1
|
Ishfaqe Q, Sami A, Zeshan Haider M, Ahmad A, Shafiq M, Ali Q, Batool A, Haider MS, Ali D, Alarifi S, Islam MS, Manzoor MA. Genome wide identification of the NPR1 gene family in plant defense mechanisms against biotic stress in chili ( Capsicum annuum L.). Front Microbiol 2024; 15:1437553. [PMID: 39161600 PMCID: PMC11332612 DOI: 10.3389/fmicb.2024.1437553] [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: 05/23/2024] [Accepted: 07/12/2024] [Indexed: 08/21/2024] Open
Abstract
Chili pepper cultivation in the Indian subcontinent is severely affected by viral diseases, prompting the need for environmentally friendly disease control methods. To achieve this, it is essential to understand the molecular mechanisms of viral resistance in chili pepper. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) genes are known to provide broad-spectrum resistance to various phytopathogens by activating systemic acquired resistance (SAR). An in-depth understanding of NPR1 gene expression during begomovirus infection and its correlation with different biochemical and physiological parameters is crucial for enhancing resistance against begomoviruses in chili pepper. Nevertheless, limited information on chili CaNPR genes and their role in biotic stress constrains their potential in breeding for biotic stress resistance. By employing bioinformatics for genome mining, we identify 5 CaNPR genes in chili. The promoter regions of 1,500 bp of CaNPR genes contained cis-elements associated with biotic stress responses, signifying their involvement in biotic stress responses. Furthermore, these gene promoters harbored components linked to light, development, and hormone responsiveness, suggesting their roles in plant hormone responses and development. MicroRNAs played a vital role in regulating these five CaNPR genes, highlighting their significance in the regulation of chili genes. Inoculation with the begomovirus "cotton leaf curl Khokhran virus (CLCuKV)" had a detrimental effect on chili plant growth, resulting in stunted development, fibrous roots, and evident virus symptoms. The qRT-PCR analysis of two local chili varieties inoculated with CLCuKV, one resistant (V1) and the other susceptible (V2) to begomoviruses, indicated that CaNPR1 likely provides extended resistance and plays a role in chili plant defense mechanisms, while the remaining genes are activated during the early stages of infection. These findings shed light on the function of chili's CaNPR in biotic stress responses and identify potential genes for biotic stress-resistant breeding. However, further research, including gene cloning and functional analysis, is needed to confirm the role of these genes in various physiological and biological processes. This in-silico analysis enhances our genome-wide understanding of how chili CaNPR genes respond during begomovirus infection.
Collapse
Affiliation(s)
- Qandeel Ishfaqe
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Arsalan Ahmad
- Department of Entomology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shafiq
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Alia Batool
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Saleem Haider
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Daoud Ali
- Department of Zoology College of Science King Saud University, Riyadh, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology College of Science King Saud University, Riyadh, Saudi Arabia
| | - Md Samiul Islam
- Graduate School of Agriculture, Hokkaido University/Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Zhao M, Lei Y, Wu L, Qi H, Song Z, Xu M. The miR159a-PeMYB33 module regulates poplar adventitious rooting through the abscisic acid signal pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:879-891. [PMID: 38271219 DOI: 10.1111/tpj.16643] [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: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a-PeMYB33 module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of miR159a increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of PeMYB33 decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of PeMYB33 using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a-PeMYB33 module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a-PeMYB33 module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth.
