | - Y Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaan Xi, China
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2
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Zhou D, Ding M, Wen S, Tian Q, Zhang X, Fang Y, Xue D. Characterization of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Its Response to Abiotic Stress in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1010. [PMID: 38611539 PMCID: PMC11013768 DOI: 10.3390/plants13071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/30/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024]
Abstract
Fatty acyl-CoA reductase (FAR) is an important NADPH-dependent enzyme that can produce primary alcohol from fatty acyl-CoA or fatty acyl-carrier proteins as substrates. It plays a pivotal role in plant growth, development, and stress resistance. Herein, we performed genome-wide identification and expression analysis of FAR members in rice using bioinformatics methods. A total of eight OsFAR genes were identified, and the OsFARs were comprehensively analyzed in terms of phylogenetic relationships, duplication events, protein motifs, etc. The cis-elements of the OsFARs were predicted to respond to growth and development, light, hormones, and abiotic stresses. Gene ontology annotation analysis revealed that OsFAR proteins participate in biological processes as fatty acyl-CoA reductase during lipid metabolism. Numerous microRNA target sites were present in OsFARs mRNAs. The expression analysis showed that OsFARs were expressed at different levels during different developmental periods and in various tissues. Furthermore, the expression levels of OsFARs were altered under abiotic stresses, suggesting that FARs may be involved in abiotic stress tolerance in rice. The findings presented here serve as a solid basis for further exploring the functions of OsFARs.
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Affiliation(s)
- Danni Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Mingyu Ding
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Shuting Wen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
| | - Quanxiang Tian
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (D.Z.); (M.D.); (S.W.); (Q.T.); (X.Z.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 311121, China
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3
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Wen S, Zhou C, Tian C, Yang N, Zhang C, Zheng A, Chen Y, Lai Z, Guo Y. Identification and Validation of the miR156 Family Involved in Drought Responses and Tolerance in Tea Plants ( Camellia sinensis (L.) O. Kuntze). PLANTS (BASEL, SWITZERLAND) 2024; 13:201. [PMID: 38256754 PMCID: PMC10819883 DOI: 10.3390/plants13020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024]
Abstract
The microRNA156 (miR156) family, one of the first miRNA families discovered in plants, plays various important roles in plant growth and resistance to various abiotic stresses. Previously, miR156s were shown to respond to drought stress, but miR156s in tea plants (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. Herein, we identify 47 mature sequences and 28 precursor sequences in tea plants. Our evolutionary analysis and multiple sequence alignment revealed that csn-miR156s were highly conserved during evolution and that the rates of the csn-miR156 members' evolution were different. The precursor sequences formed typical and stable stem-loop structures. The prediction of cis-acting elements in the CsMIR156s promoter region showed that the CsMIR156s had diverse cis-acting elements; of these, 12 CsMIR156s were found to be drought-responsive elements. The results of reverse transcription quantitative PCR (RT-qPCR) testing showed that csn-miR156 family members respond to drought and demonstrate different expression patterns under the conditions of drought stress. This suggests that csn-miR156 family members may be significantly involved in the response of tea plants to drought stress. Csn-miR156f-2-5p knockdown significantly reduced the Fv/Fm value and chlorophyll content and led to the accumulation of more-reactive oxygen species and proline compared with the control. The results of target gene prediction showed that csn-miR156f-2-5p targeted SQUAMOSA promoter binding protein-like (SPL) genes. Further analyses showed that CsSPL14 was targeted by csn-miR156f-2-5p, as confirmed through RT-qPCR, 5' RLM-RACE, and antisense oligonucleotide validation. Our results demonstrate that csn-miR156f-2-5p and CsSPL14 are involved in drought response and represent a new strategy for increasing drought tolerance via the breeding of tea plants.
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Affiliation(s)
- Shengjing Wen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Caiyun Tian
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Niannian Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Cheng Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Anru Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Yixing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (C.Z.); (C.T.); (N.Y.); (C.Z.); (A.Z.); (Y.C.); (Z.L.)
- Anxi College of Tea Science (College of Digital Economy), Fujian Agriculture and Forestry University, Quanzhou 362400, China
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4
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Maniatis G, Tani E, Katsileros A, Avramidou EV, Pitsoli T, Sarri E, Gerakari M, Goufa M, Panagoulakou M, Xipolitaki K, Klouvatos K, Megariti S, Pappi P, Papadakis IE, Bebeli PJ, Kapazoglou A. Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 13:27. [PMID: 38202337 PMCID: PMC10780352 DOI: 10.3390/plants13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.
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Affiliation(s)
- Grigorios Maniatis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Anastasios Katsileros
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Ilisia, 11528 Athens, Greece;
| | - Theodora Pitsoli
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Goufa
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Panagoulakou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Konstantina Xipolitaki
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Kimon Klouvatos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Stamatia Megariti
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Polixeni Pappi
- Laboratory of Plant Virology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA (ELGO-DIMITRA), Kastorias 32A, Mesa Katsampas, 71307 Heraklion, Crete, Greece;
| | - Ioannis E. Papadakis
- Laboratory of Pomology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
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5
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Inal B, Mirzapour M, Tufekci ED, Rustemoglu M, Kaba A, Albalawi MA, Alalawy AI, Sakran M, Alqurashi M, Ditta A. Drought-Induced miRNA Expression Correlated with Heavy Metal, Phenolic Acid, and Protein and Nitrogen Levels in Five Chickpea Genotypes. ACS OMEGA 2023; 8:35746-35754. [PMID: 37810661 PMCID: PMC10552140 DOI: 10.1021/acsomega.3c03003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Drought is a prime stress, drastically affecting plant growth, development, and yield. Plants have evolved various physiological, molecular, and biochemical mechanisms to cope with drought. Investigating specific biochemical pathways related to drought tolerance mechanisms of plants through biotechnology approaches is one of the quickest and most effective strategies for enhancing crop production. Among them, microRNAs (miRNAs) are the principal post-transcriptional regulators of gene expression in plants during plant growth under biotic and abiotic stresses. In this study, five different chickpea genotypes (İnci, Hasan bey, Arda, Seçkin, and Diyar 95) were grown under normal and drought stress. We recorded the expression levels of microRNAs in these genotypes and found differential expression (miRNA396, miR408, miRNA414, miRNA528, and miRNA1533) under contrasting conditions. Results revealed that miRNA414 and miRNA528 considerably increased in all genotypes under drought stress, and expression levels of miRNA418, miRNA1533, and miRNA396 (except for the Seçkin genotype) were found to be higher under the watered conditions. These genotypes were also investigated for heavy metal, phenolic acid, protein, and nitrogen concentrations under normal and drought stress conditions. The Arda genotype showed a significant increase in nitrogen (5.46%) and protein contents (28.3%), while protein contents were decreased in the Hasan bey and Seçkin genotypes subjected to drought stress. In the case of metals, iron was the most abundant element in all genotypes (İnci = 15.4 ppm, Hasan bey = 29.6 ppm, Seçkin = 37.8 ppm, Arda = 26.3 ppm, and Diyar 95 = 40.8 ppm) under normal conditions. Interestingly, these results were related to miRNA expression in the chickpea genotypes and hint at the regulation of multiple pathways under drought conditions. Overall, the present study will help us to understand the miRNA-mediated regulation of various pathways in chickpea genotypes.
