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Gaude AA, Siqueira RH, Botelho SB, Jalmi SK. Epigenetic arsenal for stress mitigation in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130620. [PMID: 38636616 DOI: 10.1016/j.bbagen.2024.130620] [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: 11/07/2023] [Revised: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Plant's ability to perceive, respond to, and ultimately adapt to various stressors is a testament to their remarkable resilience. In response to stresses, plants activate a complex array of molecular and physiological mechanisms. These include the rapid activation of stress-responsive genes, the manufacturing of protective compounds, modulation of cellular processes and alterations in their growth and development patterns to enhance their chances of survival. Epigenetic mechanisms play a pivotal role in shaping the responses of plants to environmental stressors. This review explores the intricate interplay between epigenetic regulation and plant stress mitigation. We delve into the dynamic landscape of epigenetic modifications, highlighting their influence on gene expression and ultimately stress tolerance. This review assembles current research, shedding light on the promising strategies within plants' epigenetic arsenal to thrive amidst adverse conditions.
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Affiliation(s)
- Aishwarya Ashok Gaude
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Roxiette Heromina Siqueira
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Savia Bernadette Botelho
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Siddhi Kashinath Jalmi
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
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Kaur A, Madhu, Sharma A, Singh K, Upadhyay SK. Investigation of two-pore K + (TPK) channels in Triticum aestivum L. suggests their role in stress response. Heliyon 2024; 10:e27814. [PMID: 38533012 PMCID: PMC10963239 DOI: 10.1016/j.heliyon.2024.e27814] [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: 10/17/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Madhu
- Department of Botany, Panjab University, Chandigarh, India, 160014
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh, India, 160014
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474001, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Chang L, Jin X, Rao Y, Zhang X. Predicting abiotic stress-responsive miRNA in plants based on multi-source features fusion and graph neural network. PLANT METHODS 2024; 20:33. [PMID: 38402152 PMCID: PMC10894500 DOI: 10.1186/s13007-024-01158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/14/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND More and more studies show that miRNA plays a crucial role in plants' response to different abiotic stresses. However, traditional experimental methods are often expensive and inefficient, so it is important to develop efficient and economical computational methods. Although researchers have developed machine learning-based method, the information of miRNAs and abiotic stresses has not been fully exploited. Therefore, we propose a novel approach based on graph neural networks for predicting potential miRNA-abiotic stress associations. RESULTS In this study, we fully considered the multi-source feature information from miRNAs and abiotic stresses, and calculated and integrated the similarity network of miRNA and abiotic stress from different feature perspectives using multiple similarity measures. Then, the above multi-source similarity network and association information between miRNAs and abiotic stresses are effectively fused through heterogeneous networks. Subsequently, the Restart Random Walk (RWR) algorithm is employed to extract global structural information from heterogeneous networks, providing feature vectors for miRNA and abiotic stress. After that, we utilized the graph autoencoder based on GIN (Graph Isomorphism Networks) to learn and reconstruct a miRNA-abiotic stress association matrix to obtain potential miRNA-abiotic stress associations. The experimental results show that our model is superior to all known methods in predicting potential miRNA-abiotic stress associations, and the AUPR and AUC metrics of our model achieve 98.24% and 97.43%, respectively, under five-fold cross-validation. CONCLUSIONS The robustness and effectiveness of our proposed model position it as a valuable approach for advancing the field of miRNA-abiotic stress association prediction.
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Affiliation(s)
- Liming Chang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Xiu Jin
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Yuan Rao
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaodan Zhang
- College of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China.
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agricultural University, Hefei, 230036, China.
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Yang W, Chen Y, Gao R, Chen Y, Zhou Y, Xie J, Zhang F. MicroRNA2871b of Dongxiang Wild Rice ( Oryza rufipogon Griff.) Negatively Regulates Cold and Salt Stress Tolerance in Transgenic Rice Plants. Int J Mol Sci 2023; 24:14502. [PMID: 37833950 PMCID: PMC10572564 DOI: 10.3390/ijms241914502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21-24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR.
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Affiliation(s)
- Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Yong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Rifang Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Yaling Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (W.Y.); (Y.C.); (R.G.); (Y.C.); (Y.Z.); (J.X.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Qiao H, Jiao B, Wang J, Yang Y, Yang F, Geng Z, Zhao G, Liu Y, Dong F, Wang Y, Zhou S. Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat. Genes (Basel) 2023; 14:1586. [PMID: 37628637 PMCID: PMC10454085 DOI: 10.3390/genes14081586] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.
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Affiliation(s)
- Hualiang Qiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Bo Jiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Jiao Wang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yang Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fan Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yongwei Liu
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fushuang Dong
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Shuo Zhou
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
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Ma Q, Niu C, Wang C, Chen C, Li Y, Wei M. Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.). BMC Genomics 2023; 24:250. [PMID: 37165319 PMCID: PMC10173649 DOI: 10.1186/s12864-023-09337-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption. RESULTS The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively. CONCLUSION Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.
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Affiliation(s)
- Qiang Ma
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chenxu Niu
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chao Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Chunhua Chen
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Yan Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Min Wei
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China.
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China.
- State Key Laboratory of Crop Biology, Taian, 271018, China.
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China.
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Zhang Q, Li J, Wen X, Deng C, Yang X, Dai S. Genome-wide identification and characterization analysis of RWP-RK family genes reveal their role in flowering time of Chrysanthemum lavandulifolium. BMC PLANT BIOLOGY 2023; 23:197. [PMID: 37061708 PMCID: PMC10105424 DOI: 10.1186/s12870-023-04201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND RWP-RKs are plant specific transcription factors, which are widely distributed in plants in the form of polygenic families and play key role in nitrogen absorption and utilization, and are crucial to plant growth and development. However, the genome-wide identification and function of RWP-RK in Compositae plants are widely unknown. RESULTS In this study, 101 RWP-RKs in Chrysanthemum lavandulifolium were identified and tandem repeat was an important way for the expansion of RWP-RKs in Compositae species. 101 RWP-RKs contain 38 NIN-like proteins (NLPs) and 31 RWP- RK domain proteins (RKDs), as well as 32 specific expansion members. qRT-PCR results showed that 7 ClNLPs in leaves were up-regulated at the floral transition stage, 10 ClNLPs were negatively regulated by low nitrate conditions, and 3 of them were up-regulated by optimal nitrate conditions. In addition, the flowering time of Chrysanthemum lavandulifolium was advanced under optimal nitrate conditions, the expression level of Cryptochromes (ClCRYs), phytochrome C (ClPHYC) and the floral integration genes GIGANTEA (ClGI), CONSTANS-LIKE (ClCOL1, ClCOL4, ClCOL5), FLOWERING LOCUS T (ClFT), FLOWERING LOCUS C (ClFLC), SUPPRESSOR OF OVER-EXPRESSION OF CONSTANS 1 (ClSOC1) also were up-regulated. The expression level of ClCRY1a, ClCRY1c, ClCRY2a and ClCRY2c in the vegetative growth stage induced by optimal nitrate reached the expression level induced by short-day in the reproductive growth stage, which supplemented the induction effect of short-day on the transcription level of floral-related genes in advance. CONCLUSIONS It was speculated that ClNLPs may act on the photoperiodic pathway under optimal nitrate environment, and ultimately regulate the flowering time by up-regulating the transcription level of ClCRYs. These results provide new perspective for exploring the mechanism of nitrate/nitrogen affecting flowering in higher plants.
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Affiliation(s)
- Qiuling Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Junzhuo Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohui Wen
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | | | - Xiuzhen Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Pradhan UK, Meher PK, Naha S, Rao AR, Kumar U, Pal S, Gupta A. ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Funct Integr Genomics 2023; 23:92. [PMID: 36939943 DOI: 10.1007/s10142-023-01014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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Chen P, Wei Q, Yao Y, Wei J, Qiu L, Zhang B, Liu H. Inoculation with Azorhizobium caulinodans ORS571 enhances plant growth and salt tolerance of switchgrass (Panicum virgatum L.) seedlings. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:35. [PMID: 36864528 PMCID: PMC9983177 DOI: 10.1186/s13068-023-02286-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/18/2023] [Indexed: 03/04/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is an important biofuel crop that may contribute to replacing petroleum fuels. However, slow seedling growth and soil salinization affect the growth and development of switchgrass. An increasing number of studies have shown that beneficial microorganisms promote plant growth and increase tolerance to salinity stress. However, the feasibility of inoculating switchgrass with Azorhizobium caulinodans ORS571 to enhance the growth and salt tolerance of its seedlings is unclear. Our previous study showed that A. caulinodans ORS571 could colonize wheat (Triticum aestivum L.) and thereby promote its growth and development and regulate the gene expression levels of microRNAs (miRNAs). RESULTS In this study, we systematically studied the impact of A. caulinodans ORS571 on switchgrass growth and development and the response to salinity stress; we also studied the underlying mechanisms during these biological processes. Inoculation with A. caulinodans ORS571 significantly alleviated the effect of salt stress on seedling growth. Under normal conditions, A. caulinodans ORS571 significantly increased fresh plant weight, chlorophyll a content, protein content, and peroxidase (POD) activity in switchgrass seedlings. Under salt stress, the fresh weight, dry weight, shoot and root lengths, and chlorophyll contents were all significantly increased, and some of these parameters even recovered to normal levels after inoculation with A. caulinodans ORS571. Soluble sugar and protein contents and POD and superoxide dismutase (SOD) activities were also significantly increased, contrary to the results for proline. Additionally, A. caulinodans ORS571 may alleviate salt stress by regulating miRNAs. Twelve selected miRNAs were all upregulated to different degrees under salt stress in switchgrass seedlings. However, the levels of miR169, miR171, miR319, miR393, miR535, and miR854 were decreased significantly after inoculation with A. caulinodans ORS571 under salt stress, in contrast to the expression level of miR399. CONCLUSION This study revealed that A. caulinodans ORS571 increased the salt tolerance of switchgrass seedlings by increasing their water content, photosynthetic efficiency, osmotic pressure maintenance, and reactive oxygen species (ROS) scavenging abilities and regulating miRNA expression. This work provides a new, creative idea for improving the salt tolerance of switchgrass seedlings.