Collapse
Affiliation(s)
- Meiqi Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yijing Lei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ling Wu
- Jiangsu Yanjiang Institute of Agricultural Science, Nantong, Jiangsu, 226541, China
| | - Haoran Qi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zihe Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| |
Collapse
|
4
|
Li Q, Zhang Z, Li K, Zhu Y, Sun K, He C. Identification of microRNAs and their target genes associated with chasmogamous and cleistogamous flower development in Viola prionantha. PLANTA 2024; 259:116. [PMID: 38592549 DOI: 10.1007/s00425-024-04398-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: 01/12/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024]
Abstract
MAIN CONCLUSION Differentially expressed microRNAs were found associated with the development of chasmogamous and cleistogamous flowers in Viola prionantha, revealing potential roles of microRNAs in the developmental evolution of dimorphic flowers. In Viola prionantha, chasmogamous (CH) flowers are induced by short daylight, while cleistogamous (CL) flowers are triggered by long daylight. How environmental factors and microRNAs (miRNAs) affect dimorphic flower formation remains unknown. In this study, small RNA sequencing was performed on CH and CL floral buds at different developmental stages in V. prionantha, differentially expressed miRNAs (DEmiRNAs) were identified, and their target genes were predicted. In CL flowers, Viola prionantha miR393 (vpr-miR393a/b) and vpr-miRN3366 were highly expressed, while in CH flowers, vpr-miRN2005, vpr-miR172e-2, vpr-miR166m-3, vpr-miR396f-2, and vpr-miR482d-2 were highly expressed. In the auxin-activated signaling pathway, vpr-miR393a/b and vpr-miRN2005 could target Vpr-TIR1/AFB and Vpr-ARF2, respectively, and other DEmiRNAs could target genes involved in the regulation of transcription, e.g., Vpr-AP2-7. Moreover, Vpr-UFO and Vpr-YAB5, the main regulators in petal and stamen development, were co-expressed with Vpr-TIR1/AFB and Vpr-ARF2 and showed lower expression in CL flowers than in CH flowers. Some V. prionantha genes relating to the stress/defense responses were co-expressed with Vpr-TIR1/AFB, Vpr-ARF2, and Vpr-AP2-7 and highly expressed in CL flowers. Therefore, in V. prionantha, CH-CL flower development may be regulated by the identified DEmiRNAs and their target genes, thus providing the first insight into the formation of dimorphic flowers in Viola.
Collapse
Affiliation(s)
- Qiaoxia Li
- Life Science College, Northwest Normal University, Anning East Road 967, Anning, Lanzhou, 730070, Gansu, China.
| | - Zuoming Zhang
- Life Science College, Northwest Normal University, Anning East Road 967, Anning, Lanzhou, 730070, Gansu, China
| | - Kunpeng Li
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyuan Zhu
- Life Science College, Northwest Normal University, Anning East Road 967, Anning, Lanzhou, 730070, Gansu, China
| | - Kun Sun
- Life Science College, Northwest Normal University, Anning East Road 967, Anning, Lanzhou, 730070, Gansu, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
5
|
López de Las Hazas MDC, Tomé-Carneiro J, Balaguer L, de la Peña G, Chapado LA, Alonso-Bernáldez M, Del Saz-Lara A, Gil-Zamorano J, Burgos-Ramos E, Rodríguez-Pérez M, Gómez-Coronado D, Dávalos A. Dietary plant microRNAs as potential regulators of cellular cholesterol efflux. CLINICA E INVESTIGACION EN ARTERIOSCLEROSIS : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ARTERIOSCLEROSIS 2024:S0214-9168(24)00021-4. [PMID: 38584064 DOI: 10.1016/j.arteri.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 04/09/2024]
Abstract
AIM Epidemiological evidence suggests adherence to vegetable-rich diets is associated to atheroprotective effects and bioactive components are most likely to play a relevant role. The notion of inter-kingdom regulation has opened a new research paradigm and perhaps microRNAs (miRNAs) from edible vegetables could influence consumer gene expression and lead to biological effects. We aimed to investigate the potential impact of broccoli-derived miRNAs on cellular cholesterol efflux in vitro. METHODS Four miRNAs (miR159a, miR159b, miR166a and miR403) from Brassica oleracea var. italica (broccoli), a widely consumed cruciferous vegetable, were selected for further investigation, based on their high abundancy in this vegetable and their presence in other plants. Selected miRNAs were synthesized with a 3'-terminal 2'-O-methylation and their cellular toxicity, in vitro gastrointestinal resistance and cellular uptake were evaluated. Potential target genes within the mammalian transcriptome were assessed in silico following pathway analysis. In vitro cholesterol efflux was assessed in human THP-1-derived macrophages. RESULTS miRNAs survival to in vitro GI digestion was around 1%, although some variation was seen between the four candidates. Cellular uptake by mammalian cells was confirmed, and an increase in cholesterol efflux was observed. Pathway analysis suggested these miRNAs are involved in biological processes related to phosphorylation, phosphatidylinositol and Wnt signaling, and to the insulin/IGF pathway. CONCLUSIONS Health-promoting properties attributed to cruciferous vegetables, might be mediated (at least in part) through miRNA-related mechanisms.