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Affiliation(s)
- Behcet Inal
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Mohsen Mirzapour
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Ebru Derelli Tufekci
- Food
and Agriculture Vocational High School, Department of Field Crops, Cankiri Karatekin University, Cankiri 18100, Turkey
| | - Mustafa Rustemoglu
- Faculty
of Agriculture, Department of Plant Protection, Sirnak University, Sirnak 73000, Turkey
| | - Adem Kaba
- Faculty
of Agriculture, Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
| | - Marzough Aziz Albalawi
- Department
of Chemistry, University College at Alwajh, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Adel I. Alalawy
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
| | - Mohamed Sakran
- Department
of Biochemistry, Faculty of Science, University
of Tabuk, Tabuk 73000, Kingdom
of Saudi Arabia
- Biochemistry
Section, Chemistry Department, Faculty of Science, Tanta University, Tanta31527,Egypt
| | - Mohammed Alqurashi
- Department
of Biotechnology, Faculty of Science, Taif
University, Taif 21974, Saudi Arabia
| | - Allah Ditta
- Department
of Environmental Sciences, Shaheed Benazir
Bhutto University Sheringal, Dir (U), Khyber Pakhtunkhwa 18000, Pakistan
- School
of Biological Sciences, The University of
Western Australia, 35
Stirling Highway, Perth, WA 6009, Australia
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Favreau B, Gaal C, Pereira de Lima I, Droc G, Roques S, Sotillo A, Guérard F, Cantonny V, Gakière B, Leclercq J, Lafarge T, de Raissac M. A multi-level approach reveals key physiological and molecular traits in the response of two rice genotypes subjected to water deficit at the reproductive stage. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:229-257. [PMID: 37822730 PMCID: PMC10564380 DOI: 10.1002/pei3.10121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 10/13/2023]
Abstract
Rice is more vulnerable to drought than maize, wheat, and sorghum because its water requirements remain high throughout the rice life cycle. The effects of drought vary depending on the timing, intensity, and duration of the events, as well as on the rice genotype and developmental stage. It can affect all levels of organization, from genes to the cells, tissues, and/or organs. In this study, a moderate water deficit was applied to two contrasting rice genotypes, IAC 25 and CIRAD 409, during their reproductive stage. Multi-level transcriptomic, metabolomic, physiological, and morphological analyses were performed to investigate the complex traits involved in their response to drought. Weighted gene network correlation analysis was used to identify the specific molecular mechanisms regulated by each genotype, and the correlations between gene networks and phenotypic traits. A holistic analysis of all the data provided a deeper understanding of the specific mechanisms regulated by each genotype, and enabled the identification of gene markers. Under non-limiting water conditions, CIRAD 409 had a denser shoot, but shoot growth was slower despite better photosynthetic performance. Under water deficit, CIRAD 409 was weakly affected regardless of the plant level analyzed. In contrast, IAC 25 had reduced growth and reproductive development. It regulated transcriptomic and metabolic activities at a high level, and activated a complex gene regulatory network involved in growth-limiting processes. By comparing two contrasting genotypes, the present study identified the regulation of some fundamental processes and gene markers, that drive rice development, and influence its response to water deficit, in particular, the importance of the biosynthetic and regulatory pathways for cell wall metabolism. These key processes determine the biological and mechanical properties of the cell wall and thus influence plant development, organ expansion, and turgor maintenance under water deficit. Our results also question the genericity of the antagonism between morphogenesis and organogenesis observed in the two genotypes.
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Affiliation(s)
- Bénédicte Favreau
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Camille Gaal
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | | | - Gaétan Droc
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Sandrine Roques
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Armel Sotillo
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Florence Guérard
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Valérie Cantonny
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Bertrand Gakière
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Julie Leclercq
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Tanguy Lafarge
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Marcel de Raissac
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
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7
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Dong W, Tu J, Deng W, Zhang J, Xu Y, Gu A, An H, Fan K, Wang R, Zhang J, Kui L, Li X. Genome-wide identification of DUF506 gene family in Oryzasativa and expression profiling under abiotic stresses. PeerJ 2023; 11:e16168. [PMID: 37790624 PMCID: PMC10544316 DOI: 10.7717/peerj.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/03/2023] [Indexed: 10/05/2023] Open
Abstract
The domain of unknown function 560 (DUF560), also known as the PDDEXK_6 family, is a ubiquitous plant protein that has been confirmed to play critical roles in Arabidopsis root development as well as ABA and abiotic responses. However, genome-wide identification and expression pattern analysis in rice (Oryza sativa) still need to be improved. Based on the phylogenetic relationship, 10 OsDUF506 genes were identified and classified into four subfamilies. Segmental duplication was essential to the expansion of OsDUF506s, which were subjected to purifying selective pressure. Except for OsDUF50609 and OsDUF50610, the OsDUF506s shared colinear gene pairs with five monocot species, showing that they were conserved in evolution. Furthermore, the conserved domains, gene structures, SNPs distribution, and targeting miRNAs were systematically investigated. Massive cis-regulatory elements were discovered in promoter regions, implying that OsDUF506s may be important in hormone regulation and abiotic stress response. Therefore, we analyzed plant hormone-induced transcriptome data and performed qRT-PCR on eight OsDUF506s under drought, cold, and phosphorus-deficient stresses. The results revealed that most OsDUF506s respond to ABA and JA treatment, as well as drought and cold conditions. In conclusion, our findings provided insights into the evolution and function of OsDUF506s, which could benefit crop breeding in the future.
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Affiliation(s)
- Wei Dong
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jian Tu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Wei Deng
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Jianhua Zhang
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Yuran Xu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Anyu Gu
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Hua An
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Kui Fan
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | - Rui Wang
- Yunnan Grain Industry Group Co., Ltd, Kunming, China
| | | | - Limei Kui
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
| | - Xiaolin Li
- Yunnan Academy of Agricultural Sciences, Food Crops Research Institute, Kunming, China
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8
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Qi F, Wang F, Xiaoyang C, Wang Z, Lin Y, Peng Z, Zhang J, Wang N, Zhang J. Gene Expression Analysis of Different Organs and Identification of AP2 Transcription Factors in Flax ( Linum usitatissimum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:3260. [PMID: 37765422 PMCID: PMC10535939 DOI: 10.3390/plants12183260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023]
Abstract
Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops.