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Affiliation(s)
- Pengyang Chen
- grid.144022.10000 0004 1760 4150College of Life Sciences, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Qiannan Wei
- grid.144022.10000 0004 1760 4150College of Life Sciences, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Yifei Yao
- grid.144022.10000 0004 1760 4150College of Life Sciences, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Jiaqi Wei
- grid.144022.10000 0004 1760 4150College of Life Sciences, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Li Qiu
- grid.144022.10000 0004 1760 4150College of Veterinary Medicine, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Huawei Liu
- College of Life Sciences, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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10
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Wan X, Wang Z, Duan W, Huang T, Song H, Xu X. Knockdown of Sly-miR164a Enhanced Plant Salt Tolerance and Improved Preharvest and Postharvest Fruit Nutrition of Tomato. Int J Mol Sci 2023; 24:ijms24054639. [PMID: 36902070 PMCID: PMC10003209 DOI: 10.3390/ijms24054639] [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: 12/13/2022] [Revised: 02/19/2023] [Accepted: 02/25/2023] [Indexed: 03/04/2023] Open
Abstract
Salinity stress is a serious limitation to tomato growth and development. The aim of this study was to investigate the effects of Sly-miR164a on tomato growth and fruit nutritional quality under salt stress. The results showed that the root length, fresh weight, plant height, stem diameter and ABA content of miR164a#STTM (knockdown of Sly-miR164a) lines were higher than those of WT and miR164a#OE (overexpression of Sly-miR164a) lines under salt stress. Compared with WT, miR164a#STTM tomato lines exhibited lower ROS accumulation under salt stress. In addition, the fruits of miR164a#STTM tomato lines had higher soluble solids, lycopene, ascorbic acid (ASA) and carotenoid content compared with WT. The study indicated that tomato plants were more sensitive to salt when Sly-miR164a was overexpressed, while knockdown of Sly-miR164a enhanced plant salt tolerance and improved fruit nutritional value.
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11
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Xu Y, Liu J, Ji X, Zhao G, Zhao T, Wang X, Wang L, Gao S, Hao Y, Gao Y, Gao Y, Weng X, Jia L, Chen Z. Integrative analysis of microRNAs and mRNAs reveals the regulatory networks of triterpenoid saponin metabolism in Soapberry ( Sapindus mukorossi Gaertn.). FRONTIERS IN PLANT SCIENCE 2023; 13:1037784. [PMID: 36699854 PMCID: PMC9869041 DOI: 10.3389/fpls.2022.1037784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/19/2022] [Indexed: 06/13/2023]
Abstract
Triterpenoid saponin are important secondary metabolites and bioactive constituents of soapberry (Sapindus mukorossi Gaertn.) and are widely used in medicine and toiletry products. However, little is known about the roles of miRNAs in the regulation of triterpenoid saponin biosynthesis in soapberry. In this study, a total of 3036 miRNAs were identified, of which 1372 miRNAs were differentially expressed at different stages of pericarp development. Important KEGG pathways, such as terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, and basal transcription factors were highlighted, as well the roles of some key miRNAs, such as ath-miR5021, han-miR3630-3p, and ppe-miR858, which may play important roles in regulating triterpenoid saponin biosynthesis. In addition, 58 miRNAs might participate in saponin biosynthesis pathways by predicting the targets of those miRNAs to 53 saponin biosynthesis structural genes. And 75 miRNAs were identified to potentially play vital role in saponin accumulation by targeting transcript factor genes, bHLH, bZIP, ERF, MYB, and WRKY, respectively, which are candidate regulatory genes in the pathway of saponin biosynthesis. The results of weighted gene coexpression network analysis (WGCNA) suggested that two saponin-specific miRNA modules and 10 hub miRNAs may participate in saponin biosynthesis. Furthermore, multiple miRNA-mRNA regulatory networks potentially involved in saponin biosynthesis were generated, e.g., ath-miR5021-SmIDI2/SmGPS5/SmbAS1/SmCYP71D-3/SmUGT74G-2, han-miR3630-3p-SmCYP71A-14/SmbHLH54/SmMYB135/SmWRKY32, and ppe-miR858-SmMYB5/SmMYB32. qRT-PCR analysis validated the expression patterns of nine miRNAs and 12 corresponding target genes. This study represents the first comprehensive analysis of miRNAs in soapberry and lays the foundation for further understanding of miRNA-based regulation in triterpenoid saponin biosynthesis.
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Affiliation(s)
- Yuanyuan Xu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Jiming Liu
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xiangqin Ji
- Bioinformatics Analysis Department, Hangzhou KaiTai Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Guochun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Tianyun Zhao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Xin Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Lixian Wang
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Shilun Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yingying Hao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuhan Gao
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Yuan Gao
- Planning and Design Institute of Forest Products Industry, National Forestry and Grassland Administration, Beijing, China
| | - Xuehuang Weng
- Research and Development Department, Yuanhua Forestry Biological Technology Co., Ltd., Sanming, Fujian, China
| | - Liming Jia
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
| | - Zhong Chen
- Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
- National Energy R&D Center for Non-food Biomass, Beijing Forestry University, Beijing, China
- National Innovation Alliance of Sapindus Industry, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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12
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Overexpression of Mtr-miR319a Contributes to Leaf Curl and Salt Stress Adaptation in Arabidopsis thaliana and Medicago truncatula. Int J Mol Sci 2022; 24:ijms24010429. [PMID: 36613873 PMCID: PMC9820427 DOI: 10.3390/ijms24010429] [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: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering.
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Rehman B, Javed J, Rauf M, Khan SA, Arif M, Hamayun M, Gul H, Khilji SA, Sajid ZA, Kim WC, Lee IJ. ACC deaminase-producing endophytic fungal consortia promotes drought stress tolerance in M.oleifera by mitigating ethylene and H 2O 2. FRONTIERS IN PLANT SCIENCE 2022; 13:967672. [PMID: 36618664 PMCID: PMC9814162 DOI: 10.3389/fpls.2022.967672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Drought has become more prevalent due to dramatic climate change worldwide. Consequently, the most compatible fungal communities collaborate to boost plant development and ecophysiological responses under environmental constraints. However, little is known about the specific interactions between non-host plants and endophytic fungal symbionts that produce growth-promoting and stress-alleviating hormones during water deficits. METHODS The current research was rationalized and aimed at exploring the influence of the newly isolated, drought-resistant, ACC deaminase enzyme-producing endophytic fungi Trichoderma gamsii (TP), Fusarium proliferatum (TR), and its consortium (TP+TR) from a xerophytic plant Carthamus oxycantha L. on Moringa oleifera L. grown under water deficit induced by PEG-8000 (8% osmoticum solution). RESULTS The current findings revealed that the co-inoculation promoted a significant enhancement in growth traits such as dry weight (217%), fresh weight (123%), root length (65%), shoot length (53%), carotenoids (87%), and chlorophyll content (76%) in comparison to control plants under water deficit. Total soluble sugars (0.56%), proteins (132%), lipids (43%), flavonoids (52%), phenols (34%), proline (55%), GA3 (86%), IAA (35%), AsA (170%), SA (87%), were also induced, while H2O2 (-45%), ABA (-60%) and ACC level (-77%) was decreased by co-inoculation of TP and TR in M. oleifera plants, compared with the non-inoculated plants under water deficit. The co-inoculum (TP+TR) also induced the antioxidant potential and enzyme activities POX (325%), CAT activity (166%), and AsA (21%), along with a lesser decrease (-2%) in water potential in M. oleifera plants with co-inoculation under water deficit compared with non-inoculated control. The molecular analysis for gene expression unraveled the reduced expression of ethylene biosynthesis and signaling-related genes up to an optimal level, with an induction of antioxidant enzymatic genes by endophytic co-inoculation in M. oleifera plants under water deficit, suggesting their role in drought stress tolerance as an essential regulatory function. CONCLUSION The finding may alert scientists to consider the impacts of optimal reduction of ethylene and induction of antioxidant potential on drought stress tolerance in M. oleifera. Hence, the present study supports the use of compatible endophytic fungi to build a bipartite mutualistic symbiosis in M. oleifera non-host plants to mitigate the negative impacts of water scarcity in arid regions throughout the world.
