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Hussain SS, Ali A, Abbas M, Sun Y, Li Y, Li Q, Ragauskas AJ. Harnessing miRNA156: A molecular Toolkit for reshaping plant development and achieving ideal architecture. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109071. [PMID: 39186849 DOI: 10.1016/j.plaphy.2024.109071] [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: 05/22/2024] [Revised: 08/07/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
Achieving ideal plant architecture is of utmost importance for plant improvement to meet the demands of ever-increasing population. The wish list of ideal plant architecture traits varies with respect to its utilization and environmental conditions. Late seed development in woody plants poses difficulties for their propagation, and an increase in regeneration capacity can overcome this problem. The transition of a plant through sequential developmental stages e.g., embryonic, juvenile, and maturity is a well-orchestrated molecular and physiological process. The manipulation in the timing of phase transition to achieve ideal plant traits and regulation of metabolic partitioning will unlock new plant potential. Previous studies demonstrate that micro RNA156 (miR156) impairs the expression of its downstream genes to resist the juvenile-adult-reproductive phase transition to prolonged juvenility. The phenomenon behind prolonged juvenility is the maintenance of stem cell integrity and regeneration is an outcome of re-establishment of the stem cell niche. The previously reported vital and diverse functions of miR156 make it a more important case of study to explore its functions and possible ways to use it in molecular breeding. In this review, we proposed how genetic manipulation of miR156 can be used to reshape plant development phase transition and achieve ideal plant architecture. We have summarized recent studies on miR156 to describe its functional pattern and networking with up and down-stream molecular factors at each stage of the plant developmental life cycle. In addition, we have highlighted unaddressed questions, provided insights and devised molecular pathways that will help researchers to design their future studies.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China; Department of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China.
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Manzar Abbas
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animals, Hohhot, China
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
| | - Quanzi Li
- Department of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China.
| | - Arthur J Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA; Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Nowak K, Wójcik AM, Konopka K, Jarosz A, Dombert K, Gaj MD. miR156-SPL and miR169-NF-YA Modules Regulate the Induction of Somatic Embryogenesis in Arabidopsis via LEC- and Auxin-Related Pathways. Int J Mol Sci 2024; 25:9217. [PMID: 39273166 PMCID: PMC11394981 DOI: 10.3390/ijms25179217] [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: 06/30/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The embryogenic transition of plant somatic cells to produce somatic embryos requires extensive reprogramming of the cell transcriptome. The prominent role of transcription factors (TFs) and miRNAs in controlling somatic embryogenesis (SE) induction in plants was documented. The profiling of MIRNA expression in the embryogenic culture of Arabidopsis implied the contribution of the miR156 and miR169 to the embryogenic induction. In the present study, the function of miR156 and miR169 and the candidate targets, SPL and NF-YA genes, were investigated in Arabidopsis SE. The results showed that misexpression of MIRNA156 and candidate SPL target genes (SPL2, 3, 4, 5, 9, 10, 11, 13, 15) negatively affected the embryogenic potential of transgenic explants, suggesting that specific fine-tuning of the miR156 and target genes expression levels seems essential for efficient SE induction. The results revealed that SPL11 under the control of miR156 might contribute to SE induction by regulating the master regulators of SE, the LEC (LEAFY COTYLEDON) genes (LEC1, LEC2, FUS3). Moreover, the role of miR169 and its candidate NF-YA targets in SE induction was demonstrated. The results showed that several miR169 targets, including NF-YA1, 3, 5, 8, and 10, positively regulated SE. We found, that miR169 via NF-YA5 seems to modulate the expression of a master SE regulator LEC1/NF-YA and other auxin-related genes: YUCCA (YUC4, 10) and PIN1 in SE induction. The study provided new insights into miR156-SPL and miR169-NF-YA functions in the auxin-related and LEC-controlled regulatory network of SE.
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Affiliation(s)
- Katarzyna Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
| | - Anna M Wójcik
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
| | - Katarzyna Konopka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
| | - Alicja Jarosz
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
| | - Katarzyna Dombert
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
| | - Małgorzata D Gaj
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, 40-007 Katowice, Poland
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3
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Wang H, Zhu S, Yang C, Zeng D, Luo C, Dai C, Cheng D, Lv X. Expression and Functional Identification of SPL6/7/9 Genes under Drought Stress in Sugarbeet Seedlings. Int J Mol Sci 2024; 25:8989. [PMID: 39201675 PMCID: PMC11354545 DOI: 10.3390/ijms25168989] [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: 07/04/2024] [Revised: 08/10/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Sugar beet is a significant sugar crop in China, primarily cultivated in arid regions of the north. However, drought often affects sugar beet cultivation, leading to reduced yield and quality. Therefore, understanding the impact of drought on sugar beets and studying their drought tolerance is crucial. Previous research has examined the role of SPL (SQUAMOSA promoter-binding protein-like) transcription factors in plant stress response; however, the precise contribution of SPLs to the drought stress response in sugar beets has yet to be elucidated. In this study, we identified and examined the BvSPL6, BvSPL7, and BvSPL9 genes in sugar beets, investigating their performance during the seedling stage under drought stress. We explored their drought resistance characteristics using bioinformatics, quantitative analysis, physiological experiments, and molecular biology experiments. Drought stress and rehydration treatments were applied to sugar beet seedlings, and the expression levels of BvSPL6, BvSPL7, and BvSPL9 genes in leaves were quantitatively analyzed at 11 different time points to evaluate sugar beets' response and tolerance to drought stress. Results indicated that the expression level of the BvSPL6/9 genes in leaves was upregulated during the mid-stage of drought stress and downregulated during the early and late stages. Additionally, the expression level of the BvSPL7 gene gradually increased with the duration of drought stress. Through analyzing changes in physiological indicators during different time periods of drought stress and rehydration treatment, we speculated that the regulation of BvSPL6/7/9 genes is associated with sugar beet drought resistance and their participation in drought stress response. Furthermore, we cloned the CDS sequences of BvSPL6, BvSPL7, and BvSPL9 genes from sugar beets and conducted sequence alignment with the database to validate the results. Subsequently, we constructed overexpression vectors, named 35S::BvSPL6, 35S::BvSPL7, and 35S::BvSPL9, and introduced them into sugar beets using Agrobacterium-mediated methods. Real-time fluorescence quantitative analysis revealed that the expression levels of BvSPL6/7/9 genes in transgenic sugar beets increased by 40% to 80%. The drought resistance of transgenic sugar beets was significantly enhanced compared with the control group.
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Affiliation(s)
- Hui Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (H.W.); (S.Z.); (C.L.)
| | - Shengyi Zhu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (H.W.); (S.Z.); (C.L.)
| | - Chao Yang
- School of Astronautics, Harbin Institute of Technology, Harbin 150001, China;
| | - Deyong Zeng
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China;
| | - Chengfei Luo
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (H.W.); (S.Z.); (C.L.)
| | - Cuihong Dai
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China;
| | - Dayou Cheng
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China; (H.W.); (S.Z.); (C.L.)
| | - Xiaohong Lv
- Heilongjiang Academy of Forestry, Harbin 150001, China;
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Nazari M, Kordrostami M, Ghasemi-Soloklui AA, Eaton-Rye JJ, Pashkovskiy P, Kuznetsov V, Allakhverdiev SI. Enhancing Photosynthesis and Plant Productivity through Genetic Modification. Cells 2024; 13:1319. [PMID: 39195209 DOI: 10.3390/cells13161319] [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: 06/19/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024] Open
Abstract
Enhancing crop photosynthesis through genetic engineering technologies offers numerous opportunities to increase plant productivity. Key approaches include optimizing light utilization, increasing cytochrome b6f complex levels, and improving carbon fixation. Modifications to Rubisco and the photosynthetic electron transport chain are central to these strategies. Introducing alternative photorespiratory pathways and enhancing carbonic anhydrase activity can further increase the internal CO2 concentration, thereby improving photosynthetic efficiency. The efficient translocation of photosynthetically produced sugars, which are managed by sucrose transporters, is also critical for plant growth. Additionally, incorporating genes from C4 plants, such as phosphoenolpyruvate carboxylase and NADP-malic enzymes, enhances the CO2 concentration around Rubisco, reducing photorespiration. Targeting microRNAs and transcription factors is vital for increasing photosynthesis and plant productivity, especially under stress conditions. This review highlights potential biological targets, the genetic modifications of which are aimed at improving photosynthesis and increasing plant productivity, thereby determining key areas for future research and development.