Collapse
Affiliation(s)
| | - Joao Tomé-Carneiro
- Laboratory of Functional Foods, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Livia Balaguer
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Gema de la Peña
- Department of Biochemistry-Research, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Luis A Chapado
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Marta Alonso-Bernáldez
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Andrea Del Saz-Lara
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Judit Gil-Zamorano
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain
| | - Emma Burgos-Ramos
- Biochemistry Area, Faculty of Environmental Sciences and Biochemistry, Universidad Castilla-La Mancha, Toledo, Spain
| | - María Rodríguez-Pérez
- Biochemistry Area, Faculty of Environmental Sciences and Biochemistry, Universidad Castilla-La Mancha, Toledo, Spain
| | - Diego Gómez-Coronado
- Department of Biochemistry-Research, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Instituto Madrileño de Estudios Avanzados (IMDEA)-Alimentación, CEI UAM+CSIC, Madrid, Spain; Consorcio CIBER de la Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
6
|
Wu T, Liu Z, Yu T, Zhou R, Yang Q, Cao R, Nie F, Ma X, Bai Y, Song X. Flowering genes identification, network analysis, and database construction for 837 plants. HORTICULTURE RESEARCH 2024; 11:uhae013. [PMID: 38585015 PMCID: PMC10995624 DOI: 10.1093/hr/uhae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/02/2024] [Indexed: 04/09/2024]
Abstract
Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183 720 genes across eight pathways, along with 10 155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the Plant Flowering-time Gene Database (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.
Collapse
Affiliation(s)
- Tong Wu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Yu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, Aarhus 8200, Denmark
| | - Qihang Yang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei 066600, China
| | - Yun Bai
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| |
Collapse
|
7
|
Kumar S, Sharma N, Sopory SK, Sanan-Mishra N. miRNAs and genes as molecular regulators of rice grain morphology and yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108363. [PMID: 38281341 DOI: 10.1016/j.plaphy.2024.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
Collapse
Affiliation(s)
- Sudhir Kumar
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| |
Collapse
|
8
|
Maniatis G, Tani E, Katsileros A, Avramidou EV, Pitsoli T, Sarri E, Gerakari M, Goufa M, Panagoulakou M, Xipolitaki K, Klouvatos K, Megariti S, Pappi P, Papadakis IE, Bebeli PJ, Kapazoglou A. Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 13:27. [PMID: 38202337 PMCID: PMC10780352 DOI: 10.3390/plants13010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/06/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.
Collapse
Affiliation(s)
- Grigorios Maniatis
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Anastasios Katsileros
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Ilisia, 11528 Athens, Greece;
| | - Theodora Pitsoli
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Goufa
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Maria Panagoulakou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Konstantina Xipolitaki
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Kimon Klouvatos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Stamatia Megariti
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Polixeni Pappi
- Laboratory of Plant Virology, Department of Viticulture, Vegetable Crops, Floriculture and Plant Protection, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA (ELGO-DIMITRA), Kastorias 32A, Mesa Katsampas, 71307 Heraklion, Crete, Greece;
| | - Ioannis E. Papadakis
- Laboratory of Pomology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (G.M.); (A.K.); (E.S.); (Μ.G.); (M.G.); (M.P.); (K.X.); (K.K.); (S.M.); (P.J.B.)