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Affiliation(s)
- Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Yujie Lin
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun 130000, China;
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130000, China; (F.Q.); (F.W.); (C.X.); (Z.W.); (Y.L.); (J.Z.)
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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9
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Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [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: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
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10
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Kaur S, Seem K, Kumar S, Kaundal R, Mohapatra T. Comparative Genome-Wide Analysis of MicroRNAs and Their Target Genes in Roots of Contrasting Indica Rice Cultivars under Reproductive-Stage Drought. Genes (Basel) 2023; 14:1390. [PMID: 37510295 PMCID: PMC10379292 DOI: 10.3390/genes14071390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Recurrent occurrence of drought stress in varying intensity has become a common phenomenon in the present era of global climate change, which not only causes severe yield losses but also challenges the cultivation of rice. This raises serious concerns for sustainable food production and global food security. The root of a plant is primarily responsible to perceive drought stress and acquire sufficient water for the survival/optimal growth of the plant under extreme climatic conditions. Earlier studies reported the involvement/important roles of microRNAs (miRNAs) in plants' responses to environmental/abiotic stresses. A number (738) of miRNAs is known to be expressed in different tissues under varying environmental conditions in rice, but our understanding of the role, mode of action, and target genes of the miRNAs are still elusive. Using contrasting rice [IR-64 (reproductive-stage drought sensitive) and N-22 (drought-tolerant)] cultivars, imposed with terminal (reproductive-stage) drought stress, we demonstrate differential expression of 270 known and 91 novel miRNAs in roots of the contrasting rice cultivars in response to the stress. Among the known miRNAs, osamiR812, osamiR166, osamiR156, osamiR167, and osamiR396 were the most differentially expressed miRNAs between the rice cultivars. In the root of N-22, 18 known and 12 novel miRNAs were observed to be exclusively expressed, while only two known (zero novels) miRNAs were exclusively expressed in the roots of IR-64. The majority of the target gene(s) of the miRNAs were drought-responsive transcription factors playing important roles in flower, grain development, auxin signaling, root development, and phytohormone-crosstalk. The novel miRNAs identified in this study may serve as good candidates for the genetic improvement of rice for terminal drought stress towards developing climate-smart rice for sustainable food production.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
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11
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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12
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Balyan S, Kansal S, Jajo R, Behere PR, Chatterjee R, Raghuvanshi S. Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice. Funct Integr Genomics 2023; 23:187. [PMID: 37243818 DOI: 10.1007/s10142-023-01111-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ringyao Jajo
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pratyush Rajiv Behere
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rishika Chatterjee
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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13
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Mishra S, Chaudhary R, Sharma P. Temporal expression analysis of microRNAs and their target GRAS genes induced by osmotic stress in two contrasting wheat genotypes. Mol Biol Rep 2023:10.1007/s11033-023-08486-2. [PMID: 37179268 DOI: 10.1007/s11033-023-08486-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important nonprotein-coding genes in plants which participate in almost all biological processes during abiotic and biotic stresses. Understanding how plants respond to various environmental conditions requires the identification of stress-related miRNAs. In recent years, there has been an increased interest in studying miRNA genes and gene expression. Drought is one of the common environmental stresses limiting plant growth and development. Stress-specific miRNAs and their GRAS gene targets were validated to understand the role of miRNAs in response to osmotic stress. RESULTS In this study, expression patterns of the ten stress-responsive miRNAs involved in osmotic stress adaptation were examined in order to undertand the regulation behavior of abiotic stress and miRNAs in two contrasting wheat genotype C-306 (drought tolerant) and WL-711 (drought sensitive). Three miRNAs were discovered to be upregulated under stress, whereas seven miRNAs were showed to be down-regulated as a consequence of the study. In contrast to miRNA, it was also discovered that GRAS genes as their targets were up-regulated during osmotic stress. In addition, the expression level of miR159, miR408 along with their targets, TaGRAS178 and TaGRAS84 increased in response to osmotic stress. Nevertheless, miR408 is highly conserved miRNA that regulates plant growth, development and stress response. As a result, variation in the expression levels of studied miRNAs in the presence of target genes provides a plausible explanation for miRNA-based abiotic stress regulation. A regulatory network of miRNA and their targets revealed that fourteen miRNA interact with 55 GRAS targets from various subfamilies that contribute in the plant growth and development. CONCLUSIONS These findings provide evidence for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock, and they may aid in determining the potential.
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Affiliation(s)
- Shefali Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Reeti Chaudhary
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India.
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14
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Praveen A, Dubey S, Singh S, Sharma VK. Abiotic stress tolerance in plants: a fascinating action of defense mechanisms. 3 Biotech 2023; 13:102. [PMID: 36866326 PMCID: PMC9971429 DOI: 10.1007/s13205-023-03519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Climate fluctuation mediated abiotic stress consequences loss in crop yields. These stresses have a negative impact on plant growth and development by causing physiological and molecular changes. In this review, we have attempted to outline recent studies (5 years) associated with abiotic stress resistance in plants. We investigated the various factors that contribute to coping with abiotic challenges, such as transcription factors (TFs), microRNAs (miRNAs), epigenetic changes, chemical priming, transgenic breeding, autophagy, and non-coding RNAs. Stress responsive genes are regulated mostly by TFs, and these can be used to enhance stress resistance in plants. Plants express some miRNA during stress imposition that act on stress-related target genes to help them survive. Epigenetic alterations govern gene expression and facilitate stress tolerance. Chemical priming enhances growth in plants by modulating physiological parameters. Transgenic breeding enables identification of genes involved in precise plant responses during stressful situations. In addition to protein coding genes, non-coding RNAs also influence the growth of the plant by causing alterations at gene expression levels. For achieving sustainable agriculture for a rising world population, it is crucial to develop abiotic-resistant crops with anticipated agronomical traits. To achieve this objective, understanding the diverse mechanisms by which plants protect themselves against abiotic stresses is imperative. This review emphasizes on recent progress and future prospects for abiotic stress tolerance and productivity in plants.