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Affiliation(s)
- Mansoureh Nazari
- Department of Horticultural Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 91779-48974, Iran
| | - Mojtaba Kordrostami
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj 31485-498, Iran
| | - Ali Akbar Ghasemi-Soloklui
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj 31485-498, Iran
| | - Julian J Eaton-Rye
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Pavel Pashkovskiy
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya St. 35, Moscow 127276, Russia
| | - Vladimir Kuznetsov
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya St. 35, Moscow 127276, Russia
| | - Suleyman I Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya St. 35, Moscow 127276, Russia
- Faculty of Engineering and Natural Sciences, Bahcesehir University, 34349 Istanbul, Turkey
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Zhang HX, Zhang Y, Zhang BW. Pepper SBP-box transcription factor, CaSBP13, plays a negatively role in drought response. FRONTIERS IN PLANT SCIENCE 2024; 15:1412685. [PMID: 39070917 PMCID: PMC11272568 DOI: 10.3389/fpls.2024.1412685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
The SBP-box gene significantly influences plant growth, development, and stress responses, yet its function in pepper plants during drought stress remains unexplored. Using virus-induced gene silencing and overexpression strategies, we examined the role of CaSBP13 during drought stress in plants. The results revealed that the expression of CaSBP13 can be induced by drought stress. Silencing of CaSBP13 in pepper notably boosted drought resistance, as evident by decreased active oxygen levels. Furthermore, the water loss rate, relative electrical conductivity, malondialdehyde content, and stomatal density were reduced in CaSBP13-silenced plants compared to controls. In contrast, CaSBP13 overexpression in Nicotiana benthamiana decreased drought tolerance with elevated reactive oxygen levels and stomatal density. Additionally, ABA signaling pathway genes (CaPP2C, CaAREB) exhibited reduced expression levels in CaSBP13-silenced plants post drought stress, as compared to control plants. On the contrary, CaPYL9 and CaSNRK2.4 showed heightened expression in CaSBP13-sienced plants under the same conditions. However, a converse trend for NbAREB, NbSNRK2.4, and NbPYL9 was observed post-four day drought in CaSBP13-overexpression plants. These findings suggest that CaSBP13 negatively regulates drought tolerance in pepper, potentially via ROS and ABA signaling pathways.
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Affiliation(s)
- Huai-Xia Zhang
- College of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
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Fan H, Wang X, Zhong H, Quan K, Yu R, Ma S, Song S, Lin M. Integrated analysis of miRNAs, transcriptome and phytohormones in the flowering time regulatory network of tea oil camellia. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:945-956. [PMID: 38974357 PMCID: PMC11222345 DOI: 10.1007/s12298-024-01473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
Camellia oleifera is a crucial cash crop in the southern region of China. Timely flowering is a crucial characteristic for maximizing crop productivity. Nevertheless, the cold temperature and wet weather throughout the fall and winter seasons in South China impact the timing of flowering and the yield produced by C. oleifera. This study examined the miRNAs, transcriptomes, and phytohormones that are part of the flowering time regulatory networks in distinct varieties of C. oleifera (Sep, Oct, and Nov). This study provides evidence that phytohormones significantly impact the timing of flowering in C. oleifera leaves. There is a positive correlation between the accumulation variations of zeatin (cZ), brassinolide (BL), salicylic acid (SA), 1-amino cyclopropane carboxylic acid (ACC), and jasmonic acid (JA) and flowering time. This means that blooming occurs earlier when the quantity of these substances in leaves increases. Abscisic acid (ABA), trans-zeatin-riboside (tZR), dihydrozeatin (dh-Z), and IP (N6-Isopentenyladenine) exhibit contrasting effects. Furthermore, both miR156 and miR172 play a crucial function in regulating flowering time in C. oleifera leaves by modulating the expression of SOC1, primarily through the miR156-SPL and miR172-AP2 pathways. These findings establish a strong basis for future research endeavors focused on examining the molecular network associated with the flowering period of C. oleifera and controlling flowering time management through external treatments. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01473-2.
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Affiliation(s)
- Haixiao Fan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Xiaoling Wang
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Huiqi Zhong
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Kehui Quan
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Ruohan Yu
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Shiying Ma
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Siqiong Song
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
| | - Mengfei Lin
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi China
- Jiangxi Kiwifruit Engineering Research Center, Nanchang, Jiangxi China
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Božić M, Ignjatović Micić D, Delić N, Nikolić A. Maize miRNAs and their putative target genes involved in chilling stress response in 5-day old seedlings. BMC Genomics 2024; 25:479. [PMID: 38750515 PMCID: PMC11094857 DOI: 10.1186/s12864-024-10403-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND In the context of early sowing of maize as a promising adaptation strategy that could significantly reduce the negative effects of climate change, an in-depth understanding of mechanisms underlying plant response to low-temperature stress is demanded. Although microRNAs (miRNAs) have been recognized as key regulators of plant stress response, research on their role in chilling tolerance of maize during early seedling stages is scarce. Therefore, it is of great significance to explore chilling-responsive miRNAs, reveal their expression patterns and associated target genes, as well as to examine the possible functions of the conserved and novel miRNAs. In this study, the role of miRNAs was examined in 5d-old maize seedlings of one tolerant and one sensitive inbred line exposed to chilling (10/8 °C) stress for 6 h and 24 h, by applying high throughput sequencing. RESULTS A total of 145 annotated known miRNAs belonging to 30 families and 876 potentially novel miRNAs were identified. Differential expression (DE) analysis between control and stress conditions identified 98 common miRNAs for both genotypes at one time point and eight miRNAs at both time points. Target prediction and enrichment analysis showed that the DE zma-miR396, zma-miR156, zma-miR319, and zma-miR159 miRNAs modulate growth and development. Furthermore, it was found that several other DE miRNAs were involved in abiotic stress response: antioxidative mechanisms (zma-miR398), signal transduction (zma-miR156, zma-miR167, zma-miR169) and regulation of water content (zma-miR164, zma-miR394, zma-miR396). The results underline the zma-miRNAs involvement in the modulation of their target genes expression as an important aspect of the plant's survival strategy and acclimation to chilling stress conditions. CONCLUSIONS To our understanding, this is the first study on miRNAs in 5-d old seedlings' response to chilling stress, providing data on the role of known and novel miRNAs post-transcriptional regulation of expressed genes and contributing a possible platform for further network and functional analysis.
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Affiliation(s)
- Manja Božić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Dragana Ignjatović Micić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia.
| | - Nenad Delić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Laboratory for Molecular Genetics and Physiology, Research and Development Department, Maize Research Institute Zemun Polje, Belgrade, Serbia
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Sun X, Zhang L, Xu W, Zheng J, Yan M, Zhao M, Wang X, Yin Y. A Comprehensive Analysis of the Peanut SQUAMOSA Promoter Binding Protein-like Gene Family and How AhSPL5 Enhances Salt Tolerance in Transgenic Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1057. [PMID: 38674467 PMCID: PMC11055087 DOI: 10.3390/plants13081057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
SPL (SQUAMOSA promoter binding protein-like), as one family of plant transcription factors, plays an important function in plant growth and development and in response to environmental stresses. Despite SPL gene families having been identified in various plant species, the understanding of this gene family in peanuts remains insufficient. In this study, thirty-eight genes (AhSPL1-AhSPL38) were identified and classified into seven groups based on a phylogenetic analysis. In addition, a thorough analysis indicated that the AhSPL genes experienced segmental duplications. The analysis of the gene structure and protein motif patterns revealed similarities in the structure of exons and introns, as well as the organization of the motifs within the same group, thereby providing additional support to the conclusions drawn from the phylogenetic analysis. The analysis of the regulatory elements and RNA-seq data suggested that the AhSPL genes might be widely involved in peanut growth and development, as well as in response to environmental stresses. Furthermore, the expression of some AhSPL genes, including AhSPL5, AhSPL16, AhSPL25, and AhSPL36, were induced by drought and salt stresses. Notably, the expression of the AhSPL genes might potentially be regulated by regulatory factors with distinct functionalities, such as transcription factors ERF, WRKY, MYB, and Dof, and microRNAs, like ahy-miR156. Notably, the overexpression of AhSPL5 can enhance salt tolerance in transgenic Arabidopsis by enhancing its ROS-scavenging capability and positively regulating the expression of stress-responsive genes. These results provide insight into the evolutionary origin of plant SPL genes and how they enhance plant tolerance to salt stress.