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Affiliation(s)
- Bushra Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Javeria Javed
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mamoona Rauf
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sumera Afzal Khan
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Humaira Gul
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sheza Ayaz Khilji
- Department of Botany, Division of Science and Technology, University of Education, Township, Lahore, Pakistan
| | | | - Won-Chan Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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14
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Chen QJ, Zhang LP, Song SR, Wang L, Xu WP, Zhang CX, Wang SP, Liu HF, Ma C. vvi-miPEP172b and vvi-miPEP3635b increase cold tolerance of grapevine by regulating the corresponding MIRNA genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111450. [PMID: 36075277 DOI: 10.1016/j.plantsci.2022.111450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
As a kind of small molecular weight proteins, many peptides have been discovered, including peptides encoded by pri-miRNA (miPEPs). Similar as traditional phytohormone or signaling molecular, these peptides participate in numerous plant growth processes. MicroRNAs (miRNAs) play an important regulatory role in plant stress response. While the roles of miPEPs in response to abiotic stress has not been studied now. In this study, to explore whether miPEPs could contribute to low temperature (4ºC) tolerance of plants, the expression pattern of 23 different vvi-MIRs were analyzed by qRT-PCR in 'Thompson Seedless' (Vitis vinifera) plantlets under cold stress (4ºC) firstly, and vvi-MIR172b and vvi-MIR3635b which showed an elevated expression levels were selected to identify miPEPs. Through transient expression, one small open reading frame (sORF) in each of the two pri-miRNAs could increase the expression of corresponding vvi-MIR, and the amino acid sequences of sORFs were named vvi-miPEP172b and vvi-miPEP3635b, respectively. The synthetic vvi-miPEP172b and vvi-miPEP3635b were applied to the grape plantlets, and the tissue culture plantlets exhibited a higher cold tolerance compared with the control groups. These results revealed the effective roles of miPEPs in plant cold stress resistance for the first time, providing a theoretical basis for the future application of miPEPs to agricultural production.
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Affiliation(s)
- Qiu-Ju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Li-Peng Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Shi-Ren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wen-Ping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cai-Xi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Ping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huai-Feng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China; Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, Xinjiang, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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15
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MicroRNA398: A Master Regulator of Plant Development and Stress Responses. Int J Mol Sci 2022; 23:ijms231810803. [PMID: 36142715 PMCID: PMC9502370 DOI: 10.3390/ijms231810803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.
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16
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MicroRNAs Mediated Plant Responses to Salt Stress. Cells 2022; 11:cells11182806. [PMID: 36139379 PMCID: PMC9496875 DOI: 10.3390/cells11182806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/17/2022] Open
Abstract
One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.
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17
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Ullah I, Kamel EAR, Shah ST, Basit A, Mohamed HI, Sajid M. Application of RNAi technology: a novel approach to navigate abiotic stresses. Mol Biol Rep 2022; 49:10975-10993. [PMID: 36057876 DOI: 10.1007/s11033-022-07871-7] [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: 05/01/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output. METHODS Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations. RESULTS As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses. CONCLUSION The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.
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Affiliation(s)
- Izhar Ullah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Ehab A R Kamel
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt
| | - Syed Tanveer Shah
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Abdul Basit
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
| | - Muhammad Sajid
- Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture, Peshawar, 25120, Pakistan
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18
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Jiang J, Zhu H, Li N, Batley J, Wang Y. The miR393-Target Module Regulates Plant Development and Responses to Biotic and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23169477. [PMID: 36012740 PMCID: PMC9409142 DOI: 10.3390/ijms23169477] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs), a class of endogenous small RNAs, are broadly involved in plant development, morphogenesis and responses to various environmental stresses, through manipulating the cleavage, translational expression, or DNA methylation of target mRNAs. miR393 is a conserved miRNA family present in many plants, which mainly targets genes encoding the transport inhibitor response1 (TIR1)/auxin signaling F-box (AFB) auxin receptors, and thus greatly affects the auxin signal perception, Aux/IAA degradation, and related gene expression. This review introduces the advances made on the miR393/target module regulating plant development and the plant’s responses to biotic and abiotic stresses. This module is valuable for genetic manipulation of optimized conditions for crop growth and development and would also be helpful in improving crop yield through molecular breeding.
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Affiliation(s)
- Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Haotian Zhu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Na Li
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: (J.B.); (Y.W.)
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (J.B.); (Y.W.)
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19
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Zhu M, Wang X, Zhou Y, Tan J, Zhou Y, Gao F. Small RNA Sequencing Revealed that miR4415, a Legume-Specific miRNA, was Involved in the Cold Acclimation of Ammopiptanthus nanus by Targeting an L-Ascorbate Oxidase Gene and Regulating the Redox State of Apoplast. Front Genet 2022; 13:870446. [PMID: 35444684 PMCID: PMC9013972 DOI: 10.3389/fgene.2022.870446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous single-stranded RNAs that regulate plant growth, development, and environmental stress response posttranscriptionally. Ammopiptanthus nanus, a rare evergreen broad-leaved shrub in the temperate area of Central Asia, can tolerate freezing stress as low as -30 degrees centigrade in winter, and miRNA might be involved in the cold acclimation which enables A. nanus to obtain tolerance to freezing stress. Systematic identification and functional analysis of the miRNAs involved in the cold acclimation in A. nanus may promote understanding of the miRNA-mediated gene regulation network underlying cold acclimation. Here, based on small RNA and degradome sequencing, 256 miRNAs and 1,808 miRNA-target pairs were identified in A. nanus. A total of 39 cold-responsive miRNAs were identified, of which 29 were upregulated and ten were downregulated. These cold-responsive miRNAs may participate in the cold acclimation by regulating redox homeostasis (miR398, miR4415, and miR408), calcium signaling (miR5225 and miR5211), growth and development (miR159 and miR390), and small RNA-mediated gene silencing (miR168 and miR1515). We found that miR4415, a legume-specific miRNA, is involved in the cold acclimation of A. nanus by targeting an L-ascorbate oxidase gene and then regulating the redox state of the apoplast. Our study provides important data for understanding the regulatory role of miRNA in the cold acclimation of A. nanus.
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Affiliation(s)
- Ming Zhu
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Xue Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yanqiu Zhou
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jinhua Tan
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yijun Zhou
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
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Salamon S, Żok J, Gromadzka K, Błaszczyk L. Expression Patterns of miR398, miR167, and miR159 in the Interaction between Bread Wheat ( Triticum aestivum L.) and Pathogenic Fusarium culmorum and Beneficial Trichoderma Fungi. Pathogens 2021; 10:1461. [PMID: 34832616 PMCID: PMC8624912 DOI: 10.3390/pathogens10111461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is an agronomically significant cereal cultivated worldwide. Wheat breeding is limited by numerous abiotic and biotic stresses. One of the most deleterious factors is biotic stress provoked by the Fusarium culmorum fungus. This pathogen is a causative agent of Fusarium root rot and Fusarium head blight. Beneficial fungi Trichoderma atroviride and T. cremeum are strong antagonists of mycotoxigenic Fusarium spp. These fungi promote plant growth and enhance their tolerance of negative environmental conditions. The aim of the study was to determine and compare the spatial (in above- and underground organs) and temporal (early: 6 and 22 hpi; and late: 5 and 7 dpi reactions) expression profiles of three mature miRNAs (miR398, miR167, and miR159) in wheat plants inoculated with two strains of F. culmorum (KF846 and EW49). Moreover, the spatial expression patterns in wheat response between plants inoculated with beneficial T. atroviride (AN35) and T. cremeum (AN392) were assessed. Understanding the sophisticated role of miRNAs in wheat-fungal interactions may initiate a discussion concerning the use of this knowledge to protect wheat plants from the harmful effects of fungal pathogens. With the use of droplet digital PCR (ddPCR), the absolute quantification of the selected miRNAs in the tested material was carried out. The differential accumulation of miR398, miR167, and miR159 in the studied groups was observed. The abundance of all analyzed miRNAs in the roots demonstrated an increase in the early and reduction in late wheat response to F. culmorum inoculation, suggesting the role of these particles in the initial wheat reaction to the studied fungal pathogen. The diverse expression patterns of the studied miRNAs between Trichoderma-inoculated or F. culmorum-inoculated plants and control wheat, as well as between Trichoderma-inoculated and F. culmorum-inoculated plants, were noticed, indicating the need for further analysis.
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Affiliation(s)
- Sylwia Salamon
- Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (S.S.); (J.Ż.)
| | - Julia Żok
- Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (S.S.); (J.Ż.)
| | - Karolina Gromadzka
- Department of Chemistry, Poznan University of Life Sciences, 60-625 Poznan, Poland;
| | - Lidia Błaszczyk
- Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (S.S.); (J.Ż.)