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Affiliation(s)
- Afsana Praveen
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Sonali Dubey
- National Botanical Research Institute, Uttar Pradesh, Lukhnow, 226001 India
| | - Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Varun Kumar Sharma
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
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15
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Asakura H, Tanaka M, Tamura T, Saito Y, Yamakawa T, Abe K, Asakura T. Genes related to cell wall metabolisms are targeted by miRNAs in immature tomato fruits under drought stress. Biosci Biotechnol Biochem 2023; 87:290-302. [PMID: 36572396 DOI: 10.1093/bbb/zbac209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022]
Abstract
The metabolism of tomato fruits changes when plants experience drought stress. In this study, we investigated changes in microRNA (miRNA) abundance and detected 32 miRNAs whose expression changes in fruit. The candidate target genes for each miRNA were predicted from the differentially expressed genes identified by transcriptome analysis at the same fruit maturation stage. The predicted targeted genes were related to cell wall metabolisms, response to pathogens, and plant hormones. Among these, we focused on cell wall metabolism-related genes and performed a dual luciferase assay to assess the targeting of their mRNAs by their predicted miRNA. As a result, sly-miR10532 and sly-miR7981e suppress the expression of mRNAs of galacturonosyltransferase-10 like encoding the main enzyme of pectin biosynthesis, while sly-miR171b-5p targets β-1,3-glucosidase mRNAs involved in glucan degradation. These results will allow the systematic characterization of miRNA and their target genes in the tomato fruit under drought stress conditions.
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Affiliation(s)
- Hiroko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Mayui Tanaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tomoko Tamura
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Yoshikazu Saito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takashi Yamakawa
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Keiko Abe
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan.,Kanagawa Institute of Industrial Science and Technology (KISTEC), Life Science & Environmental Research Center (LiSE), 705-1, Imaizumi, Ebina, Kanagawa, Japan
| | - Tomiko Asakura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, Japan
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16
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Hassan HM, Hadifa AA, El-leithy SA, Batool M, Sherif A, Al-Ashkar I, Ueda A, Rahman MA, Hossain MA, Elsabagh A. Variable level of genetic dominance controls important agronomic traits in rice populations under water deficit condition. PeerJ 2023; 11:e14833. [PMID: 36815980 PMCID: PMC9933770 DOI: 10.7717/peerj.14833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/10/2023] [Indexed: 02/15/2023] Open
Abstract
Plant hybridization is an important breeding technique essential for producing a genotype (hybrid) with favorable traits (e.g., stress tolerance, pest resistance, high yield potential etc.) to increase agronomic, economic and commercial values. Studying of genetic dominance among the population helps to determine gene action, heritability and candidate gene selection for plant breeding program. Therefore, this investigation was aimed to evaluate gene action, heritability, genetic advance and heterosis of rice root, agronomic, and yield component traits under water deficit conditions. In this study, crossing was performed among the four different water-deficit tolerant rice genotypes to produce better hybrid (F1), segregating (F2) and back-cross (BC1 and BC2) populations. The Giza 178, WAB56-204, and Sakha104 × WAB56-104 populations showed the better physiological and agronomical performances, which provided better adaptability of the populations to water deficit condition. Additionally, the estimation of heterosis and heterobeltiosis of some quantitative traits in rice populations were also studied. The inheritance of all studied traits was influenced by additive gene actions. Dominance gene actions played a major role in controlling the genetic variance among studied traits in both crossed populations under well-watered and drought conditions. The additive × additive type of gene interactions was essential for the inheritance of root length, root/shoot ratio, 1,000-grain weight, and sterility % of two crossed populations under both conditions. On the contrary, the additive × dominance type of gene interactions was effective in the inheritance of all studied traits, except duration in Giza178 × Sakha106, and plant height in Sakha104 × WAB56-104 under water deficit condition. In both crosses, the dominance × dominance type of gene interactions was effective in the inheritance of root volume, root/shoot ratio, number of panicles/plant and 1,000-grain weight under both conditions. Moreover, dominance × dominance type of gene interaction played a major role in the inheritance of root length, number of roots/plant, plant height, panicle length, number of filled grain/panicle and grain yield/plant in Giza178 × Sakha106 under both conditions. The studied traits in both crossed populations indicated better genetic advance as they showed advanced qualitative and quantitative characters in rice populations under water deficit condition. Overall, our findings open a new avenue of future phenotypic and genotypic association studies in rice. These insights might be useful to the plant breeders and farmers for developing water deficit tolerant rice cultivars.
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Affiliation(s)
- Hamada M. Hassan
- Department of Rice Research, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Adel A. Hadifa
- Department of Rice Research, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Sara A. El-leithy
- Department of Rice Research, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Maria Batool
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Ahmed Sherif
- Department of Rice Research, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Ibrahim Al-Ashkar
- Department of Plant Production, College of Food and Agriculture, King Saud University, Riyadh, Saudi Arabia
| | - Akihiro Ueda
- Graduate School of Integrated Sciences for Life, Hiroshima University of Economics, Hiroshima, Japan
| | - Md Atikur Rahman
- Grassland and Forage Division, National Institute of Animal Science, Rural Development Administration, Cheonan, Republic of Korea
| | - Mohammad Anwar Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ayman Elsabagh
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Shaikh, Egypt
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17
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Byregowda R, Prasad SR, Oelmüller R, Nataraja KN, Prasanna Kumar MK. Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes. Int J Mol Sci 2022; 23:ijms23169194. [PMID: 36012460 PMCID: PMC9408852 DOI: 10.3390/ijms23169194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.
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Affiliation(s)
- Roopashree Byregowda
- Department of Seed Science and Technology, University of Agricultural Sciences, Bangalore 560065, India
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
| | | | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
- Correspondence:
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore 560065, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore 560065, India
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18
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Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review. Curr Issues Mol Biol 2022; 44:3695-3710. [PMID: 36005149 PMCID: PMC9406886 DOI: 10.3390/cimb44080253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.
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19
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Chen Y, Fan Y, Yang W, Ding G, Xie J, Zhang F. Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.). Funct Integr Genomics 2022; 22:1153-1157. [PMID: 35916988 DOI: 10.1007/s10142-022-00891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
Rice production worldwide has continued to decline due to various environmental stresses, with drought stress being a prominent factor, as rice is a semi-aquatic plant. Thus, development of drought stress-resistant rice varieties is of great importance for rice production. In our previous study, we found that microRNAs (miRNAs) play a crucial role in the response to drought stress in Dongxiang wild rice (DXWR) (Oryza rufipogon Griff.). Developing drought stress-responsive miRNA-based single sequence repeat (SSR) markers for DXWR will be of great value for the efficient identification and utilization of miRNA genes to breed drought stress-resistant rice varieties. In this study, ninety-nine novel SSR markers were developed based on the drought stress-responsive miRNAs of DXWR. These markers were distributed in all 12 rice chromosomes, and most were in chromosomes 2 and 6, with di- and tri-nucleotides being the most abundant repeat motifs. Twelve out of fourteen synthesized markers displayed high levels of genetic diversity in the genomes of three populations of DXWR and 40 modern rice varieties worldwide. The number of alleles per locus ranged from 2 to 7, with an average of 4.67; the genetic diversity index ranged from 0.21 to 0.76, with an average of 0.58; and the polymorphism information content value ranged from 0.18 to 0.72, with an average of 0.53. These novel molecular markers developed from the drought stress-responsive miRNAs of DXWR could be additional tools for mapping elite miRNA genes and breeding drought stress-resistant rice varieties.