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Affiliation(s)
| | | | | | | | | | | | - Xinyu Wang
- Yantai Academy of Agricultural Sciences, Yantai 265500, China; (X.S.); (L.Z.); (W.X.); (J.Z.); (M.Y.); (M.Z.)
| | - Yan Yin
- Yantai Academy of Agricultural Sciences, Yantai 265500, China; (X.S.); (L.Z.); (W.X.); (J.Z.); (M.Y.); (M.Z.)
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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Madhuvanthi CK, Muthulakshmi E, Ghosh Dasgupta M. Integrated mRNA and small RNA sequencing reveals post-transcriptional regulation of the sesquiterpene pathway in Santalum album L. (Indian sandalwood). 3 Biotech 2023; 13:387. [PMID: 37942052 PMCID: PMC10628100 DOI: 10.1007/s13205-023-03816-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/15/2023] [Indexed: 11/10/2023] Open
Abstract
Key message In sandalwood, negative pattern of regulation by miRNAs was documented in key genes from the sesquiterpene pathway, with cytochrome P450 reductase showing maximum miRNA targets, followed by sesquisabianene synthase 1. Abstract A comprehensive knowledge of the molecular regulation of sesquiterpene biosynthetic pathway through transcriptomic studies is well established in Santalum album (Indian Sandalwood). However, the post-transcriptional regulation of the genes regulating the pathway is still elusive in this genus. In the present study, an integrated analysis of wood transcriptome and small RNA datasets was conducted to investigate the role of miRNAs in regulating the expression of transcripts involved in santalol production mediated by the sesquiterpene biosynthesis pathway. A total of 24,237 transcripts were annotated from the wood transcriptome, and 45 transcripts were mapped to the sesquiterpenoid pathway. Small RNA data analysis identified 257 conserved miRNAs belonging to 50 families and 7 novel putative miRNAs. Sa-miR156, Sa-miR396, Sa-miR166, and Sa-miR319 had the most number of members among the miRNA families. An integrated analysis predicted 69 miRNA members belonging to 12 families that targeted 12 transcripts from the sesquiterpene pathway, with a maximum of 24 miRNAs regulating cytochrome P450 reductase, followed by sesquisabianene synthase 1, which was targeted by 23 miRNAs. Validation of miRNA-mRNA interaction by qRT-PCR revealed a negative pattern of regulation in six miRNA-mRNA target pairs across wood tissues sourced from four genotypes. The present study provides the first crucial insight into the post-transcriptional regulation of the sesquiterpene pathway genes in the genus Santalum and opens up a new perspective in metabolite engineering for enhanced essential oil production in sandalwood. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03816-4.
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Affiliation(s)
- Chandramouli K. Madhuvanthi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
| | - Eswaran Muthulakshmi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
| | - Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu 641002 India
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11
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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12
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Yuan J, Wang X, Qu S, Shen T, Li M, Zhu L. The roles of miR156 in abiotic and biotic stresses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108150. [PMID: 37922645 DOI: 10.1016/j.plaphy.2023.108150] [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: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.
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Affiliation(s)
- Jing Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengtao Qu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tian Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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13
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Pietrykowska H, Alisha A, Aggarwal B, Watanabe Y, Ohtani M, Jarmolowski A, Sierocka I, Szweykowska-Kulinska Z. Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development. PLANT MOLECULAR BIOLOGY 2023; 113:121-142. [PMID: 37991688 PMCID: PMC10721683 DOI: 10.1007/s11103-023-01392-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/19/2023] [Indexed: 11/23/2023]
Abstract
A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.
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Affiliation(s)
- Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Alisha Alisha
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192, Nara, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Chiba, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Kanagawa, Japan
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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14
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Jadhao KR, Kale SS, Chavan NS, Janjal PH. Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus). Cell Stress Chaperones 2023; 28:943-958. [PMID: 37938528 PMCID: PMC10746691 DOI: 10.1007/s12192-023-01388-z] [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: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.
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Affiliation(s)
- Kundansing R Jadhao
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Nilesh S Chavan
- Department of Microbiology and Environmental Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Pandharinath H Janjal
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India
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15
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Chen X, Chen H, Shen T, Luo Q, Xu M, Yang Z. The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress. Int J Mol Sci 2023; 24:14655. [PMID: 37834103 PMCID: PMC10572226 DOI: 10.3390/ijms241914655] [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: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Masson pine (Pinus massoniana Lamb.) is a major fast-growing woody tree species and pioneer species for afforestation in barren sites in southern China. However, the regulatory mechanism of gene expression in P. massoniana under drought remains unclear. To uncover candidate microRNAs, their expression profiles, and microRNA-mRNA interactions, small RNA-seq was used to investigate the transcriptome from seedling roots under drought and rewatering in P. massoniana. A total of 421 plant microRNAs were identified. Pairwise differential expression analysis between treatment and control groups unveiled 134, 156, and 96 differential expressed microRNAs at three stages. These constitute 248 unique microRNAs, which were subsequently categorized into six clusters based on their expression profiles. Degradome sequencing revealed that these 248 differentially expressed microRNAs targeted 2069 genes. Gene Ontology enrichment analysis suggested that these target genes were related to translational and posttranslational regulation, cell wall modification, and reactive oxygen species scavenging. miRNAs such as miR482, miR398, miR11571, miR396, miR166, miRN88, and miRN74, along with their target genes annotated as F-box/kelch-repeat protein, 60S ribosomal protein, copper-zinc superoxide dismutase, luminal-binding protein, S-adenosylmethionine synthase, and Early Responsive to Dehydration Stress may play critical roles in drought response. This study provides insights into microRNA responsive to drought and rewatering in Masson pine and advances the understanding of drought tolerance mechanisms in Pinus.
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Affiliation(s)
- Xinhua Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, 682 Guangshan Road 1, Guangzhou 510520, China;
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China;
- Engineering Research Center of Masson Pine of State Forestry Administration, Engineering Research Center of Masson Pine of Guangxi, Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China; (H.C.); (Q.L.)
| | - Hu Chen
- Engineering Research Center of Masson Pine of State Forestry Administration, Engineering Research Center of Masson Pine of Guangxi, Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China; (H.C.); (Q.L.)
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China;
| | - Qunfeng Luo
- Engineering Research Center of Masson Pine of State Forestry Administration, Engineering Research Center of Masson Pine of Guangxi, Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China; (H.C.); (Q.L.)
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China;
| | - Zhangqi Yang
- Engineering Research Center of Masson Pine of State Forestry Administration, Engineering Research Center of Masson Pine of Guangxi, Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning 530002, China; (H.C.); (Q.L.)
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16
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Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
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Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
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17
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Taylor RE, Waterworth W, West CE, Foyer CH. WHIRLY proteins maintain seed longevity by effects on seed oxygen signalling during imbibition. Biochem J 2023; 480:941-956. [PMID: 37351567 PMCID: PMC10422932 DOI: 10.1042/bcj20230008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 06/24/2023]
Abstract
The WHIRLY (WHY) family of DNA/RNA binding proteins fulfil multiple but poorly characterised functions in plants. We analysed WHY protein functions in the Arabidopsis Atwhy1, Atwhy3, Atwhy1why3 single and double mutants and wild type controls. The Atwhy3 and Atwhy1why3 double mutants showed a significant delay in flowering, having more siliques per plant but with fewer seeds per silique than the wild type. While germination was similar in the unaged high-quality seeds of all lines, significant decreases in vigour and viability were observed in the aged mutant seeds compared with the wild type. Imbibition of unaged high-quality seeds was characterised by large increases in transcripts that encode proteins involved in oxygen sensing and responses to hypoxia. Seed aging resulted in a disruption of the imbibition-induced transcriptome profile such that transcripts encoding RNA metabolism and processing became the most abundant components of the imbibition signature. The imbibition-related profile of the Atwhy1why3 mutant seeds, was characterised by decreased expression of hypoxia-related and oxygen metabolism genes even in the absence of aging. Seed aging further decreased the abundance of hypoxia-related and oxygen metabolism transcripts relative to the wild type. These findings suggest that the WHY1 and WHY3 proteins regulate the imbibition-induced responses to oxygen availability and hypoxia. Loss of WHY1 and WHY3 functions decreases the ability of Arabidopsis seeds to resist the adverse effects of seed aging.