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21
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Fasani E, DalCorso G, Zorzi G, Vitulo N, Furini A. Comparative analysis identifies micro-RNA associated with nutrient homeostasis, development and stress response in Arabidopsis thaliana upon high Zn and metal hyperaccumulator Arabidopsis halleri. PHYSIOLOGIA PLANTARUM 2021; 173:920-934. [PMID: 34171137 PMCID: PMC8597110 DOI: 10.1111/ppl.13488] [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: 01/11/2021] [Accepted: 06/21/2021] [Indexed: 05/05/2023]
Abstract
miRNAs have been found to be key players in mineral homeostasis, both in the control of nutrient balance and in the response to toxic trace elements. However, the effect of Zn excess on miRNAs has not been elucidated; moreover, no data are present regarding miRNAs in hyperaccumulator species, where metal homeostasis is tightly regulated. Therefore, expression levels of mature miRNAs were measured by RNA-Seq in Zn-sensitive Arabidopsis thaliana grown in control conditions and upon high Zn, in soil and in Zn-hyperaccumulator Arabidopsis halleri grown in control conditions. Differential expression of notable miRNAs and their targets was confirmed by real-time RT-PCR. The comparison in A. thaliana revealed a small subset modulated upon Zn treatment that is associated with stress response and nutrient homeostasis. On the other hand, a more consistent group of miRNAs was differentially expressed in A. halleri compared with A. thaliana, reflecting inherent differences in nutritional requirements and response to stresses and plant growth and development. Overall, these results confirm the involvement of miRNAs in Zn homeostasis and support the hypothesis of distinct regulatory pathways in hyperaccumulator species.
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Affiliation(s)
- Elisa Fasani
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | | | - Gianluca Zorzi
- Department of BiotechnologyUniversity of VeronaVeronaItaly
| | - Nicola Vitulo
- Department of BiotechnologyUniversity of VeronaVeronaItaly
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Abdellatef E, Kamal NM, Tsujimoto H. Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses. Int J Mol Sci 2021; 22:ijms22147687. [PMID: 34299307 PMCID: PMC8306419 DOI: 10.3390/ijms22147687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Crop yield is severely affected by biotic and abiotic stresses. Plants adapt to these stresses mainly through gene expression reprogramming at the transcriptional and post-transcriptional levels. Recently, the exogenous application of double-stranded RNAs (dsRNAs) and RNA interference (RNAi) technology has emerged as a sustainable and publicly acceptable alternative to genetic transformation, hence, small RNAs (micro-RNAs and small interfering RNAs) have an important role in combating biotic and abiotic stresses in plants. RNAi limits the transcript level by either suppressing transcription (transcriptional gene silencing) or activating sequence-specific RNA degradation (post-transcriptional gene silencing). Using RNAi tools and their respective targets in abiotic stress responses in many crops is well documented. Many miRNAs families are reported in plant tolerance response or adaptation to drought, salinity, and temperature stresses. In biotic stress, the spray-induced gene silencing (SIGS) provides an intelligent method of using dsRNA as a trigger to silence target genes in pests and pathogens without producing side effects such as those caused by chemical pesticides. In this review, we focus on the potential of SIGS as the most recent application of RNAi in agriculture and point out the trends, challenges, and risks of production technologies. Additionally, we provide insights into the potential applications of exogenous RNAi against biotic stresses. We also review the current status of RNAi/miRNA tools and their respective targets on abiotic stress and the most common responsive miRNA families triggered by stress conditions in different crop species.
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Affiliation(s)
- Eltayb Abdellatef
- Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan;
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Behavioural and Chemical Ecology Unit, International Centre of Insect Physiology and Ecology, P.O. Box 30772, Nairobi 00100, Kenya
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Agricultural Research Corporation, P.O. Box 30, Khartoum North 11111, Sudan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan;
- Correspondence:
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Dong W, Ren W, Wang X, Mao Y, He Y. MicroRNA319a regulates plant resistance to Sclerotinia stem rot. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3540-3553. [PMID: 33606883 DOI: 10.1093/jxb/erab070] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
MicroRNA319a (miR319a) controls cell division arrest in plant leaves by inhibiting the expression of TCP (TEOSINTE BRANCHED 1/CYCLOIDEA/PCF) family genes. However, it is unclear whether miR319a influences infection by necrotrophic pathogens and host susceptibility. In this study, we revealed that miR319a affects plant resistance to stem rot disease caused by Sclerotinia sclerotiorum. In Brassica rapa plants infected with S. sclerotiorum, miR319a levels increased while the expression levels of several BraTCP genes significantly decreased compared with those of uninfected plants. Overexpression of BraMIR319a in B. rapa increased the susceptibility of the plants to S. sclerotiorum and aggravated stem rot disease, whereas overexpression of BraTCP4-1 promoted plant resistance. RNA sequencing data revealed a potential relationship between miR319a and pathogen-related WRKY genes. Chromatin immunoprecipitation, electrophoretic mobility shift, and reporter transaction assays showed that BraTCP4-1 could bind to the promoters of WRKY75, WRKY70, and WRKY33 and directly activate these pathogen-related genes. Moreover, the expression levels of WRKY75, WRKY70, and WRKY33 in plants overexpressing BraMIR319a decreased significantly, whereas those of plants overexpressing BraTCP4-1 increased significantly, relative to the wild type. These results suggest that miR319a and its target gene BraTCP4 control stem rot resistance through pathways of WRKY genes.
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Affiliation(s)
- Weiguo Dong
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Ren
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xuan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanfei Mao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuke He
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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Xu T, Zhang L, Yang Z, Wei Y, Dong T. Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:665439. [PMID: 34220888 PMCID: PMC8247772 DOI: 10.3389/fpls.2021.665439] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 05/07/2023]
Abstract
Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.
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Affiliation(s)
- Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Tao Xu,
| | - Long Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tingting Dong,
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26
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Chakraborty A, Viswanath A, Malipatil R, Rathore A, Thirunavukkarasu N. Structural and Functional Characteristics of miRNAs in Five Strategic Millet Species and Their Utility in Drought Tolerance. Front Genet 2020; 11:608421. [PMID: 33363575 PMCID: PMC7753210 DOI: 10.3389/fgene.2020.608421] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
Millets are the strategic food crops in arid and drought-prone ecologies. Millets, by virtue of nature, are very well-adapted to drought conditions and able to produce sustainable yield. Millets have important nutrients that can help prevent micro-nutrient malnutrition. As a result of the adverse effect of climate change and widespread malnutrition, millets have attained a strategic position to sustain food and nutritional security. Although millets can adapt well to the drought ecologies where other cereals fail completely, the yield level is very low under stress. There is a tremendous opportunity to increase the genetic potential of millet crops in dry lands when the genetics of the drought-tolerance mechanism is fully explained. MicroRNAs (miRNAs) are the class of small RNAs that control trait expression. They are part of the gene regulation but little studied in millets. In the present study, novel miRNAs and gene targets were identified from the genomic resources of pearl millet, sorghum, foxtail millet, finger millet, and proso millet through in silico approaches. A total of 1,002 miRNAs from 280 families regulating 23,158 targets were identified using different filtration criteria in five millet species. The unique as well as conserved structural features and functional characteristics of miRNA across millets were explained. About 84 miRNAs were conserved across millets in different species combinations, which explained the evolutionary relationship of the millets. Further, 215 miRNAs controlling 155 unique major drought-responsive genes, transcription factors, and protein families revealed the genetics of drought tolerance that are accumulated in the millet genomes. The miRNAs regulating the drought stress through specific targets or multiple targets showed through a network analysis. The identified genes regulated by miRNA genes could be useful in developing functional markers and used for yield improvement under drought in millets as well as in other crops.
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Affiliation(s)
- Animikha Chakraborty
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Aswini Viswanath
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Renuka Malipatil
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Abhishek Rathore
- Statistics, Bioinformatics and Data Management, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Nepolean Thirunavukkarasu
- Genomics and Molecular Breeding Lab, Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
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Husain T, Fatima A, Suhel M, Singh S, Sharma A, Prasad SM, Singh VP. A brief appraisal of ethylene signaling under abiotic stress in plants. PLANT SIGNALING & BEHAVIOR 2020; 15:1782051. [PMID: 32692940 PMCID: PMC8550184 DOI: 10.1080/15592324.2020.1782051] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
For years, ethylene has been known to humankind as the plant hormone responsible for fruit ripening. However, the multitasking aspect of ethylene is still being investigated as ever. It is one of the most diversified signaling molecules which acclimatize plant under adverse conditions. It promotes adventitious root formation, stem and petiole elongation, opening and closing of stomatal aperture, reduces salinity and metal stress, etc. Presence of ethylene checks the production and scavenging of reactive oxygen species by strengthening the antioxidant machinery. Meanwhile, it interacts with other signaling molecules and initiates a cascade of adaptive responses. In the present mini review, the biosynthesis and sources of ethylene production, interaction with other signaling molecules, and its exogenous application under different abiotic stresses have been discussed.