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Lykovrysi, 14123 Athens, Greece;
| |
Collapse
|
9
|
Szymonik K, Klimek-Chodacka M, Lukasiewicz A, Macko-Podgórni A, Grzebelus D, Baranski R. Comparative analysis of the carrot miRNAome in response to salt stress. Sci Rep 2023; 13:21506. [PMID: 38057586 PMCID: PMC10700493 DOI: 10.1038/s41598-023-48900-0] [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: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.
Collapse
Affiliation(s)
- Kamil Szymonik
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Aneta Lukasiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| |
Collapse
|
10
|
Amini Z, Salehi H, Chehrazi M, Etemadi M, Xiang M. miRNAs and Their Target Genes Play a Critical Role in Response to Heat Stress in Cynodon dactylon (L.) Pers. Mol Biotechnol 2023; 65:2004-2017. [PMID: 36913082 DOI: 10.1007/s12033-023-00713-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023]
Abstract
Annual global temperature is increasing rapidly. Therefore, in the near future, plants will be exposed to severe heat stress. However, the potential of microRNAs-mediated molecular mechanism for modulating the expression of their target genes is unclear. To investigate the changes of miRNAs in thermo-tolerant plants, in this study, we first investigated the impact of four high temperature regimes including 35/30 °C, 40/35 °C, 45/40 °C, and 50/45 °C in a day/night cycle for 21 days on the physiological traits (total chlorophyll, relative water content and electrolyte leakage and total soluble protein), antioxidant enzymes activities (superoxide dismutase, ascorbic peroxidase, catalase and peroxidase), and osmolytes (total soluble carbohydrates and starch) in two bermudagrass accessions named Malayer and Gorgan. The results showed that more chlorophyll and the relative water content, lower ion leakage, more efficient protein and carbon metabolism and activation of defense proteins (such as antioxidant enzymes) in Gorgan accession, led to better maintained plant growth and activity during heat stress. In the next stage, to investigate the role of miRNAs and their target genes in response to heat stress in a thermo-tolerant plant, the impact of severe heat stress (45/40 °C) was evaluated on the expression of three miRNAs (miRNA159a, miRNA160a and miRNA164f) and their target genes (GAMYB, ARF17 and NAC1, respectively). All measurements were performed in leaves and roots simultaneously. Heat stress significantly induced the expression of three miRNAs in leaves of two accession, while having different effects on the expression of these miRNAs in roots. The results showed that a decrease in the expression of the transcription factor ARF17, no change in the expression of the transcription factor NAC1, and an increase in the expression of the transcription factor GAMYB in leaf and root tissues of Gorgan accession led to improved heat tolerance in it. These results also showed that the effect of miRNAs on the modulating expression of target mRNAs in leaves and roots is different under heat stress, and miRNAs and mRNAs show spatiotemporal expression. Therefore, the simultaneous analysis of miRNAs and mRNAs expressions in shoot and roots is needed to comprehensively understand miRNAs regulatory function under heat stress.
Collapse
Affiliation(s)
- Zohreh Amini
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Salehi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Mehrangiz Chehrazi
- Department of Horticultural Science, School of Agriculture, Shahid Chamran University, Ahvaz, Iran
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Mingying Xiang
- Department of Horticulture and Landscape Architecture, Oklahoma State University, Stillwater, OK, 74078, USA
| |
Collapse
|
11
|
Fu T, Wang C, Yang Y, Yang X, Wang J, Zhang L, Wang Z, Wang Y. Function identification of miR159a, a positive regulator during poplar resistance to drought stress. HORTICULTURE RESEARCH 2023; 10:uhad221. [PMID: 38077498 PMCID: PMC10709547 DOI: 10.1093/hr/uhad221] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/24/2023] [Indexed: 03/08/2024]
Abstract
Drought seriously affects the growth and development of plants. MiR159 is a highly conserved and abundant microRNA family that plays a crucial role in plant growth and stress responses. However, studies of its function in woody plants are still lacking. Here, the expression of miR159a was significantly upregulated after drought treatment in poplar, and the overexpression of miR159a (OX159a) significantly reduced the open area of the stomata and improved water-use efficiency in poplar. After drought treatment, OX159a lines had better scavenging ability of reactive oxygen species and damage of the membrane system was less than that in wild-type lines. MYB was the target gene of miR159a, as verified by psRNATarget prediction, RT-qPCR, degradome sequencing, and 5' rapid amplification of cDNA ends (5' RACE). Additionally, miR159a-short tandem target mimic suppression (STTM) poplar lines showed increased sensitivity to drought stress. Transcriptomic analysis comparing OX159a lines with wild-type lines revealed upregulation of a series of genes related to response to water deprivation and metabolite synthesis. Moreover, drought-responsive miR172d and miR398 were significantly upregulated and downregulated respectively in OX159a lines. This investigation demonstrated that miR159a played a key role in the tolerance of poplar to drought by reducing stomata open area, increasing the number and total area of xylem vessels, and enhancing water-use efficiency, and provided new insights into the role of plant miR159a and crucial candidate genes for the molecular breeding of trees with tolerance to drought stress.