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Affiliation(s)
- Yong Chen
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yuanwei Fan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
- Department of Biology and Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Wanling Yang
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Gumu Ding
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| | - Fantao Zhang
- Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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20
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A WRKY Protein, MfWRKY40, of Resurrection Plant Myrothamnus flabellifolia Plays a Positive Role in Regulating Tolerance to Drought and Salinity Stresses of Arabidopsis. Int J Mol Sci 2022; 23:ijms23158145. [PMID: 35897721 PMCID: PMC9330732 DOI: 10.3390/ijms23158145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 02/06/2023] Open
Abstract
WRKY transcription factors (TFs), one of the largest transcription factor families in plants, play an important role in abiotic stress responses. The resurrection plant, Myrothamnus flabellifolia, has a strong tolerance to dehydration, but only a few WRKY proteins related to abiotic stress response have been identified and functionally characterized in M. flabellifolia. In this study, we identified an early dehydration-induced gene, MfWRKY40, of M. flabellifolia. The deduced MfWRKY40 protein has a conserved WRKY motif but lacks a typical zinc finger motif in the WRKY domain and is localized in the nucleus. To investigate its potential roles in abiotic stresses, we overexpressed MfWRKY40 in Arabidopsis and found that transgenic lines exhibited better tolerance to both drought and salt stresses. Further detailed analysis indicated that MfWRKY40 promoted primary root length elongation and reduced water loss rate and stomata aperture (width/length) under stress, which may provide Arabidopsis the better water uptake and retention abilities. MfWRKY40 also facilitated osmotic adjustment under drought and salt stresses by accumulating more osmolytes, such as proline, soluble sugar, and soluble protein. Additionally, the antioxidation ability of transgenic lines was also significantly enhanced, represented by higher chlorophyll content, less malondialdehyde and reactive oxygen species accumulations, as well as higher antioxidation enzyme activities. All these results indicated that MfWRKY40 might positively regulate tolerance to drought and salinity stresses. Further investigation on the relationship of the missing zinc finger motif of MfWRKY40 and its regulatory role is necessary to obtain a better understanding of the mechanism underlying the excellent drought tolerance of M. flabellifolia.
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21
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Premachandran Y. Triggered in distress: a miRNA-controlled switch for drought-induced ABA biosynthesis in rice. PLANT PHYSIOLOGY 2022; 189:447-449. [PMID: 35266538 PMCID: PMC9157111 DOI: 10.1093/plphys/kiac105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Yadukrishnan Premachandran
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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22
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Gao W, Li M, Yang S, Gao C, Su Y, Zeng X, Jiao Z, Xu W, Zhang M, Xia K. miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice. PLANT PHYSIOLOGY 2022; 189:889-905. [PMID: 35188194 PMCID: PMC9157147 DOI: 10.1093/plphys/kiac071] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/15/2022] [Indexed: 05/27/2023]
Abstract
Mediating induced abscisic acid (ABA) biosynthesis is important for enhancing plant stress tolerance. Here, we found that rice (Oryza sativa L.) osa-miR2105 (miR2105) and the Stress/ABA-activated protein kinase (OsSAPK10) coordinately regulate the rice basic region-leucine zipper transcription factor (bZIP TF; OsbZIP86) at the posttranscriptional and posttranslational levels to control drought-induced ABA biosynthesis via modulation of rice 9-cis-epoxycarotenoid dioxygenase (OsNCED3) expression. OsbZIP86 expression is regulated by miR2105-directed cleavage of the OsbZIP86 mRNA. OsbZIP86 encodes a nuclear TF that binds to the promoter of the ABA biosynthetic gene OsNCED3. OsSAPK10 can phosphorylate and activate OsbZIP86 to enhance the expression of OsNCED3. Under normal growth conditions, altered expression of miR2105 and OsbZIP86 displayed no substantial effect on rice growth. However, under drought conditions, miR2105 knockdown or OsbZIP86 overexpression transgenic rice plants showed higher ABA content, enhanced tolerance to drought, lower rates of water loss, and more stomatal closure of seedlings, compared with wild-type rice Zhonghua 11; in contrast, miR2105 overexpression, OsbZIP86 downregulation, and OsbZIP86 knockout plants displayed opposite phenotypes. Collectively, our results show that the "miR2105-(OsSAPK10)-OsbZIP86-OsNCED3" module regulates the drought-induced ABA biosynthesis without penalty on rice growth under normal conditions, suggesting candidates for improving drought tolerance in rice.
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Affiliation(s)
- Weiwei Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingkang Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chunzhi Gao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yan Su
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuan Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhengli Jiao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weijuan Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of life Science, University of Chinese Academy of Sciences, Beijing 10049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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23
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Yang X, Liu C, Niu X, Wang L, Li L, Yuan Q, Pei X. Research on lncRNA related to drought resistance of Shanlan upland rice. BMC Genomics 2022; 23:336. [PMID: 35490237 PMCID: PMC9055766 DOI: 10.1186/s12864-022-08546-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported. Results In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR. Conclusion Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08546-0.
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Affiliation(s)
- Xinsen Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoling Niu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Liu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Laiyi Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Qianhua Yuan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-Resources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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24
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Hao Z, Ma S, Liang L, Feng T, Xiong M, Lian S, Zhu J, Chen Y, Meng L, Li M. Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. Int J Mol Sci 2022; 23:ijms23074016. [PMID: 35409377 PMCID: PMC8999833 DOI: 10.3390/ijms23074016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 01/24/2023] Open
Abstract
Drought and salinity stresses are significant abiotic factors that limit rice yield. Exploring the co-response mechanism to drought and salt stress will be conducive to future rice breeding. A total of 1748 drought and salt co-responsive genes were screened, most of which are enriched in plant hormone signal transduction, protein processing in the endoplasmic reticulum, and the MAPK signaling pathways. We performed gene-coding sequence haplotype (gcHap) network analysis on nine important genes out of the total amount, which showed significant differences between the Xian/indica and Geng/japonica population. These genes were combined with related pathways, resulting in an interesting mechanistic draft called the ‘gcHap-network pathway’. Meanwhile, we collected a lot of drought and salt breeding varieties, especially the introgression lines (ILs) with HHZ as the parent, which contained the above-mentioned nine genes. This might imply that these ILs have the potential to improve the tolerance to drought and salt. In this paper, we focus on the relationship of drought and salt co-response gene gcHaps and their related pathways using a novel angle. The haplotype network will be helpful to explore the desired haplotypes that can be implemented in haplotype-based breeding programs.