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Affiliation(s)
- Tajammul Husain
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Abreeq Fatima
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Mohammad Suhel
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Samiksha Singh
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Sheo Mohan Prasad
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, India
- Sheo Mohan Prasad Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of Allahabad, Prayagraj, 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, India
- CONTACT Vijay Pratap Singh Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj211002, India
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Jiang W, Geng Y, Liu Y, Chen S, Cao S, Li W, Chen H, Ma D, Yin J. Genome-wide identification and characterization of SRO gene family in wheat: Molecular evolution and expression profiles during different stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:590-611. [PMID: 32912491 DOI: 10.1016/j.plaphy.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/27/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
SRO (SIMILAR TO RCD ONE), a type of plant-specific small protein family, play important roles in plant growth and development, as well as in response to biotic/abiotic stresses. Although characterization of SROs have been performed in model plants, little is known about their function in wheat, especially under stress conditions. In this study, 30 SRO genes were identified from the wheat genome (TaSRO). They were phylogenetically separated into two groups with distinct structures. The cis-regulatory elements in the promoter region of TaSROs were analyzed and numerous elements functionally associated with stress responding and hormones were interpreted, implying the reason for induction expression patterns of TaSROs during abiotic and biotic stresses in wheat. Whole-genome replication events in the SRO gene family of wheat and seven other species (Arabidopsis thaliana, rice, maize, barley, soybean, upland cotton, and cucumber) were analyzed, resulting in 1, 12, 9, 23, 6, 5, and 3 of gene pairs, respectively. The tissue-specific expression pattern profiling revealed that most TaSROs are highly expressed in one or more tissues and may play an important role in wheat growth and development. In addition, qRT-PCR results further confirmed that these TaSRO genes are involved in wheat stress response. In summary, our study laid a theoretical basis for molecular function deciphering of TaSROs, especially in plant hormones and biotic/abiotic stress responses.
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Affiliation(s)
- Wenqiang Jiang
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210014, Jiangsu, China
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Shuhui Chen
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China.
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/College of Agriculture, Yangtze University, Jingzhou, 434000, Hubei, China; Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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29
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Smoczynska A, Pacak AM, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes (Basel) 2020; 11:genes11050488. [PMID: 32365647 PMCID: PMC7290300 DOI: 10.3390/genes11050488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
The regulation of mRNA (messenger RNA) levels by microRNA-mediated activity is especially important in plant responses to environmental stresses. In this work, we report six novel barley microRNAs, including two processed from the same precursor that are severely downregulated under drought conditions. For all analyzed microRNAs, we found target genes that were upregulated under drought conditions and that were known to be involved in a plethora of processes from disease resistance to chromatin–protein complex formation and the regulation of transcription in mitochondria. Targets for novel barley microRNAs were confirmed through degradome data analysis and RT-qPCR using primers flanking microRNA-recognition site. Our results show a broad transcriptional response of barley to water deficiency conditions through microRNA-mediated gene regulation and facilitate further research on drought tolerance in crops.
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Affiliation(s)
- Aleksandra Smoczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Andrzej M. Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Przemysław Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-712 Poznan, Poland;
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland; (A.S.); (A.M.P.); (P.N.); (A.S.-B.); (K.K.); (A.J.)
- Correspondence: ; Tel.: +48-61-829-5950
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30
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Weng ST, Kuo YW, King YC, Lin HH, Tu PY, Tung KS, Jeng ST. Regulation of micoRNA2111 and its target IbFBK in sweet potato on wounding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110391. [PMID: 32005396 DOI: 10.1016/j.plantsci.2019.110391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 05/14/2023]
Abstract
Plant microRNAs (miRNAs) are non-coding RNAs, which are composed of 20-24 nucleotides. MiRNAs play important roles in plant growth and responses to biotic and abiotic stresses. Wounding is one of the most serious stresses for plants; however, the regulation of miRNAs in plants upon wounding is not well studied. In this study, miR2111, a wound-repressed miRNA, identified previously in sweet potato (Ipomoea batatas cv Tainung 57) by small RNA deep sequencing was chosen for further analysis. Based on sweet potato transcriptome database, F-box/kelch repeat protein (IbFBK), a target gene of miR2111, was identified. IbFBK is a wound-inducible gene, and the miR2111-induced cleavage site in IbFBK mRNA is between the 10th and 11th nucleotides of miR2111. IbFBK is a component of the E3 ligase SCF (SKP1-Cullin-F-box) complex participating in protein ubiquitination and degradation. The results of yeast two-hybrid and bimolecular fluorescence complementation assays demonstrate that IbFBK was conjugated with IbSKP1 through the F-box domain in IbFBK N-terminus to form SCF complex, and interacted with IbCNR8 through the kelch-repeat domain in IbFBK C-terminus. The interaction of IbFBK and IbCNR8 may lead to the ubiquitination and degradation of IbCNR8. In conclusion, the suppression of miR2111 resulted in the increase of IbFBK, and may regulate protein degradation of IbCNR8 in sweet potato responding to wounding.
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Affiliation(s)
- Shiau-Ting Weng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan; Academy of Agricultural Sciences, Sanming 365000, Fujian, China.
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pin-Yang Tu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Kuei-Shu Tung
- Institute of Molecular and Cellular Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.
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Asefpour Vakilian K. Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses. Sci Rep 2020; 10:3041. [PMID: 32080299 PMCID: PMC7033123 DOI: 10.1038/s41598-020-59981-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/06/2020] [Indexed: 12/03/2022] Open
Abstract
During the last two decades, human has increased his knowledge about the role of miRNAs and their target genes in plant stress response. Biotic and abiotic stresses result in simultaneous tissue-specific up/down-regulation of several miRNAs. In this study, for the first time, feature selection algorithms have been used to investigate the contribution of individual plant miRNAs in Arabidopsis thaliana response towards different levels of several abiotic stresses including drought, salinity, cold, and heat. Results of information theory-based feature selection revealed that miRNA-169, miRNA-159, miRNA-396, and miRNA-393 had the highest contributions to plant response towards drought, salinity, cold, and heat, respectively. Furthermore, regression models, i.e., decision tree (DT), support vector machines (SVMs), and Naïve Bayes (NB) were used to predict the plant stress by having the plant miRNAs' concentration. SVM with Gaussian kernel was capable of predicting plant stress (R2 = 0.96) considering miRNA concentrations as input features. Findings of this study prove the performance of machine learning as a promising tool to investigate some aspects of miRNAs' contribution to plant stress responses that have been undiscovered until today.
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Affiliation(s)
- Keyvan Asefpour Vakilian
- Department of Agrotechnology, College of Abouraihan, University of Tehran, Tehran, Iran.
- Private Laboratory of Biosensor Applications, Hamadan, Iran.
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Liu Y, Li D, Yan J, Wang K, Luo H, Zhang W. MiR319 mediated salt tolerance by ethylene. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2370-2383. [PMID: 31094071 PMCID: PMC6835123 DOI: 10.1111/pbi.13154] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 05/04/2019] [Accepted: 05/10/2019] [Indexed: 05/03/2023]
Abstract
Salinity-induced accumulation of certain microRNAs accompanied by gaseous phytohormone ethylene production has been recognized as a mechanism of plant salt tolerance. MicroRNA319 (miR319) has been characterized as an important player in abiotic stress resistance in some C3 plants, such as Arabidopsis thaliana and rice. However, its role in the dedicated biomass plant switchgrass (Panicum virgatum L.), a C4 plant, has not been reported. Here, we show crosstalk between miR319 and ethylene (ET) for increasing salt tolerance. By overexpressing Osa-MIR319b and a target mimicry form of miR319 (MIM319), we showed that miR319 positively regulated ET synthesis and salt tolerance in switchgrass. By experimental treatments, we demonstrated that ET-mediated salt tolerance in switchgrass was dose-dependent, and miR319 regulated the switchgrass salt response by fine-tuning ET synthesis. Further experiments showed that the repression of a miR319 target, PvPCF5, in switchgrass also led to enhanced ethylene accumulation and salt tolerance in transgenic plants. Genome-wide transcriptome analysis demonstrated that overexpression of miR319 (OE-miR319) down-regulated the expression of key genes in the methionine (Met) cycle but promoted the expression of genes in ethylene synthesis. The results enrich our understanding of the synergistic effects of the miR319-PvPCF5 module and ethylene synthesis in the salt tolerance of switchgrass, a C4 bioenergy plant.