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Affiliation(s)
- Rachel E. Taylor
- The Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Wanda Waterworth
- The Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Christopher E West
- The Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, U.K
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18
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Dabravolski SA, Isayenkov SV. The Role of Anthocyanins in Plant Tolerance to Drought and Salt Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2558. [PMID: 37447119 DOI: 10.3390/plants12132558] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Drought and salinity affect various biochemical and physiological processes in plants, inhibit plant growth, and significantly reduce productivity. The anthocyanin biosynthesis system represents one of the plant stress-tolerance mechanisms, activated by surplus reactive oxygen species. Anthocyanins act as ROS scavengers, protecting plants from oxidative damage and enhancing their sustainability. In this review, we focus on molecular and biochemical mechanisms underlying the role of anthocyanins in acquired tolerance to drought and salt stresses. Also, we discuss the role of abscisic acid and the abscisic-acid-miRNA156 regulatory node in the regulation of drought-induced anthocyanin production. Additionally, we summarise the available knowledge on transcription factors involved in anthocyanin biosynthesis and development of salt and drought tolerance. Finally, we discuss recent progress in the application of modern gene manipulation technologies in the development of anthocyanin-enriched plants with enhanced tolerance to drought and salt stresses.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, Karmiel 2161002, Israel
| | - Stanislav V Isayenkov
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, The National Academy of Sciences of Ukraine, Baidi-Vyshneveckogo Str., 2a, 04123 Kyiv, Ukraine
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19
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Quezada M, Giorello FM, Da Silva CC, Aguilar I, Balmelli G. Single-step genome-wide association study for susceptibility to Teratosphaeria nubilosa and precocity of vegetative phase change in Eucalyptus globulus. FRONTIERS IN PLANT SCIENCE 2023; 14:1124768. [PMID: 37465383 PMCID: PMC10350686 DOI: 10.3389/fpls.2023.1124768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/24/2023] [Indexed: 07/20/2023]
Abstract
Introduction Mycosphaerella leaf disease (MLD) is one of the most prevalent foliar diseases of Eucalyptus globulus plantations around the world. Since resistance management strategies have not been effective in commercial plantations, breeding to develop more resistant genotypes is the most promising strategy. Available genomic information can be used to detect genomic regions associated with resistance to MLD, which could significantly speed up the process of genetic improvement. Methods We investigated the genetic basis of MLD resistance in a breeding population of E. globulus which was genotyped with the EUChip60K SNP array. Resistance to MLD was evaluated through resistance of the juvenile foliage, as defoliation and leaf spot severity, and through precocity of change to resistant adult foliage. Genome-wide association studies (GWAS) were carried out applying four Single-SNP models, a Genomic Best Linear Unbiased Prediction (GBLUP-GWAS) approach, and a Single-step genome-wide association study (ssGWAS). Results The Single-SNP (model K) and GBLUP-GWAS models detected 13 and 16 SNP-trait associations in chromosomes 2, 3 y 11; whereas the ssGWAS detected 66 SNP-trait associations in the same chromosomes, and additional significant SNP-trait associations in chromosomes 5 to 9 for the precocity of phase change (proportion of adult foliage). For this trait, the two main regions in chromosomes 3 and 11 were identified for the three approaches. The SNPs identified in these regions were positioned near the key miRNA genes, miR156.5 and miR157.4, which have a main role in the regulation of the timing of vegetative change, and also in the response to environmental stresses in plants. Discussion Our results demonstrated that ssGWAS was more powerful in detecting regions that affect resistance than conventional GWAS approaches. Additionally, the results suggest a polygenic genetic architecture for the heteroblastic transition in E. globulus and identified useful SNP markers for the development of marker-assisted selection strategies for resistance to MLD.
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Affiliation(s)
- Marianella Quezada
- Programa Nacional de Investigación en Producción de Leche, Estación Experimental “Wilson Ferreira Adulnate”, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Facundo Matias Giorello
- PDU Espacio de Biología Vegetal del Noreste, sede Tacuarembó, CENUR Noreste, Universidad de la República, Tacuarembó, Uruguay
| | - Cecilia Corina Da Silva
- PDU Espacio de Biología Vegetal del Noreste, sede Tacuarembó, CENUR Noreste, Universidad de la República, Tacuarembó, Uruguay
| | - Ignacio Aguilar
- Programa Nacional de Investigación en Producción de Leche, Estación Experimental “Wilson Ferreira Adulnate”, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
| | - Gustavo Balmelli
- Programa Nacional de Investigación en Producción Forestal, Estación Experimental del Norte, Instituto Nacional de Investigación Agropecuaria, Tacuarembó, Uruguay
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20
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Niazi A, Iranbakhsh A, Esmaeel Zadeh M, Ebadi M, Oraghi Ardebili Z. Zinc oxide nanoparticles (ZnONPs) influenced seed development, grain quality, and remobilization by affecting the transcription of microRNA 171 (miR171), miR156, NAM, and SUT genes in wheat (Triticum aestivum): a biological advantage and risk assessment study. PROTOPLASMA 2023; 260:839-851. [PMID: 36318315 DOI: 10.1007/s00709-022-01817-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Limited studies have been conducted on the role of microRNAs (miRs) and transcription factors in regulating plant cell responses to nanoparticles. This study attempted to address whether the foliar application of zinc oxide nanoparticles (ZnONPs; 0, 10, 25, and 50 mgL-1) can affect miRs, gene expression, and wheat grain quality. The seedlings were sprayed with ZnONPs (0, 10, 25, and 50 mgL-1) or bulk counterpart (BZnO) five times at 72 h intervals. The application of ZnONPs at 10 mgL-1 increased the number of spikelets and seed weight, while the nano-supplement at 50 mgL-1 was accompanied by severe restriction on developing spikes and grains. ZnONPs, in a dose-dependent manner, transcriptionally influenced miR156 and miR171. The expression of miR171 showed a similar trend to that of miR156. The ZnONPs at optimum concentration upregulated the NAM transcription factor and sucrose transporter (SUT) at transcriptional levels. However, the transcription of both NAM and SUT genes displayed a downward trend in response to the toxic dose of ZnONPs (50 mgL-1). Utilization of ZnONPs increased proline and total soluble phenolic content. Monitoring the accumulation of carbohydrates, including fructan, glucose, fructose, and sucrose, revealed that ZnONPs at 10 mgL-1 modified the source/sink communication and nutrient remobilization. The molecular and physiological data revealed that the expression of miR156 and miR171 is tightly linked to seed grain development, remobilization of carbohydrates, and genes involved in nutrient transportation. This study establishes a novel strategy for obtaining higher yields in crops. This biological risk assessment investigation also displays the potential hazard of applying ZnONPs at the flowering developmental phase.
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Affiliation(s)
- Atefe Niazi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Mohsen Esmaeel Zadeh
- Seed and Plant Improvement Institute, Agricultural Research Education & Extension Organization, Karaj, Iran
| | - Mostafa Ebadi
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
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21
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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. FRONTIERS IN PLANT SCIENCE 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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22
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Islam W, Waheed A, Idrees A, Rashid J, Zeng F. Role of plant microRNAs and their corresponding pathways in fluctuating light conditions. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119304. [PMID: 35671849 DOI: 10.1016/j.bbamcr.2022.119304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/03/2023]
Abstract
In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Abdul Waheed
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Atif Idrees
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | | | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Lu Z, Yang Z, Tian Z, Gui Q, Dong R, Chen C. Genome-wide analysis and identification of microRNAs in Medicago truncatula under aluminum stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1137764. [PMID: 36778703 PMCID: PMC9911878 DOI: 10.3389/fpls.2023.1137764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Numerous studies have shown that plant microRNAs (miRNAs) play key roles in plant growth and development, as well as in response to biotic and abiotic stresses; however, the role of miRNA in legumes under aluminum (Al) stress have rarely been reported. Therefore, here, we aimed to investigate the role of miRNAs in and their mechanism of Al tolerance in legumes. To this end, we sequenced a 12-strand-specific library of Medicago truncatula under Al stress. A total of 195.80 M clean reads were obtained, and 876 miRNAs were identified, of which, 673 were known miRNAs and 203 were unknown. A total of 55 miRNAs and their corresponding 2,502 target genes were differentially expressed at various time points during Al stress. Further analysis revealed that mtr-miR156g-3p was the only miRNA that was significantly upregulated at all time points under Al stress and could directly regulate the expression of genes associated with root cell growth. Three miRNAs, novel_miR_135, novel_miR_182, and novel_miR_36, simultaneously regulated the expression of four Al-tolerant transcription factors, GRAS, MYB, WRKY, and bHLH, at an early stage of Al stress, indicating a response to Al stress. In addition, legume-specific miR2119 and miR5213 were involved in the tolerance mechanism to Al stress by regulating F-box proteins that have protective effects against stress. Our results contribute to an improved understanding of the role of miRNAs in Al stress in legumes and provide a basis for studying the molecular mechanisms of Al stress regulation.