Collapse
Affiliation(s)
- Tiantian Fu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuzhang Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jing Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lichun Zhang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Zeqi Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
12
|
Sumbur B, Gao F, Liu Q, Feng D, Bing J, Dorjee T, Li X, Sun H, Zhou Y. The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress. Biomolecules 2023; 13:1721. [PMID: 38136592 PMCID: PMC10741500 DOI: 10.3390/biom13121721] [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: 10/31/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.
Collapse
Affiliation(s)
- Batu Sumbur
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Dandan Feng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Jie Bing
- College of Life Sciences, Beijing Normal University, Beijing 100080, China;
| | - Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xuting Li
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Huigai Sun
- School of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; (B.S.); (F.G.); (Q.L.); (D.F.); (T.D.); (X.L.)
- Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| |
Collapse
|
13
|
Liu Y, Zhu QF, Li WY, Chen P, Xue J, Yu Y, Feng YZ. The Pivotal Role of Noncoding RNAs in Flowering Time Regulation. Genes (Basel) 2023; 14:2114. [PMID: 38136936 PMCID: PMC10742506 DOI: 10.3390/genes14122114] [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: 10/21/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Noncoding RNAs constitute a substantial portion of the transcriptome and play pivotal roles in plant growth and development. Among these processes, flowering stands out as a crucial trait, ensuring reproductive success and seed set, and is meticulously controlled by genetic and environmental factors. With remarkable advancements in the identification and characterization of noncoding RNAs in plants, it has become evident that noncoding RNAs are intricately linked to the regulation of flowering time. In this article, we present an overview of the classification of plant noncoding RNAs and delve into their functions in the regulation of flowering time. Furthermore, we review their molecular mechanisms and their involvement in flowering pathways. Our comprehensive review enhances the understanding of how noncoding RNAs contribute to the regulation of flowering time and sheds light on their potential implications in crop breeding.
Collapse
Affiliation(s)
| | | | | | | | | | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
| | - Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Y.L.); (Q.-F.Z.); (W.-Y.L.); (P.C.); (J.X.)
| |
Collapse
|
14
|
Wang Q, Wan J, Dang K, Meng S, Hu D, Lin Y, Qiu X, Guo Z, Fu Z, Ding D, Tang J. zma-miR159 targets ZmMYB74 and ZmMYB138 transcription factors to regulate grain size and weight in maize. PLANT PHYSIOLOGY 2023; 193:2430-2441. [PMID: 37590954 DOI: 10.1093/plphys/kiad455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 08/19/2023]
Abstract
Endosperm cell number is critical in determining grain size in maize (Zea mays). Here, zma-miR159 overexpression led to enlarged grains in independent transgenic lines, suggesting that zma-miR159 contributes positively to maize grain size. Targeting of ZmMYB74 and ZmMYB138 transcription factor genes by zma-miR159 was validated using 5' RACE and dual-luciferase assay. Lines in which ZmMYB74 was knocked out using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) presented a similar enlarged grain phenotype as those with zma-miR159 overexpression. Downstream genes regulating cell division were identified through DNA affinity purification sequencing using ZmMYB74 and ZmMYB138. Our results suggest that zma-miR159-ZmMYB modules act as an endosperm development hub, participating in the division and proliferation of endosperm cells.