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Affiliation(s)
- Yanrong Liu
- Department of Grassland ScienceChina Agricultural UniversityBeijingChina
| | - Dayong Li
- Beijing Vegetable Research Center (BVRC)Beijing Academy of Agricultural and Forestry SciencesNational Engineering Research Center for VegetablesBeijingChina
| | - Jianping Yan
- Department of Grassland ScienceChina Agricultural UniversityBeijingChina
| | - Kexin Wang
- Department of Grassland ScienceChina Agricultural UniversityBeijingChina
| | - Hong Luo
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Wanjun Zhang
- Department of Grassland ScienceChina Agricultural UniversityBeijingChina
- National Energy R&D Center for Biomass (NECB)China Agricultural UniversityBeijingChina
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Asefpour Vakilian K. Gold nanoparticles-based biosensor can detect drought stress in tomato by ultrasensitive and specific determination of miRNAs. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 145:195-204. [PMID: 31706222 DOI: 10.1016/j.plaphy.2019.10.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 05/16/2023]
Abstract
Drought stress can significantly affect the yield and quality of tomato production. However, the development of a sensitive and specific method for the determination of drought stress is somehow challenging since plant common morpho-physiological and biochemical characteristic are not generally specific to biotic and abiotic stresses. As a solution, the concentration of miRNAs in plant tissues can be a selective and specific indicator of plant stress. In this study, an optical biosensor based on gold nanoparticles is introduced to determine miRNA-1886 in tomato plant roots. Results showed that irrigation levels from 100% to 60% of field capacity increased the concentration of miRNA-1886 in a range from ca. 100 to 6800 fM (fM) causing a linear change in the biosensor response (R2 = 0.97). Results also revealed that in contrast with plant conventional morpho-physiological and biochemical characteristic, miRNA-1886 concentration was not significantly affected (P < 0.01) by other stresses, i.e., salinity and temperature during the growth period. The biosensor introduced in this study is a reliable method to study stress-related functions of miRNAs in plants and their application in specific plant stress determination.
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Affiliation(s)
- Keyvan Asefpour Vakilian
- Department of Agrotechnology, College of Abouraihan, University of Tehran, Tehran, Iran; Private Laboratory of Biosensor Applications, Hamadan, Iran.
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Zhou C, Zhu C, Fu H, Li X, Chen L, Lin Y, Lai Z, Guo Y. Genome-wide investigation of superoxide dismutase (SOD) gene family and their regulatory miRNAs reveal the involvement in abiotic stress and hormone response in tea plant (Camellia sinensis). PLoS One 2019; 14:e0223609. [PMID: 31600284 PMCID: PMC6786557 DOI: 10.1371/journal.pone.0223609] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
Superoxide dismutases (SODs), as a family of metalloenzymes related to the removal of reactive oxygen species (ROS), have not previously been investigated at genome-wide level in tea plant. In this study, 10 CsSOD genes were identified in tea plant genome, including 7 Cu/Zn-SODs (CSDs), 2 Fe-SODs (FSDs) and one Mn-SOD (MSD), and phylogenetically classified in three subgroups, respectively. Physico-chemical characteristic, conserved motifs and potential protein interaction analyses about CsSOD proteins were carried out. Exon-intron structures and codon usage bias about CsSOD genes were also examined. Exon-intron structures analysis revealed that different CsSOD genes contained various number of introns. On the basis of the prediction of regulatory miRNAs of CsSODs, a modification 5’ RNA ligase-mediated (RLM)-RACE was performed and validated that csn-miR398a-3p-1 directly cleaves CsCSD4. By prediction of cis-acting elements, the expression patterns of 10 CsSOD genes and their regulatory miRNAs were detected under cold, drought, exogenous methyl jasmonate (MeJA) and gibberellin (GA3) treatments. The results showed that most of CsSODs except for CsFSD2 were induced under cold stress and CsCSDs may play primary roles under drought stress; exogenous GA3 and MeJA could also stimulated/inhibited distinct CsSODs at different stages. In addition, we found that csn-miR398a-3p-1 negatively regulated the expression of CsCSD4 may be a crucial regulatory mechanism under cold stress. This study provides a certain basis for the studies about stress resistance in tea plants, even provide insight into comprehending the classification, evolution, diverse functions and influencing factors of expression patterns for CsSOD genes.
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Affiliation(s)
- Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Tea Science of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- * E-mail:
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36
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Li YF, Wei K, Wang M, Wang L, Cui J, Zhang D, Guo J, Zhao M, Zheng Y. Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field. Front Genet 2019; 10:779. [PMID: 31552091 PMCID: PMC6737308 DOI: 10.3389/fgene.2019.00779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022] Open
Abstract
Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5'RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.
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Affiliation(s)
- Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Kangning Wei
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junxia Cui
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Daijing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Junqiang Guo
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
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37
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Li Y, Cao X, Zhu Y, Yang X, Zhang K, Xiao Z, Wang H, Zhao J, Zhang L, Li G, Zheng Y, Fan J, Wang J, Chen X, Wu X, Zhao J, Dong OX, Chen X, Chern M, Wang W. Osa-miR398b boosts H 2 O 2 production and rice blast disease-resistance via multiple superoxide dismutases. THE NEW PHYTOLOGIST 2019; 222:1507-1522. [PMID: 30632163 PMCID: PMC6593823 DOI: 10.1111/nph.15678] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/03/2019] [Indexed: 05/18/2023]
Abstract
miRNAs contribute to plant resistance against pathogens. Previously, we found that the function of miR398b in immunity in rice differs from that in Arabidopsis. However, the underlying mechanisms are unclear. In this study, we characterized the mutants of miR398b target genes and demonstrated that multiple superoxide dismutase genes contribute to miR398b-regulated rice immunity against the blast fungus Magnaporthe oryzae. Out of the four target genes of miR398b, mutations in Cu/Zn-Superoxidase Dismutase1 (CSD1), CSD2 and Os11g09780 (Superoxide DismutaseX, SODX) led to enhanced resistance to M. oryzae and increased hydrogen peroxide (H2 O2 ) accumulation. By contrast, mutations in Copper Chaperone for Superoxide Dismutase (CCSD) resulted in enhanced susceptibility. Biochemical studies revealed that csd1, csd2 and sodx displayed altered expression of CSDs and other superoxide dismutase (SOD) family members, leading to increased total SOD enzyme activity that positively contributed to higher H2 O2 production. By contrast, the ccsd mutant showed CSD protein deletion, resulting in decreased CSD and total SOD enzyme activity. Our results demonstrate the roles of different SODs in miR398b-regulated resistance to rice blast disease, and uncover an integrative regulatory network in which miR398b boosts total SOD activity to upregulate H2 O2 concentration and thereby improve disease resistance.
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Affiliation(s)
- Yan Li
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Xiao‐Long Cao
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Yong Zhu
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Xue‐Mei Yang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Kai‐Ni Zhang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Zhi‐Yuan Xiao
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - He Wang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Jing‐Hao Zhao
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Ling‐Li Zhang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Guo‐Bang Li
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Ya‐Ping Zheng
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Jing Fan
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Jing Wang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Xiao‐Qiong Chen
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Xian‐Jun Wu
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River BasinSichuan Agricultural UniversityChengdu611131China
| | - Ji‐Qun Zhao
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
| | - Oliver Xiaoou Dong
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Xue‐Wei Chen
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River BasinSichuan Agricultural UniversityChengdu611131China
| | - Mawsheng Chern
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Wen‐Ming Wang
- Rice Research Institute and Key Lab for Major Crop DiseasesSichuan Agricultural UniversityChengdu611131China
- Collaborative Innovation Center for Hybrid Rice in Yangtze River BasinSichuan Agricultural UniversityChengdu611131China
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Alzahrani SM, Alaraidh IA, Khan MA, Migdadi HM, Alghamdi SS, Alsahli AA. Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. Genes (Basel) 2019; 10:E303. [PMID: 30999691 PMCID: PMC6523927 DOI: 10.3390/genes10040303] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/02/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Salt stress has detrimental effects on plant growth and development. MicroRNAs (miRNAs) are a class of noncoding RNAs that are involved in post-transcriptional gene expression regulation. In this study, small RNA sequencing was employed to identify the salt stress-responsive miRNAs of the salt-sensitive Hassawi-3 and the salt-tolerant ILB4347 genotypes of faba bean, growing under salt stress. A total of 527 miRNAs in Hassawi-3 plants, and 693 miRNAs in ILB4347 plants, were found to be differentially expressed. Additionally, 284 upregulated and 243 downregulated miRNAs in Hassawi-3, and 298 upregulated and 395 downregulated miRNAs in ILB4347 plants growing in control and stress conditions were recorded. Target prediction and annotation revealed that these miRNAs regulate specific salt-responsive genes, which primarily included genes encoding transcription factors and laccases, superoxide dismutase, plantacyanin, and F-box proteins. The salt-responsive miRNAs and their targets were functionally enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, which showed that the miRNAs were involved in salt stress-related biological pathways, including the ABC transporter pathway, MAPK signaling pathway, plant hormone signal transduction, and the phosphatidylinositol signaling system, among others, suggesting that the miRNAs play an important role in the salt stress tolerance of the ILB4347 genotype. These results offer a novel understanding of the regulatory role of miRNAs in the salt response of the salt-tolerant ILB4347 and the salt-sensitive Hassawi-3 faba bean genotypes.
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Affiliation(s)
- Saud M Alzahrani
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Ibrahim A Alaraidh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Muhammad A Khan
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
- Plant Biotechnology Department, National Agricultural Research Center, Baq'a 19381, Jordan.