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Affiliation(s)
- Zhongjie Lu
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
| | - Zhengyu Yang
- Department of Vehicle Engineering, Guizhou Technological College of Machinery and Electricity, Duyun, China
| | - Zheng Tian
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
| | - Qihui Gui
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
| | - Rui Dong
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
| | - Chao Chen
- Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China
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24
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Chen F, Zhang H, Li H, Lian L, Wei Y, Lin Y, Wang L, He W, Cai Q, Xie H, Zhang H, Zhang J. IPA1 improves drought tolerance by activating SNAC1 in rice. BMC PLANT BIOLOGY 2023; 23:55. [PMID: 36698063 PMCID: PMC9875436 DOI: 10.1186/s12870-023-04062-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/13/2023] [Indexed: 05/27/2023]
Abstract
Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H2O2, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H2O2 as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.
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Affiliation(s)
- Feihe Chen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Haomin Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Hong Li
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Ling Lian
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Yuelong Lin
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Lanning Wang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Wei He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China
| | - Hua Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350018, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops/Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China.
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25
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Lu G, Tian Z, Hao Y, Xu M, Lin Y, Wei J, Zhao Y. Overexpression of soybean microRNA156b enhanced tolerance to phosphorus deficiency and seed yield in Arabidopsis. Sci Rep 2023; 13:652. [PMID: 36635356 PMCID: PMC9837069 DOI: 10.1038/s41598-023-27847-2] [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: 11/01/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
microRNAs (miRNAs) are endogenous small RNAs that are key regulatory factors participating in various biological activities such as the signaling of phosphorus deficiency in the plant. Previous studies have shown that miR156 expression was modulated by phosphorus starvation in Arabidopsis and soybean. However, it is not clear whether the over-expression of soybean miR156b (GmmiR156b) can improve a plant's tolerance to phosphorus deficiency and affect yield component traits. In this study, we generated Arabidopsis transgenic lines overexpressing GmmiR156b and investigated the plant's response to phosphorus deficiency. Compared with the wild type, the transgenic Arabidopsis seedlings had longer primary roots and higher phosphorus contents in roots under phosphorus-deficit conditions, but lower fresh weight root/shoot ratios under either phosphorus-deficient or sufficient conditions. Moreover, the GmmiR156b overexpression transgenic lines had higher phosphorus content in shoots of adult plants and grew better than the wide type under phosphorus-deficient conditions, and exhibited increased seed yields as well as strong pleiotropic developmental morphology such as dwarfness, prolonged growth period, bushy shoot/branching, and shorter silique length, suggesting that the transgenic lines were more tolerant to phosphorus deficiency. In addition, the expression level of four SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes (i.e., AtSPL4/5/6/15) were markedly suppressed in transgenic plants, indicating that they were the main targets negatively regulated by GmmiR156b (especially AtSPL15) and that the enhanced tolerance to phosphorus deficiency and seed yield is conferred mainly by the miR156-mediated downregulation of AtSPL15.
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Affiliation(s)
- Guangyuan Lu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Zhitao Tian
- grid.35155.370000 0004 1790 4137College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430062 People’s Republic of China
| | - Yifan Hao
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Meihua Xu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongxin Lin
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Jinxing Wei
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, People's Republic of China.
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26
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Waheed S, Liang F, Zhang M, He D, Zeng L. High-Throughput Sequencing Reveals Novel microRNAs Involved in the Continuous Flowering Trait of Longan ( Dimocarpus longan Lour.). Int J Mol Sci 2022; 23:15565. [PMID: 36555206 PMCID: PMC9779457 DOI: 10.3390/ijms232415565] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
A major determinant of fruit production in longan (Dimocarpus longan Lour.) is the difficulty of blossoming. In this study, high-throughput microRNA sequencing (miRNA-Seq) was carried out to compare differentially expressed miRNAs (DEmiRNAs) and their target genes between a continuous flowering cultivar 'Sijimi' (SJ), and a unique cultivar 'Lidongben' (LD), which blossoms only once in the season. Over the course of our study, 1662 known miRNAs and 235 novel miRNAs were identified and 13,334 genes were predicted to be the target of 1868 miRNAs. One conserved miRNA and 29 new novel miRNAs were identified as differently expressed; among them, 16 were upregulated and 14 were downregulated. Through the KEGG pathway and cluster analysis of DEmiRNA target genes, three critical regulatory pathways, plant-pathogen interaction, plant hormone signal transduction, and photosynthesis-antenna protein, were discovered to be strongly associated with the continuous flowering trait of the SJ. The integrated correlation analysis of DEmiRNAs and their target mRNAs revealed fourteen important flowering-related genes, including COP1-like, Casein kinase II, and TCP20. These fourteen flowering-related genes were targeted by five miRNAs, which were novel-miR137, novel-miR76, novel-miR101, novel-miR37, and csi-miR3954, suggesting these miRNAs might play vital regulatory roles in flower regulation in longan. Furthermore, novel-miR137 was cloned based on small RNA sequencing data analysis. The pSAK277-miR137 transgenic Arabidopsis plants showed delayed flowering phenotypes. This study provides new insight into molecular regulation mechanisms of longan flowering.
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Affiliation(s)
| | | | | | | | - Lihui Zeng
- Institute of Genetics and Breeding in Horticultural Plants, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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27
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Nasrollahi V, Yuan ZC, Lu QSM, McDowell T, Kohalmi SE, Hannoufa A. Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa. PLANT MOLECULAR BIOLOGY 2022; 110:511-529. [PMID: 35976552 PMCID: PMC9684250 DOI: 10.1007/s11103-022-01303-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/17/2022] [Indexed: 05/11/2023]
Abstract
Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.
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Affiliation(s)
- Vida Nasrollahi
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Qing Shi Mimmie Lu
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Tim McDowell
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
- Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON, N6A 3K7, Canada.
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28
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Meng X, Zhang T, Chen C, Li Q, Liu J. Regulatory network of ginsenoside biosynthesis under Ro stress in the hairy roots of Panax ginseng revealed by RNA sequencing. Front Bioeng Biotechnol 2022; 10:1006386. [PMID: 36394021 PMCID: PMC9659575 DOI: 10.3389/fbioe.2022.1006386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
P. ginseng C.A. Meyer is a valuable Chinese herbal medicine that belongs to the Araliaceae family. Major obstacles to the continuous cropping of ginseng have severely restricted the sustainable development of the ginseng industry. The allelopathic effects of triterpenoid saponins play an important role in disorders related to continuous cropping; however, the mechanisms underlying the allelopathic autotoxicity of triterpenoid ginsenosides remain unknown. In this study, we performed mRNA and miRNA sequencing analyses to identify candidate genes and miRNAs that respond differentially to ginsenoside Ro stress in ginseng and their targets. The growth of the ginseng hairy roots was significantly inhibited under Ro stress (0.5 mg/L, Ro-0.5). The inhibition of root growth and injury to root-tip cells promoted the accumulation of the endogenous hormones indole-3-acetic acid and salicylic acid and inhibited the accumulation of abscisic acid and jasmonate acid. The accumulation of ginsenosides, except Rg3, was significantly inhibited under Ro-0.5 stress. An mRNA analysis of the Ro-0.5 and control groups showed that differentially expressed genes were mostly concentrated in the hormone signal transduction pathway. ARF7 and EFM were upregulated, whereas XTH23 and ZOX1 were downregulated. These genes represent important potential candidates for hormone-responsive continuous cropping diseases. In total, 74 differentially expressed miRNAs were identified based on the miRNA sequencing analysis, of which 22 were upregulated and 52 were downregulated. The target genes of ptc-miR156k_L + 1, mtr-miR156b-5p, gma-miR156a_R + 1, and mtr-miR156e all belonged to TRINITY_DN14567_c0_g4, which is a gene in the plant hormone signal transduction pathway. These four miRNAs were all negatively correlated with mRNA, indicating their likely involvement in the response of ginseng to continuous cropping disorders and the regulation of ginsenoside synthesis. Our findings provide useful insights for removing the barriers to continuous ginseng cropping and have important implications in the genetic engineering of plant stress responses.