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Affiliation(s)
- Zhiqi Hao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sai Ma
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Mengyuan Xiong
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Shangshu Lian
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jingyan Zhu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
| | - Lijun Meng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Correspondence: (L.M.); (M.L.)
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China; (Z.H.); (S.M.); (L.L.); (T.F.); (M.X.); (S.L.); (J.Z.); (Y.C.)
- Correspondence: (L.M.); (M.L.)
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25
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Shen X, He J, Ping Y, Guo J, Hou N, Cao F, Li X, Geng D, Wang S, Chen P, Qin G, Ma F, Guan Q. The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees. PLANT PHYSIOLOGY 2022; 188:1686-1708. [PMID: 34893896 PMCID: PMC8896624 DOI: 10.1093/plphys/kiab565] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/10/2021] [Indexed: 05/25/2023]
Abstract
Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.
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Affiliation(s)
- Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yikun Ping
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gege Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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26
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Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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27
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Li J, Duan Y, Sun N, Wang L, Feng S, Fang Y, Wang Y. The miR169n-NF-YA8 regulation module involved in drought resistance in Brassica napus L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111062. [PMID: 34763855 DOI: 10.1016/j.plantsci.2021.111062] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
As an ancient and conserved plant microRNA (miRNA) family, miR169 targets nuclear factor Y subunit alpha (NF-YA) family members. The miR169-NF-YA module is associated with plant development and various stress responses. However, the function of miR169 in response to drought stress in rapeseed (Brassica napus L.) is unclear. In the present study, we showed that miR169n acted as a negative regulator of drought resistance in rapeseed by targeting a nuclear factor Y-A gene, NF-YA8. miR169n was strongly down-regulated by drought stress. Expression of a miR169n target mimicry construct (MIM169n) which functioned as a sponge to trap miR169n resulted in enhanced resistance of transgenic plants to both osmotic stress at the post-germination stage and drought stress at the seedling stage. MIM169n plants had a higher relative water content (RWC) and proline content, lower relative electrolyte leakage (REL), and showed higher antioxidative capability compared with those of control (CK) plants under drought stress. Moreover, NF-YA8 was verified as a target of miR169n, and overexpression of NF-YA8 led to improved tolerance of rapeseed to osmotic stress at the post-germination stage. Overall, our findings implied that the miR169n-NF-YA8 regulatory module could serve as a potential target for genetic improvement of drought resistance in B. napus.
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Affiliation(s)
- Jian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Yujing Duan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Nianli Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Lu Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Shanshan Feng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China
| | - Yujie Fang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, China.
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, 225009, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, China.
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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Guo M, Li H, Zhu L, Wu Z, Li J, Li Z. Genome-wide identification of microRNAs associated with osmotic stress and elucidation of the role of miR319 in Medicago ruthenica seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 168:53-61. [PMID: 34619598 DOI: 10.1016/j.plaphy.2021.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/06/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Drought is a major environmental stress that affects plant growth, development, and productivity. Medicago ruthenica, a leguminous forage, has garnered attention owing to its resistance to abiotic stress. The purpose of the current study was to explore genes conferring drought resistance to M. ruthenica. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in plants and are associated with developmental plasticity and abiotic/biotic stress responses. Here, high-throughput small RNA, mRNA, and degradome sequencing analyses were performed to analyze miRNAs and their potential target genes in the leaves of M. ruthenica seedlings under osmotic stress conditions. In total, 591 miRNAs were identified. A comparison of the expression levels showed that 15 miRNAs (14 upregulated and 1 downregulated) were significantly differentially expressed following PEG6000 treatment compared with those in the control (0 h). Most miRNAs are highly conserved between M. ruthenica and Medicago truncatula. Using TargetFinder, 11 target genes were predicted; the expression of these target genes negatively correlated with that of five miRNAs related to osmotic stress response. miR319 downregulated the expression of teosinte branched/cycloidea/proliferating cell factor 4 (TCP4), which encodes plant-specific transcription factors, more significantly in the leaves than in the roots. These results were confirmed using quantitative real-time polymerase chain reaction, northern blotting, RLM 5'RACE, and a Nicotiana benthamiana transient expression system. The miR319-TCP4 module may act as a homeostasis factor in M. ruthenica roots following drought injury, and it is conserved among plant species.
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Affiliation(s)
- Maowei Guo
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Hongyan Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lin Zhu
- Grassland and Resources Environment Institute, Inner Mongolia Agriculture University, Hohhot, China
| | - Zinian Wu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jun Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China; Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China.
| | - Zhiyong Li
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China.
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Exploitation of Drought Tolerance-Related Genes for Crop Improvement. Int J Mol Sci 2021; 22:ijms221910265. [PMID: 34638606 PMCID: PMC8508643 DOI: 10.3390/ijms221910265] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
Drought has become a major threat to food security, because it affects crop growth and development. Drought tolerance is an important quantitative trait, which is regulated by hundreds of genes in crop plants. In recent decades, scientists have made considerable progress to uncover the genetic and molecular mechanisms of drought tolerance, especially in model plants. This review summarizes the evaluation criteria for drought tolerance, methods for gene mining, characterization of genes related to drought tolerance, and explores the approaches to enhance crop drought tolerance. Collectively, this review illustrates the application prospect of these genes in improving the drought tolerance breeding of crop plants.
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Can Electrophysiological Parameters Substitute for Growth, and Photosynthetic Parameters to Characterize the Response of Mulberry and Paper Mulberry to Drought? PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10091772. [PMID: 34579304 PMCID: PMC8470290 DOI: 10.3390/plants10091772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Drought is a key factor restricting plant survival, growth and development. The physiological parameters of plants are commonly used to determine the water status, in order to irrigate appropriately and save water. In this study, mulberry (Morus alba L.) and paper mulberry (Broussonetia papyrifera (L.) Vent.) seedlings were used as experimental materials, and four soil moisture treatments were set up for both plant species: 70–75% (CK: the control group, referred to as T0), 55–60% (T1: mild drought), 40–45% (T2: moderate drought), and 25–30% (T3: severe drought). The growth parameter of the plants was measured every two days from the onset of the treatment, the photosynthetic and electrophysiological parameters of the plants were measured every other week for a total of five times. The physiological responses and electrophysiological traits of leaves under different treatment levels were analyzed. The results showed that the photosynthetic and electrophysiological parameters could characterize the response of mulberry growth and development to soil water, and the growth and electrophysiological parameters could characterize the response of paper mulberry growth and development to soil water. Mild drought had no significant effects on the growth and development of mulberry and paper mulberry.