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdluaziz A Alsahli
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
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Zhu H, Zhang Y, Tang R, Qu H, Duan X, Jiang Y. Banana sRNAome and degradome identify microRNAs functioning in differential responses to temperature stress. BMC Genomics 2019; 20:33. [PMID: 30630418 PMCID: PMC6329063 DOI: 10.1186/s12864-018-5395-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/18/2018] [Indexed: 12/31/2022] Open
Abstract
Background Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in various biological processes. Harvested banana fruit can exhibit distinct symptoms in response to different temperature stresses, but the underlying miRNA-mediated regulatory mechanisms remained unknown. Results Here, we profiled temperature-responsive miRNAs in banana, using deep sequencing and computational and molecular analyses. In total 113 known miRNAs and 26 novel banana-specific miRNAs were identified. Of these miRNAs, 42 miRNAs were expressed differentially under cold and heat stresses. Degradome sequencing identified 60 target genes regulated by known miRNAs and half of these targets were regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes were further validated via qRT-PCR. Our data showed that miR535 and miR156 families may derive from a common ancestor during evolution and jointly play a role in fine-tuning SPL gene expression in banana. We also identified the miRNA-triggered phased secondary siRNAs in banana and found miR393-TIR1/AFB phasiRNA production displaying cold stress-specific enrichment. Conclusions Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana. The characterized correlations between miRNAs and their response to temperature stress could serve as markers in the breeding programs or tools for improving temperature tolerance of banana. Electronic supplementary material The online version of this article (10.1186/s12864-018-5395-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hong Zhu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Yu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruifang Tang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongxia Qu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuewu Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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40
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Kuo YW, Lin JS, Li YC, Jhu MY, King YC, Jeng ST. MicroR408 regulates defense response upon wounding in sweet potato. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:469-483. [PMID: 30403812 PMCID: PMC6322576 DOI: 10.1093/jxb/ery381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/02/2018] [Indexed: 05/08/2023]
Abstract
MiRNAs play diverse roles in plant development and defense responses by binding to their mRNA targets based on sequence complementarity. Here, we investigated a wound-related miR408 and its target genes in sweet potato (Ipomoea batatas) by small RNA deep sequencing and transcriptome analysis. The expression patterns of miR408 and the miR408 precursor were significantly repressed by wounding and jasmonate (JA). In contrast, expression of the putative target genes IbKCS (3-ketoacyl-CoA synthase 4), IbPCL (plantacyanin), and IbGAUT (galacturonosyltransferase 7-like) of miR408 was increased following wounding, whereas only IbKCS was increased after JA treatment. Target cleavage site mapping and Agrobacterium-mediated transient assay demonstrated that IbKCS, IbPCL, and IbGAUT were the targets of miR408. The expression of miR408 target genes was repressed in transgenic sweet potatoes overexpressing miR408. These data indicated a relationship between miR408 and its target genes. Notably, miR408-overexpressing plants showed a semi-dwarf phenotype and attenuated resistance to insect feeding, while transgenic plants overexpressing IbKCS exhibited more insect resistance than plants overexpressing only the empty vector. Collectively, sweet potato reduces the abundance of miR408 upon wounding to elevate the expression of IbKCS, IbPCL, and IbGAUT. The expression of IbKCS enhances the defense system against herbivore wounding.
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Affiliation(s)
- Yun-Wei Kuo
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Chi Li
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Min-Yao Jhu
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chi King
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shih-Tong Jeng
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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Qiu Z, He Y, Zhang Y, Guo J, Wang L. Characterization of miRNAs and their target genes in He-Ne laser pretreated wheat seedlings exposed to drought stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 164:611-617. [PMID: 30153643 DOI: 10.1016/j.ecoenv.2018.08.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/19/2018] [Accepted: 08/21/2018] [Indexed: 05/07/2023]
Abstract
Drought stress is considered a critical environmental factor that negatively affects wheat growth and development, which causes considerable losses in wheat yields worldwide. More recently, numerous microRNAs (miRNAs) have been found to be involved in wheat responses to drought stresses. However, there is little information regarding the effects of He-Ne laser irradiation on the expression traits of miRNAs and their targets in wheat seedlings exposed to drought stress. In the current study, therefore, a combination of physiological and molecular approaches was used to assess the effect of He-Ne laser irradiation on the expression of miRNAs and their targets in wheat seedlings exposed to drought stress. Our results demonstrated that drought stress significantly reduced plant height, root length, shoot and root fresh weight, relative water content, the expression level and activity of superoxide dismutase (SOD), enhanced malondialdehyde (MDA) concentration in the wheat seedlings. However, He-Ne laser irradiation significantly enhanced the activities of SOD, ascorbate peroxidase (APX), peroxidase (POD) and relative water content, and reduced MDA concentration of seedlings by regulating gene expression for SOD, POD, APX. In addition, in comparison with drought stress alone, miR160, miR164 and miR398 transcripts were down-regulated, and expression levels of its targets auxin response factor (ARF22), NAC domain transcription factor and Cu/Zn superoxide dismutases (CSD) were up-regulated in He-Ne laser irradiated seedlings exposed to drought stress. These results suggested that He-Ne laser irradiation could possible protection of drought stress, at least partially, by increasing the transcript levels and activities of SOD, POD and APX, and decreasing the transcript levels of miR160, miR164 and miR398. To the best of our knowledge, this is the first study to present biochemical and molecular evidence supporting the effect of He-Ne laser irradiation on the alleviation of drought stress in wheat seedlings mediated by miRNA expression.
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Affiliation(s)
- Zongbo Qiu
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China.
| | - Yanyan He
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Yimeng Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Junli Guo
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Li Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
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Liu W, Cheng C, Chen F, Ni S, Lin Y, Lai Z. High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans). BMC PLANT BIOLOGY 2018; 18:308. [PMID: 30486778 PMCID: PMC6263057 DOI: 10.1186/s12870-018-1483-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/15/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas. RESULT Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana. CONCLUSIONS In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.
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Affiliation(s)
- Weihua Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Chongqing Normal University, Daxuecheng Middle Rd, Chongqing, Shapingba Qu China
| | - Chunzhen Cheng
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Fanglan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Shanshan Ni
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Shi F, Zhou X, Yao MM, Tan Z, Zhou Q, Zhang L, Ji SJ. miRNAs play important roles in aroma weakening during the shelf life of 'Nanguo' pear after cold storage. Food Res Int 2018; 116:942-952. [PMID: 30717027 DOI: 10.1016/j.foodres.2018.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/05/2018] [Accepted: 09/09/2018] [Indexed: 10/28/2022]
Abstract
Cold storage is commonly employed to delay senescence in 'Nanguo' pear after harvest. However, this technique also causes fruit aroma weakening. MicroRNAs are regulators of gene expression at the post-transcriptional level that play important roles in plant development and in eliciting responses to abiotic environmental stressors. In this study, the miRNA transcript profiles of the fruit on the first day (C0, LT0) move in and out of cold storage and the optimum tasting period (COTP, LTOTP) during shelf life at room temperature and after cold storage were analyzed, respectively. 314 known miRNAs were identified in 'Nanguo' pear; 176 and 135 miRNAs were significantly differentially expressed on the C0 vs. LT0 and on the COTP vs. LTOTP, respectively. After prediction the target genes of these differentially expressed miRNAs, 9 s-lipoxygenase (LOX2S), 13 s-lipoxygenase (LOX1_5), hydroperoxide lyase (HPL), and alcohol dehydrogenase (ADH1) were found differentially expressed, which were the key genes during aroma formation. The expression pattern of these target genes and the related miRNAs were identified by RT-PCR. mdm-miR172a-h, mdm-miR159a/b, mdm-miR160a-e, mdm-miR395a-i, mdm-miR399a/b/c, mdm/ppe-miR535a/b, and mdm-miR7120a/b may negatively regulate the target genes expression. These results indicate that miRNAs may play key roles in aroma weakening in cold storage 'Nanguo' pear and provide valuable information for studying the molecular mechanisms of miRNAs in the aroma weakening of fruit due to low temperature.
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Affiliation(s)
- Fei Shi
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China; College of Food Science and Engineering, Shanxi Agricultural University, Taigu, Shanxi 030801, PR China
| | - Xin Zhou
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Miao-Miao Yao
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Zhuo Tan
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Qian Zhou
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Lei Zhang
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Shu-Juan Ji
- Department of Food Science, Shenyang Agricultural University, Shenyang 110866, PR China.