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Affiliation(s)
| | - Tao Zhang
- *Correspondence: Tao Zhang, ; Changbao Chen,
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Li Z, Yang Y, Chen B, Xia B, Li H, Zhou Y, He M. Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense. PeerJ 2022; 10:e14241. [PMID: 36320567 PMCID: PMC9618261 DOI: 10.7717/peerj.14241] [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: 05/23/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana, rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs, which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense. In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.
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Affiliation(s)
- Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Chen
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hongyao Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Jilin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
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Deng F, Zeng F, Shen Q, Abbas A, Cheng J, Jiang W, Chen G, Shah AN, Holford P, Tanveer M, Zhang D, Chen ZH. Molecular evolution and functional modification of plant miRNAs with CRISPR. TRENDS IN PLANT SCIENCE 2022; 27:890-907. [PMID: 35165036 DOI: 10.1016/j.tplants.2022.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.
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Affiliation(s)
- Fenglin Deng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Fanrong Zeng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Qiufang Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Jianhui Cheng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Wei Jiang
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Pakistan
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7004, Australia.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food, and Wine, University of Adelaide, Glen Osmond, SA, Australia.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia.
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Zheng Z, Xu Z, Cai C, Liao Y, Yang C, Du X, Huang R, Deng Y. Circulating exosome miRNA, is it the novel nutrient molecule through cross-kingdom regulation mediated by food chain transmission from microalgae to bivalve? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 43:101004. [PMID: 35644102 DOI: 10.1016/j.cbd.2022.101004] [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: 12/01/2021] [Revised: 05/10/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. Plant-derived miRNAs are highly enriched in animal haemolymph and regulate mammalian gene expression. However, evidence for food-derived miRNAs in Mollusca species is lacking. In this study, we fed the microalga Nannochloropsis oculata to the pearl oyster Pinctada fucata martensii and detected dietary miRNAs in exosomes isolated from the haemolymph by RNA-seq. In total, 273 endogenous miRNAs were identified in all biological replicates. We identified 23 microalgae-derived miRNAs in the exosomes of pearl oyster haemolymph. Most microalgae-derived miRNAs showed high expression levels in both exosomes and microalgae and exhibited apparent variation among individuals. These food-derived miRNAs were predicted to participate in endocytosis, apoptosis, signal transduction, energy metabolism, and biomineralization by targeting multiple genes. These findings demonstrated the cross-kingdom transport of miRNAs from microalgae to bivalves and provide insights into novel nutrient transmission through the food chain.
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Affiliation(s)
- Zhe Zheng
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Zhijie Xu
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China
| | - Caixia Cai
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China
| | - Yongshan Liao
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China
| | - Chuangye Yang
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Xiaodong Du
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China
| | - Ronglian Huang
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
| | - Yuewen Deng
- Guangdong Ocean University, Fishery College, 524088 Zhanjiang, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China.
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Zhao H, Cao H, Zhang M, Deng S, Li T, Xing S. Genome-Wide Identification and Characterization of SPL Family Genes in Chenopodium quinoa. Genes (Basel) 2022; 13:genes13081455. [PMID: 36011366 PMCID: PMC9408038 DOI: 10.3390/genes13081455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a large family of plant-specific transcription factors that play important roles in plant growth, development, and stress responses. However, there is little information available on SPL genes in Chenopodiaceae. Here, 23 SPL genes were identified and characterized in the highly nutritious crop Chenopodium quinoa. Chromosome localization analysis indicated that the 23 CqSPL genes were unevenly distributed on 12 of 18 chromosomes. Two zinc finger-like structures and a nuclear location signal were present in the SBP domains of all CqSPLs, with the exception of CqSPL21/22. Phylogenetic analysis revealed that these genes were classified into eight groups (group I–VIII). The exon–intron structure and motif composition of the genes in each group were similar. Of the 23 CqSPLs, 13 were potential targets of miR156/7. In addition, 5 putative miR156-encoding loci and 13 putative miR157-encoding loci were predicted in the quinoa genome, and they were unevenly distributed on chromosome 1–4. The expression of several Cqu-MIR156/7 loci was confirmed by reverse transcription polymerase chain reaction in seedlings. Many putative cis-elements associated with light, stress, and phytohormone responses were identified in the promoter regions of CqSPLs, suggesting that CqSPL genes are likely involved in the regulation of key developmental processes and stress responses. Expression analysis revealed highly diverse expression patterns of CqSPLs among tissues. Many CqSPLs were highly expressed in leaves, flowers, and seeds, and their expression levels were low in the roots, suggesting that CqSPLs play distinct roles in the development and growth of quinoa. The expression of 13 of 23 CqSPL genes responded to salt treatment (11 up-regulated and 2 down-regulated). A total of 22 of 23 CqSPL genes responded to drought stress (21 up-regulated and 1 down-regulated). Moreover, the expression of 14 CqSPL genes was significantly altered following cadmium treatment (3 up-regulated and 11 down-regulated). CqSPL genes are thus involved in quinoa responses to salt/drought and cadmium stresses. These findings provide new insights that will aid future studies of the biological functions of CqSPLs in C. quinoa.
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Affiliation(s)
- Hongmei Zhao
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
| | - Huaqi Cao
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Mian Zhang
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Sufang Deng
- College of Biological Sciences and Technology, Jinzhong University, Jinzhong 030600, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Tingting Li
- College of Life Science, Shanxi University, Taiyuan 030006, Shanxi, China
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
| | - Shuping Xing
- Institute of Applied Biology, Shanxi University, Taiyuan 030006, Shanxi, China
- Correspondence: ; Tel.: +86-186-0346-2517
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice. J Genet Genomics 2022; 49:766-775. [PMID: 35803541 DOI: 10.1016/j.jgg.2022.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/20/2022] [Accepted: 06/30/2022] [Indexed: 11/22/2022]
Abstract
Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown to play critical roles in salt response in Arabidopsis. However, the roles of the MPK cascade signaling in rice salt response and substrates of OsMPK remain largely unknown. Here, we report that the salt-induced OsMPK4-Ideal Plant Architecture 1 (IPA1) signaling pathway regulates the salt tolerance in rice. Under salt stress, OsMPK4 could interact with IPA1 and phosphorylate IPA1 at Thr180, leading to degradation of IPA1. Genetic evidence shows that IPA1 is a negative regulator of salt tolerance in rice, whereas OsMPK4 promotes salt response in an IPA1-dependent manner. Taken together, our results uncover an OsMPK4-IPA1 signal cascade that modulates the salt stress response in rice and sheds new light on the breeding of salt-tolerant rice varieties.
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The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23126365. [PMID: 35742808 PMCID: PMC9223653 DOI: 10.3390/ijms23126365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.
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Sun J, Li GS. Identification of genes differentially expressed between prostrate shoots and erect shoots in the lycophyte Selaginella nipponica using an RNA-seq approach. AOB PLANTS 2022; 14:plac018. [PMID: 35694642 PMCID: PMC9179412 DOI: 10.1093/aobpla/plac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Lycophytes are the earliest vascular plants and Selaginella is the most studied genus among them. Prostrate shoots are produced during early growth and erect shoots emerge later in S. nipponica, thus providing an opportunity for exploring the evolution of the mechanism underlying the transition between growth phases. Six libraries were sequenced for the prostrate and the erect shoots, and a total of 206 768 genes were identified. Some genes were differentially expressed in prostate and erect shoot, with relatively high expression in the prostate shoots being related to hormone responses and defence reactions, while higher expression in the erect shoots was related to spore formation and shoot development. Some SPL genes possessed a miR156 binding site and were highly expressed in the erect shoots, while AP2-like genes were more highly expressed in the prostrate shoots but simultaneously lacked any miR172 binding site. MiR156 was detected at a higher concentration in the prostrate shoots. Thus, the mechanism for the vegetative to reproductive transition of sporophytes probably originated in the common ancestor of vascular plants and must have experienced stepwise development during evolution.