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33
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Effects of Abiotic Stress on Soil Microbiome. Int J Mol Sci 2021; 22:ijms22169036. [PMID: 34445742 PMCID: PMC8396473 DOI: 10.3390/ijms22169036] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.
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35
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SA-Mediated Regulation and Control of Abiotic Stress Tolerance in Rice. Int J Mol Sci 2021; 22:ijms22115591. [PMID: 34070465 PMCID: PMC8197520 DOI: 10.3390/ijms22115591] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
Environmental or abiotic stresses are a common threat that remains a constant and common challenge to all plants. These threats whether singular or in combination can have devastating effects on plants. As a semiaquatic plant, rice succumbs to the same threats. Here we systematically look into the involvement of salicylic acid (SA) in the regulation of abiotic stress in rice. Studies have shown that the level of endogenous salicylic acid (SA) is high in rice compared to any other plant species. The reason behind this elevated level and the contribution of this molecule towards abiotic stress management and other underlying mechanisms remains poorly understood in rice. In this review we will address various abiotic stresses that affect the biochemistry and physiology of rice and the role played by SA in its regulation. Further, this review will elucidate the potential mechanisms that control SA-mediated stress tolerance in rice, leading to future prospects and direction for investigation.
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Shi R, Jiao W, Yun L, Zhang Z, Zhang X, Wang Q, Li Y, Mi F. Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica. FRONTIERS IN PLANT SCIENCE 2021; 12:675903. [PMID: 34413864 PMCID: PMC8369265 DOI: 10.3389/fpls.2021.675903] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/14/2021] [Indexed: 05/08/2023]
Abstract
Drought is a major limiting factor in foraging grass yield and quality. Medicago ruthenica (M. ruthenica) is a high-quality forage legume with drought resistance, cold tolerance, and strong adaptability. In this study, we integrated transcriptome, small RNA, and degradome sequencing in identifying drought response genes, microRNAs (miRNAs), and key miRNA-target pairs in M. ruthenica under drought and rewatering treatment conditions. A total of 3,905 genes and 50 miRNAs (45 conserved and 5 novel miRNAs) were significantly differentially expressed in three test conditions (CK: control, DS: plants under drought stress, and RW: plants rewatering after drought stress). The degradome sequencing (AllenScore < 4) analysis revealed that 104 miRNAs (11 novel and 93 conserved miRNAs) were identified with 263 target transcripts, forming 296 miRNA-target pairs in three libraries. There were 38 differentially expressed targets from 16 miRNAs in DS vs. CK, 31 from 11 miRNAs in DS vs. RW, and 6 from 3 miRNAs in RW vs. CK; 21, 18, and 3 miRNA-target gene pairs showed reverse expression patterns in DS vs. CK, DS vs. RW, and RW vs. CK comparison groups, respectively. These findings provide valuable information for further functional characterization of genes and miRNAs in response to abiotic stress, in general, and drought stress in M. ruthenica, and potentially contribute to drought resistance breeding of forage in the future.
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Affiliation(s)
- Rui Shi
- Key Laboratory of Grassland Resources, Ministry of Education P.R of China, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Baotou Medical College, Baotou, China
| | - Wei Jiao
- College of Mechanical and Electrical Engineering, Inner Mongolia Agricultural University, Hohhot, China
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Lan Yun
- Key Laboratory of Grassland Resources, Ministry of Education P.R of China, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiqiang Zhang
- Key Laboratory of Grassland Resources, Ministry of Education P.R of China, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Zhang
- Inner Mongolia Key Laboratory of Molecular Biology on Featured Plants, Hohhot, China
| | - Quanzhen Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Ying Li
- Key Laboratory of Grassland Resources, Ministry of Education P.R of China, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Fugui Mi
- Key Laboratory of Grassland Resources, Ministry of Education P.R of China, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Fugui Mi,
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Waziri A, Singh DK, Sharma T, Chatterjee S, Purty RS. Genome-wide analysis of PHD finger gene family and identification of potential miRNA and their PHD finger gene specific targets in Oryza sativa indica. Noncoding RNA Res 2020; 5:191-200. [PMID: 33163736 PMCID: PMC7610035 DOI: 10.1016/j.ncrna.2020.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/24/2020] [Accepted: 10/24/2020] [Indexed: 11/24/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the most important cereal crops for one third of the world population. However, the grain quality as well as yield of rice is severely affected by various abiotic stresses. Environmental stresses affect the expression of various microRNAs (miRNAs) which in turn negatively regulate gene expression at the post-transcriptional level either by degrading the target mRNA genes or suppressing translation in plants. Plant homeo-domain (PHD) finger proteins are known to be involved in the plant response to salinity stress. In the present study, we identified 44 putative OsPHD finger genes in Oryza sativa Indica, using Ensembl Plants Database. Using computational approach, potential miRNAs that target OsPHD finger genes were identified. Out of the 44 OsPHD finger genes only three OsPHD finger genes i.e., OsPHD2, OsPHD35 and OsPHD11, were found to be targeted by five newly identified putative miRNAs i.e., ath-miRf10010-akr, ath-miRf10110-akr, osa-miR1857–3p, osa-miRf10863-akr, and osa-miRf11806-akr. This is the first report of these five identified miRNAs on targeting PHD finger in Oryza sativa Indica. Further, expression analysis of 44 PHD finger genes under salinity was also performed using quantitative Real-Time PCR. The expression profile of 8 genes were found to be differentially regulated, among them two genes were significantly up regulated i.e., OsPHD6 and OsPHD12. In silico protein-protein interaction analysis using STRING database showed interaction of the OsPHD finger proteins with other protein partners that are directly or indirectly involved in development and abiotic stress tolerance. Total of 44 Plant homeo-domain (PHD) finger proteins were identified & classified into 10 groups in Oryza sativa Indica. This is the first report showing 5 newly identified putative miRNAs targeting three OsPHD genes i.e., OsPHD2, 11 and 35. Expression analysis of PHD finger genes showed up-regulation of the 2 genes OsPHD 6 & 12 under salinity stress treatment. Protein-protein network of OsPHDs showed protein partners that are involved in plant growth and abiotic stress tolerance.