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Liu Z, Wang X, Chen X, Shi G, Bai Q, Xiao K. TaMIR1139: a wheat miRNA responsive to Pi-starvation, acts a critical mediator in modulating plant tolerance to Pi deprivation. PLANT CELL REPORTS 2018; 37:1293-1309. [PMID: 29947952 DOI: 10.1007/s00299-018-2313-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/06/2018] [Indexed: 05/18/2023]
Abstract
Wheat miRNA member TaMIR1139 targets genes functional in various families and plays crucial roles in regulating plant Pi starvation tolerance. Through regulating target genes at posttranscriptional or translational level, plant miRNAs are involved in mediating diverse biological processes associated with growth, development, and responses to adverse stresses. In this study, we characterized the expression pattern and function of TaMIR1139, a miRNA member of wheat (T. aestivum) under Pi deprivation. TaMIR1139 precursor is also present in N. tabucum, suggesting the conserved nature of miR1139 across monocots and eudicots. TaMIR1139 targets seven genes within different families. The transcripts abundance of TaMIR1139 was induced upon Pi deprivation and the upregulated expression under Pi starvation was downregulated by the Pi recovery treatment, In contrast, the genes targeted by TaMIR1139 exhibited reduced transcripts upon Pi starvation and their downregulated expression was recovered by Pi-recovery condition, suggesting the regulation of them under TaMIR1139 through a cleavage mechanism. TaMIR1139 overexpression conferred the Pi-deprived plants improved phenotype, biomass, photosynthesis, and Pi acquisition. Transcriptome analysis identified numerous genes involving biological process, cellular components, and molecular function were differentially expressed in the TaMIR1139 overexpression lines, which suggests the TaMIR1139-mediated plant Pi starvation tolerance to be associated with the role of miRNA in extensively modulating the transcript profiling. A phosphate transporter (PT) gene NtPT showed significantly upregulated expression in TaMIR1139 overexpression lines; overexpression of it conferred plants improved Pi acquisition upon Pi starvation, suggesting its contribution to the TaMIR1139-mediated plant low-Pi stress resistance. Our investigation indicates that TaMIR1139 is critical in plant Pi starvation tolerance through transcriptionally regulating the target genes and modulating the Pi stress-defensiveness processes.
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Affiliation(s)
- Zhipeng Liu
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China
| | - Xiaoying Wang
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China
| | - Xi Chen
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China
| | - Guiqing Shi
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China
| | - Qianqian Bai
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China
| | - Kai Xiao
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, People's Republic of China.
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, 071001, People's Republic of China.
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Kaleem F, Shabir G, Aslam K, Rasul S, Manzoor H, Shah SM, Khan AR. An Overview of the Genetics of Plant Response to Salt Stress: Present Status and the Way Forward. Appl Biochem Biotechnol 2018; 186:306-334. [PMID: 29611134 DOI: 10.1007/s12010-018-2738-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 03/15/2018] [Indexed: 01/24/2023]
Abstract
Salinity is one of the major threats faced by the modern agriculture today. It causes multidimensional effects on plants. These effects depend upon the plant growth stage, intensity, and duration of the stress. All these lead to stunted growth and reduced yield, ultimately inducing economic loss to the farming community in particular and to the country in general. The soil conditions of agricultural land are deteriorating at an alarming rate. Plants assess the stress conditions, transmit the specific stress signals, and then initiate the response against that stress. A more complete understanding of plant response mechanisms and their practical incorporation in crop improvement is an essential step towards achieving the goal of sustainable agricultural development. Literature survey shows that investigations of plant stresses response mechanism are the focus area of research for plant scientists. Although these efforts lead to reveal different plant response mechanisms against salt stress, yet many questions still need to be answered to get a clear picture of plant strategy to cope with salt stress. Moreover, these studies have indicated the presence of a complicated network of different integrated pathways. In order to work in a progressive way, a review of current knowledge is critical. Therefore, this review aims to provide an overview of our understanding of plant response to salt stress and to indicate some important yet unexplored dynamics to improve our knowledge that could ultimately lead towards crop improvement.
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Affiliation(s)
- Fawad Kaleem
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Sumaira Rasul
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Hamid Manzoor
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Shahid Masood Shah
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Abdul Rehman Khan
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan.
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Megha S, Basu U, Kav NNV. Regulation of low temperature stress in plants by microRNAs. PLANT, CELL & ENVIRONMENT 2018; 41:1-15. [PMID: 28346818 DOI: 10.1111/pce.12956] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 05/22/2023]
Abstract
Low temperature is one of the most common environmental stresses that seriously affect the growth and development of plants. However, plants have the plasticity in their defence mechanisms enabling them to tolerate and, sometimes, even survive adverse environmental conditions. MicroRNAs (miRNAs) are small non-coding RNAs, approximately 18-24 nucleotides in length, and are being increasingly recognized as regulators of gene expression at the post-transcriptional level and have the ability to influence a broad range of biological processes. There is growing evidence in the literature that reprogramming of gene expression mediated through miRNAs is a major defence mechanism in plants enabling them to respond to stresses. To date, numerous studies have established the importance of miRNA-based regulation of gene expression under low temperature stress. Individual miRNAs can modulate the expression of multiple mRNA targets, and, therefore, the manipulation of a single miRNA has the potential to affect multiple biological processes. Numerous functional studies have attempted to identify the miRNA-target interactions and have elaborated the role of several miRNAs in cold-stress regulation. This review summarizes the current understanding of miRNA-mediated modulation of the expression of key genes as well as genetic and regulatory pathways, involved in low temperature stress responses in plants.
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Affiliation(s)
- Swati Megha
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
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Bai Q, Wang X, Chen X, Shi G, Liu Z, Guo C, Xiao K. Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes. FRONTIERS IN PLANT SCIENCE 2018; 9:499. [PMID: 29720988 PMCID: PMC5916090 DOI: 10.3389/fpls.2018.00499] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/03/2018] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNA) families act as critical regulators for plant growth, development, and responses to abiotic stresses. In this study, we characterized TaemiR408, a miRNA family member of wheat (Triticum aestivum), for the role in mediating plant responses to Pi starvation and salt stress. TaemiR408 targets six genes that encode proteins involving biochemical metabolism, microtubule organization, and signaling transduction. 5'- and 3'-RACE analyses confirmed the mRNA cleavage of target genes mediated by this wheat miRNA. TaemiR408 showed induced expression patterns upon Pi starvation and salt stress and whose upregulated expression was gradually repressed by the normal recovery treatments. The target genes of TaemiR408 exhibited reverse expression patterns to this miRNA, whose transcripts were downregulated under Pi starvation and salt stress and the reduced expression was recovered by the followed normal condition. These results suggest the regulation of the target genes under TaemiR408 through a cleavage mechanism. Tobacco lines with TaemiR408 overexpression exhibited enhanced stress tolerance, showing improved phenotype, biomass, and photosynthesis behavior compared with wild type under both Pi starvation and salt treatments, which closely associate increased P accumulation upon Pi deprivation and elevated osmolytes under salt stress, respectively. Phosphate transporter (PT) gene NtPT2 displays upregulated transcripts in the Pi-deprived TaemiR408 overexpressors; knockdown of this PT gene reduces Pi acquisition under low-Pi stress, confirming its role in improving plant Pi taken up. Likewise, NtPYL2 and NtSAPK3, genes encoding abscisic acid (ABA) receptor and SnRK2 protein, respectively, exhibited upregulated transcripts in salt-challenged TaemiR408 overexpressors; knockdown of them caused deteriorated growth and lowered osmolytes amounts of plants upon salt treatment. Thus, TaemiR408 is crucial for plant adaptations to Pi starvation and salt stress through regulating Pi acquisition under low-Pi stress and remodel ABA signaling pathway and osmoprotects biosynthesis under salt stress.
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Affiliation(s)
| | | | | | | | | | | | - Kai Xiao
- *Correspondence: Chengjin Guo, Kai Xiao,
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Wang B, Song N, Zhang Q, Wang N, Kang Z. TaMAPK4 Acts as a Positive Regulator in Defense of Wheat Stripe-Rust Infection. FRONTIERS IN PLANT SCIENCE 2018; 9:152. [PMID: 29527215 PMCID: PMC5829626 DOI: 10.3389/fpls.2018.00152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Highly conserved mitogen-activated protein kinase (MAPK) cascades regulate numerous plant processes, including hormonal responses, stress, and innate immunity. In this research, TaMAPK4 was predicted to be a target of tae-miR164. We verified the binding and suppression of TaMAPK4 by co-expression in Nicotiana benthamiana. Moreover, we found TaMAPK4 was localized in the cytoplasm and nucleus using transient expression analyses. TaMAPK4 transcripts increased following salicylic acid (SA) treatment and when host plants were infected with an avirulent race of the stripe-rust pathogen. Silencing of TaMAPK4 by virus-induced gene silencing permitted increased colonization by the avirulent pathogen race. Detailed histological results showed increased Puccinia striiformis (Pst) hyphal length, hyphal branches, and infection uredinial size compared to the non-silenced control. SA accumulation and the transcript levels of TaPR1, TaPR2, and TaPR5 were significantly down-regulated in TaMAPK4 knockdown plants. Overall, these results suggest that TaMAPK4 plays an important role in signaling during the wheat-Pst interaction. These results present new insights into MAPK signaling in wheat defense to rust pathogen.
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Affiliation(s)
- Bing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China
| | - Na Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qiong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ning Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
- *Correspondence: Zhensheng Kang,
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