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Affiliation(s)
- Jun Sun
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou 416000, China
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An J, Liu Y, Han J, He C, Chen M, Zhu X, Hu W, Song W, Hu J, Guan Y. Transcriptional multiomics reveals the mechanism of seed deterioration in Nicotiana tabacum L. and Oryza sativa L. J Adv Res 2022; 42:163-176. [PMID: 36513411 PMCID: PMC9788960 DOI: 10.1016/j.jare.2022.03.009] [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: 01/20/2022] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Mature seeds deteriorate gradually and die eventually during long-term storage. Controlled deterioration is often used to accelerate the seed deterioration rate to assess the seed vigor and physiological quality of seed lots. OBJECTIVES Although it is well known that the process of seed deterioration produced by controlled deterioration is distinct from that caused by long-term storage, the differences in transcriptional levels have not been reported. Clarifying the mechanism of seed deterioration is critical for identifying, conserving and utilizing germplasm resources. METHODS Tobacco (Nicotiana tabacum L.) seeds were studied thoroughly using transcriptome, small RNA, and degradome sequencing after long-term storage (LS) and controlled deterioration (CD). Co-expression trend analysis identified transcripts involved in tobacco seed deterioration, while phylogenetic analysis helped to uncover comparable targets in rice (Oryza sativa L.) for further verification and utilization. RESULTS In LS and CD, a total of 2,112 genes and 164 miRNAs were differentially expressed, including 20 interaction miRNA-mRNA pairs with contrasting expression. Transcriptional multiomics found that the main causes of LS were plant hormone signal transduction and protein processing in the endoplasmic reticulum, whereas the primary cause of CD was nucleotide excision repair dysfunction. The homeostatic balance of RNA degradation and the spliceosome occurred in both modes of seed deterioration. Additionally, co-expression trend analysis identified two coherent pairs, nta-miR160b-NtARF18 and nta-miR396c-NtMBD10, as being significant in LS and CD, respectively. For utilization, rice homologous targets OsARF18 and OsMBD707 were verified to play similar roles in LS and CD, respectively. CONCLUSION This study demonstrated the transcriptional mechanism of tobacco and key genes in seed deterioration. And the application of key genes in rice also verified the feasibility of the multiomics method, guiding the identification of candidate genes to precisely delay seed deterioration in other species of seed research.
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Affiliation(s)
- Jianyu An
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Yihan Liu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jiajun Han
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Can He
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Min Chen
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Xiaobo Zhu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Weimin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Wenjian Song
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Jin Hu
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China
| | - Yajing Guan
- Seed Science Center, Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China,Hainan Research Institute, Zhejiang University, Sanya, Hainan Province 572000, China,Corresponding author.
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Salvi P, Agarrwal R, Gandass N, Manna M, Kaur H, Deshmukh R. Sugar transporters and their molecular tradeoffs during abiotic stress responses in plants. PHYSIOLOGIA PLANTARUM 2022; 174:e13652. [PMID: 35174495 DOI: 10.1111/ppl.13652] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/25/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Sugars as photosynthates are well known as energy providers and as building blocks of various structural components of plant cells, tissues and organs. Additionally, as a part of various sugar signaling pathways, they interact with other cellular machinery and influence many important cellular decisions in plants. Sugar signaling is further reliant on the differential distribution of sugars throughout the plant system. The distribution of sugars from source to sink tissues or within organelles of plant cells is a highly regulated process facilitated by various sugar transporters located in plasma membranes and organelle membranes, respectively. Sugar distribution, as well as signaling, is impacted during unfavorable environments such as extreme temperatures, salt, nutrient scarcity, or drought. Here, we have discussed the mechanism of sugar transport via various types of sugar transporters as well as their differential response during environmental stress exposure. The functional involvement of sugar transporters in plant's abiotic stress tolerance is also discussed. Besides, we have also highlighted the challenges in engineering sugar transporter proteins as well as the undeciphered modules associated with sugar transporters in plants. Thus, this review provides a comprehensive discussion on the role and regulation of sugar transporters during abiotic stresses and enables us to target the candidate sugar transporter(s) for crop improvement to develop climate-resilient crops.
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Affiliation(s)
- Prafull Salvi
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | | | - Nishu Gandass
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Mrinalini Manna
- National Institute of Plant Genome Research, New Delhi, India
| | - Harmeet Kaur
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Rupesh Deshmukh
- Department of Agriculture Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab, India
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Han H, Zhou Y. Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing. Int J Mol Sci 2022; 23:2544. [PMID: 35269685 PMCID: PMC8910752 DOI: 10.3390/ijms23052544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/17/2022] Open
Abstract
MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation of miR171 by developmental cues and environmental signals. Specifically, miR171 regulates shoot meristem activity and phase transition through repressing the HAIRYMERISTEM (HAM) family genes. In the model species Arabidopsis, miR171 serves as a short-range mobile signal, which initiates in the epidermal layer of shoot meristems and moves downwards within a limited distance, to pattern the apical-basal polarity of gene expression and drive stem cell dynamics. miR171 levels are regulated by light and various abiotic stresses, suggesting miR171 may serve as a linkage between environmental factors and cell fate decisions. Furthermore, miR171 family members also demonstrate both conserved and lineage-specific functions in land plants, which are summarized and discussed here.
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Affiliation(s)
- Han Han
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA;
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
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Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa. Genes (Basel) 2022; 13:genes13020331. [PMID: 35205375 PMCID: PMC8871590 DOI: 10.3390/genes13020331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022] Open
Abstract
Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which makes it a model species for studying compound leaf development. However, transcriptomic information from alfalfa remains limited. In this study, RNA-Seq technology was used to identify 3746 differentially expressed genes (DEGs) between multifoliate and trifoliate alfalfa. Through an analysis of annotation information and expression data, SPL, one of the key regulators in modifiable plant development and abiotic stress response, was further analyzed. Here, thirty MsSPL genes were obtained from the alfalfa genome, of which 16 had the putative miR156 binding site. A tissue expression pattern analysis showed that the miR156-targeted MsSPLs were divided into two classes, namely, either tissue-specific or widely expressed in all tissues. All miR156-targeted SPLs strongly showed diversification and positive roles under drought and salt conditions. Importantly, miR156/MsSPL08 was significantly suppressed in multifoliate alfalfa. Furthermore, in the paralogous mutant of MsSPL08 isolated from Medicago truncatula, the phenotypes of mutant plants reveal that miR156/MsSPL08 is involved not only involved the branches but also especially regulates the number of leaflets. The legume is a typical compound leaf plant; the ratio of the leaflet often affects the quality of the forage. This study sheds light on new functions of SPL genes that regulate leaflet number development.
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The Mulberry SPL Gene Family and the Response of MnSPL7 to Silkworm Herbivory through Activating the Transcription of MnTT2L2 in the Catechin Biosynthesis Pathway. Int J Mol Sci 2022; 23:ijms23031141. [PMID: 35163065 PMCID: PMC8835075 DOI: 10.3390/ijms23031141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, as unique plant transcription factors, play important roles in plant developmental regulation and stress response adaptation. Although mulberry is a commercially valuable tree species, there have been few systematic studies on SPL genes. In this work, we identified 15 full-length SPL genes in the mulberry genome, which were distributed on 4 Morus notabilis chromosomes. Phylogenetic analysis clustered the SPL genes from five plants (Malus × domestica Borkh, Populus trichocarpa, M. notabilis, Arabidopsis thaliana, and Oryza sativa) into five groups. Two zinc fingers (Zn1 and Zn2) were found in the conserved SBP domain in all of the MnSPLs. Comparative analyses of gene structures and conserved motifs revealed the conservation of MnSPLs within a group, whereas there were significant structure differences among groups. Gene quantitative analysis showed that the expression of MnSPLs had tissue specificity, and MnSPLs had much higher expression levels in older mulberry leaves. Furthermore, transcriptome data showed that the expression levels of MnSPL7 and MnSPL14 were significantly increased under silkworm herbivory. Molecular experiments revealed that MnSPL7 responded to herbivory treatment through promoting the transcription of MnTT2L2 and further upregulating the expression levels of catechin synthesis genes (F3′H, DFR, and LAR).