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Affiliation(s)
- Aafrin Waziri
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Deepak Kumar Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Tarun Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Sayan Chatterjee
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Ram Singh Purty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
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Singh DK, Mehra S, Chatterjee S, Purty RS. In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress. Noncoding RNA Res 2020; 5:167-177. [PMID: 33024905 PMCID: PMC7522899 DOI: 10.1016/j.ncrna.2020.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 11/08/2022] Open
Abstract
Several biotic (bacterial and viral pathogenesis) and abiotic stress factors like salt, drought, cold, and extreme temperatures significantly reduce crop productivity and grain quality throughout the world. MicroRNAs (miRNAs) are small (~22 nucleotides) non-coding endogenous RNA molecules which negatively regulate gene expression at the post-transcriptional level either by degrading the target protein-coding mRNA genes or suppressing translation in plants. Dirigent (DIR) gene protein plays a crucial role as they are involved to dictate the stereochemistry of a compound synthesized by other enzymes as well as in lignifications against biotic and abiotic stress. In plants, several miRNAs, as well as their targets, are known to regulate stress response but systematic identification of the same is limited. The present work has been designed for in silico identification of miRNAs against a total of sixty-one DIR genes in Oryza sativa Indica followed by target prediction of identified miRNAs through the computational approach and thereafter validation of potential miRNAs in rice genotypes. We systematically identified 3 miRNA and their respective DIR specific target gene in Oryza sativa Indica. The expression of these three miRNAs and their respective DIR specific targets were validated in rice seedlings subjected to five different abiotic stress conditions (heavy metal, high temperature, low temperature, salinity and drought) by quantitative Real-Time PCR (qRT-PCR). Expression analysis indicated that miRNA under stress conditions regulates the gene expression of the DIR gene in rice. To the best of our knowledge this is this is the first report in any organism showing the expression of ath-miRf10317-akr, and osamiRf10761-akr miRNAs in response to various abiotic stresses. Total 61 DIR proteins were identified & classified into 6 groups based on phylogeny analysis in Oryza sativa Indica. Three miRNAs ath-miRf10317-akr, cre-miR910 and osa-miRf10761-akr were identified via computational approach. These 3 miRNAs in response to abiotic stresses showed inverse expression pattern in the respective target genes. This is the first report on expression of ath-miRf10317-akr, and osa-miRf10761-akr miRNAs in response to abiotic stresses.
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Affiliation(s)
- Deepak Kumar Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Shourya Mehra
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Sayan Chatterjee
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
| | - Ram Singh Purty
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sec-16C, Dwarka, New Delhi, India
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Varotto S, Tani E, Abraham E, Krugman T, Kapazoglou A, Melzer R, Radanović A, Miladinović D. Epigenetics: possible applications in climate-smart crop breeding. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5223-5236. [PMID: 32279074 PMCID: PMC7475248 DOI: 10.1093/jxb/eraa188] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/09/2020] [Indexed: 05/23/2023]
Abstract
To better adapt transiently or lastingly to stimuli from the surrounding environment, the chromatin states in plant cells vary to allow the cells to fine-tune their transcriptional profiles. Modifications of chromatin states involve a wide range of post-transcriptional histone modifications, histone variants, DNA methylation, and activity of non-coding RNAs, which can epigenetically determine specific transcriptional outputs. Recent advances in the area of '-omics' of major crops have facilitated identification of epigenetic marks and their effect on plant response to environmental stresses. As most epigenetic mechanisms are known from studies in model plants, we summarize in this review recent epigenetic studies that may be important for improvement of crop adaptation and resilience to environmental changes, ultimately leading to the generation of stable climate-smart crops. This has paved the way for exploitation of epigenetic variation in crop breeding.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy, Food, Natural Resources, Animals, and the Environment, University of Padova, Agripolis, Viale dell’Università, Padova, Italy
| | - Eleni Tani
- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Demeter (HAO-Demeter), Lykovrysi, Greece
| | - Rainer Melzer
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
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Nadarajah KK. ROS Homeostasis in Abiotic Stress Tolerance in Plants. Int J Mol Sci 2020; 21:E5208. [PMID: 32717820 PMCID: PMC7432042 DOI: 10.3390/ijms21155208] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/21/2022] Open
Abstract
Climate change-induced abiotic stress results in crop yield and production losses. These stresses result in changes at the physiological and molecular level that affect the development and growth of the plant. Reactive oxygen species (ROS) is formed at high levels due to abiotic stress within different organelles, leading to cellular damage. Plants have evolved mechanisms to control the production and scavenging of ROS through enzymatic and non-enzymatic antioxidative processes. However, ROS has a dual function in abiotic stresses where, at high levels, they are toxic to cells while the same molecule can function as a signal transducer that activates a local and systemic plant defense response against stress. The effects, perception, signaling, and activation of ROS and their antioxidative responses are elaborated in this review. This review aims to provide a purview of processes involved in ROS homeostasis in plants and to identify genes that are triggered in response to abiotic-induced oxidative stress. This review articulates the importance of these genes and pathways in understanding the mechanism of resistance in plants and the importance of this information in breeding and genetically developing crops for resistance against abiotic stress in plants.
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Affiliation(s)
- Kalaivani K Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM BANGI, Malaysia
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Anwar A, Kim JK. Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives. Int J Mol Sci 2020; 21:E2695. [PMID: 32295026 PMCID: PMC7216248 DOI: 10.3390/ijms21082695] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.
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Affiliation(s)
| | - Ju-Kon Kim
- Graduate School of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science & Technology, Seoul National University, Pyeongchang 25354, Korea;
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Wójcikowska B, Wójcik AM, Gaj MD. Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants. Int J Mol Sci 2020; 21:ijms21072307. [PMID: 32225116 PMCID: PMC7177879 DOI: 10.3390/ijms21072307] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022] Open
Abstract
Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.
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Kim Y, Chung YS, Lee E, Tripathi P, Heo S, Kim KH. Root Response to Drought Stress in Rice ( Oryza sativa L .). Int J Mol Sci 2020; 21:E1513. [PMID: 32098434 PMCID: PMC7073213 DOI: 10.3390/ijms21041513] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 01/24/2023] Open
Abstract
The current unpredictable climate changes are causing frequent and severe droughts. Such circumstances emphasize the need to understand the response of plants to drought stress, especially in rice, one of the most important grain crops. Knowledge of the drought stress response components is especially important in plant roots, the major organ for the absorption of water and nutrients from the soil. Thus, this article reviews the root response to drought stress in rice. It is presented to provide readers with information of use for their own research and breeding program for tolerance to drought stress in rice.
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Affiliation(s)
- Yoonha Kim
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.K.); (P.T.)
| | - Yong Suk Chung
- Faculty of Bioscience and Industry, College of Applied Life Science, SARI, Jeju National University, Jeju 63243, Korea;
| | - Eungyeong Lee
- National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
| | - Pooja Tripathi
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.K.); (P.T.)
| | - Seong Heo
- Ganghwa Agricultural Technology Service Center, Incheon 23038, Korea;
| | - Kyung-Hwan Kim
- National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea;
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