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Zhang N, Feng X, Zeng Q, Lin H, Wu Z, Gao X, Huang Y, Wu J, Qi Y. Integrated Analysis of miRNAs Associated With Sugarcane Responses to Low-Potassium Stress. FRONTIERS IN PLANT SCIENCE 2022; 12:750805. [PMID: 35058942 PMCID: PMC8763679 DOI: 10.3389/fpls.2021.750805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Sugarcane is among the most important global crops and a key bioenergy source. Sugarcane production is restricted by limited levels of available soil potassium (K+). The ability of plants to respond to stressors can be regulated by a range of microRNAs (miRNAs). However, there have been few studies regarding the roles of miRNAs in the regulation of sugarcane responses to K+-deficiency. To understand how these non-coding RNAs may influence sugarcane responses to low-K+ stress, we conducted expression profiling of miRNAs in sugarcane roots under low-K+ conditions via high-throughput sequencing. This approach led to the identification of 324 and 42 known and novel miRNAs, respectively, of which 36 were found to be differentially expressed miRNAs (DEMs) under low-K+ conditions. These results also suggested that miR156-x/z and miR171-x are involved in these responses as potential regulators of lateral root formation and the ethylene signaling pathway, respectively. A total of 705 putative targets of these DEMs were further identified through bioinformatics predictions and degradome analyses, and GO and KEGG enrichment analyses revealed these target mRNAs to be enriched for catalytic activity, binding functions, metabolic processes, plant hormone signal transduction, and mitogen-activated protein kinase (MAPK) signaling. In summary, these data provide an overview of the roles of miRNAs in the regulation of sugarcane response to low-K+ conditions.
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Affiliation(s)
- Nannan Zhang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaomin Feng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiaoying Zeng
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Huanzhang Lin
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zilin Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoning Gao
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Yonghong Huang
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiayun Wu
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Yongwen Qi
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
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miRNAomic Approach to Plant Nitrogen Starvation. Int J Genomics 2021; 2021:8560323. [PMID: 34796230 PMCID: PMC8595019 DOI: 10.1155/2021/8560323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.
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Perea-García A, Andrés-Bordería A, Huijser P, Peñarrubia L. The Copper-microRNA Pathway Is Integrated with Developmental and Environmental Stress Responses in Arabidopsis thaliana. Int J Mol Sci 2021; 22:9547. [PMID: 34502449 PMCID: PMC8430956 DOI: 10.3390/ijms22179547] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022] Open
Abstract
As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such as miR398 and miR408 are conserved, as well as the signal transduction pathway to induce them under Cu deficiency. The Arabidopsis thaliana SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family member SPL7 binds to the cis-regulatory motifs present in the promoter regions of genes expressed under Cu deficiency, including Cu-miRNAs. The expression of several other SPL transcription factor family members is regulated by miR156. This regulatory miR156-SPL module plays a crucial role in developmental phase transitions while integrating internal and external cues. Here, we show that Cu deficiency also affects miR156 expression and that SPL3 overexpressing plants, resistant to miR156 regulation, show a severe decrease in SPL7-mediated Cu deficiency responses. These include the expression of Cu-miRNAs and their targets and is probably due to competition between SPL7 and miR156-regulated SPL3 in binding to cis-regulatory elements in Cu-miRNA promoters. Thus, the conserved SPL7-mediated Cu-miRNA pathway could generally be affected by the miR156-SPL module, thereby underscoring the integration of the Cu-miRNA pathway with developmental and environmental stress responses in Arabidopsis thaliana.
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Affiliation(s)
- Ana Perea-García
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
| | - Amparo Andrés-Bordería
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany;
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, 46100 Burjassot, Valencia, Spain; (A.P.-G.); (A.A.-B.)
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Song N, Cheng Y, Peng W, Peng E, Zhao Z, Liu T, Yi T, Dai L, Wang B, Hong Y. Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange ( Citrus sinensis). Int J Mol Sci 2021; 22:ijms22168918. [PMID: 34445624 PMCID: PMC8396319 DOI: 10.3390/ijms22168918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/08/2021] [Accepted: 08/16/2021] [Indexed: 12/17/2022] Open
Abstract
SBP-box is an important plant-specific transcription factor family and is involved in diverse biological processes. Here, we identified a total of 15 SBP-BOX genes in the important fruit crop sweet orange (Citrus sinensis) and characterized their gene structures, conserved domain and motif, chromosomal location, and cis-acting regulatory elements. SBP genes were classified into four subfamilies based on the amino acid sequence homology, and the classification is equally strongly supported by the gene and protein structures. Our analysis revealed that segmental duplication events were the main driving force in the evolution of CsSBP genes, and gene pairs might undergo extensive purifying selection. Further synteny analysis of the SBP members among sweet orange and other plant species provides valuable information for clarifying the CsSBP family evolutionary relationship. According to publicly available RNA-seq data and qRT-PCR analysis from various sweet orange tissues, CsSBP genes may be expressed in different tissues and developmental stages. Gene expression analysis showed variable expression profiles of CsSBP genes under various abiotic stresses, such as high and low-temperature, salt, and wound treatments, demonstrating the potential role of SBP members in sweet orange response to abiotic stress. Noticeably, all CsSBP genes were also downregulated in sweet orange upon the infection of an important fungal pathogen Diaporthe citri. Our results provide valuable information for exploring the role of SBP-Box in sweet orange.
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Affiliation(s)
- Na Song
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
| | - Yulin Cheng
- School of Life Sciences, Chongqing University, Chongqing 401331, China;
| | - Weiye Peng
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - ErPing Peng
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Zengling Zhao
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Tiantian Liu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Tuyong Yi
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Bing Wang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (B.W.); (Y.H.)
| | - Yanyun Hong
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (N.S.); (W.P.); (E.P.); (Z.Z.); (T.L.); (T.Y.); (L.D.)
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (B.W.); (Y.H.)
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He F, Wei C, Zhang Y, Long R, Li M, Wang Z, Yang Q, Kang J, Chen L. Genome-Wide Association Analysis Coupled With Transcriptome Analysis Reveals Candidate Genes Related to Salt Stress in Alfalfa ( Medicago sativa L.). FRONTIERS IN PLANT SCIENCE 2021; 12:826584. [PMID: 35185967 PMCID: PMC8850473 DOI: 10.3389/fpls.2021.826584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/28/2021] [Indexed: 05/12/2023]
Abstract
Salt stress is the main abiotic factor affecting alfalfa yield and quality. However, knowledge of the genetic basis of the salt stress response in alfalfa is still limited. Here, a genome-wide association study (GWAS) involving 875,023 single-nucleotide polymorphisms (SNPs) was conducted on 220 alfalfa varieties under both normal and salt-stress conditions. Phenotypic analysis showed that breeding status and geographical origin play important roles in the alfalfa salt stress response. For germination ability under salt stress, a total of 15 significant SNPs explaining 9%-14% of the phenotypic variation were identified. For tolerance to salt stress in the seedling stage, a total of 18 significant SNPs explaining 12%-23% of the phenotypic variation were identified. Transcriptome analysis revealed 2,097 and 812 differentially expressed genes (DEGs) that were upregulated and 2,445 and 928 DEGs that were downregulated in the leaves and roots, respectively, under salt stress. Among these DEGs, many encoding transcription factors (TFs) were found, including MYB-, CBF-, NAC-, and bZIP-encoding genes. Combining the results of our GWAS analysis and transcriptome analysis, we identified a total of eight candidate genes (five candidate genes for tolerance to salt stress and three candidate genes for germination ability under salt stress). Two SNPs located within the upstream region of MsAUX28, which encodes an auxin response protein, were significantly associated with tolerance to salt stress. The two significant SNPs within the upstream region of MsAUX28 existed as three different haplotypes in this panel. Hap 1 (G/G, A/A) was under selection in the alfalfa domestication and improvement process.
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Juvenile Leaves or Adult Leaves: Determinants for Vegetative Phase Change in Flowering Plants. Int J Mol Sci 2020; 21:ijms21249753. [PMID: 33371265 PMCID: PMC7766579 DOI: 10.3390/ijms21249753] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022] Open
Abstract
Vegetative leaves in Arabidopsis are classified as either juvenile leaves or adult leaves based on their specific traits, such as leaf shape and the presence of abaxial trichomes. The timing of the juvenile-to-adult phase transition during vegetative development, called the vegetative phase change, is a critical decision for plants, as this transition is associated with crop yield, stress responses, and immune responses. Juvenile leaves are characterized by high levels of miR156/157, and adult leaves are characterized by high levels of miR156/157 targets, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. The discovery of this miR156/157-SPL module provided a critical tool for elucidating the complex regulation of the juvenile-to-adult phase transition in plants. In this review, we discuss how the traits of juvenile leaves and adult leaves are determined by the miR156/157-SPL module and how different factors, including embryonic regulators, sugar, meristem regulators, hormones, and epigenetic proteins are involved in controlling the juvenile-to-adult phase transition, focusing on recent insights into vegetative phase change. We also highlight outstanding questions in the field that need further investigation. Understanding how vegetative phase change is regulated would provide a basis for manipulating agricultural traits under various conditions.
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