Collapse
Affiliation(s)
- Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| |
Collapse
|
15
|
Jing W, Gong F, Liu G, Deng Y, Liu J, Yang W, Sun X, Li Y, Gao J, Zhou X, Ma N. Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nat Commun 2023; 14:7106. [PMID: 37925502 PMCID: PMC10625627 DOI: 10.1038/s41467-023-42914-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
The size of plant lateral organs is determined by well-coordinated cell proliferation and cell expansion. Here, we report that miR159, an evolutionarily conserved microRNA, plays an essential role in regulating cell division in rose (Rosa hybrida) petals by modulating cytokinin catabolism. We uncover that Cytokinin Oxidase/Dehydrogenase6 (CKX6) is a target of miR159 in petals. Knocking down miR159 levels results in the accumulation of CKX6 transcripts and earlier cytokinin clearance, leading to a shortened cell division period and smaller petals. Conversely, knocking down CKX6 causes cytokinin accumulation and a prolonged developmental cell division period, mimicking the effects of exogenous cytokinin application. MYB73, a R2R3-type MYB transcription repressor, recruits a co-repressor (TOPLESS) and a histone deacetylase (HDA19) to form a suppression complex, which regulates MIR159 expression by modulating histone H3 lysine 9 acetylation levels at the MIR159 promoter. Our work sheds light on mechanisms for ensuring the correct timing of the exit from the cell division phase and thus organ size regulation by controlling cytokinin catabolism.
Collapse
Affiliation(s)
- Weikun Jing
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Feifei Gong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guoqin Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yinglong Deng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiaqi Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenjing Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yonghong Li
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaofeng Zhou
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
16
|
Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
Collapse
Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| |
Collapse
|
17
|
Mejía-Mendoza MA, Garcidueñas-Piña C, Barrera-Figueroa BE, Morales-Domínguez JF. Identification and Profiling Analysis of microRNAs in Guava Fruit ( Psidium guajava L.) and Their Role during Ripening. Genes (Basel) 2023; 14:2029. [PMID: 38002972 PMCID: PMC10670931 DOI: 10.3390/genes14112029] [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: 08/01/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The guava (Psidium guajava L.) is a climacteric fruit with an accelerated post-harvest overripening. miRNAs are small RNA sequences that function as gene regulators in eukaryotes and are essential for their survival and development. In this study, miRNA libraries were constructed, sequenced and analyzed from the breaker and ripe stages of guava fruit cv. Siglo XXI. One hundred and seventy-four mature miRNA sequences from 28 miRNA families were identified. The taxonomic distribution of the guava miRNAs showed a high level of conservation among the dicotyledonous plants. Most of the predicted miRNA target genes were transcription factors and genes involved in the metabolism of phytohormones such as abscisic acid, auxins, and ethylene, as revealed through an ontology enrichment analysis. The miRNA families miR168, miR169, miR396, miR397, and miR482 were classified as being directly associated with maturation, whereas the miRNA families miR160, miR165, miR167, miR3930, miR395, miR398, and miR535 were classified as being indirectly associated. With this study, we intended to increase our knowledge and understanding of the regulatory process involved in the ripening process, thereby providing valuable information for future research on the ripening of guava fruit.
Collapse
Affiliation(s)
- Mario Alejandro Mejía-Mendoza
- Departamento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes (UAA), Av. Universidad, #940, Ciudad Universitaria, Aguascalientes 20100, Mexico; (M.A.M.-M.); (C.G.-P.)
| | - Cristina Garcidueñas-Piña
- Departamento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes (UAA), Av. Universidad, #940, Ciudad Universitaria, Aguascalientes 20100, Mexico; (M.A.M.-M.); (C.G.-P.)
| | - Blanca Estela Barrera-Figueroa
- Centro de Investigaciones Científicas, Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Circuito Central #200, Parque Industrial, Tuxtepec 68301, Mexico;
| | - José Francisco Morales-Domínguez
- Departamento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes (UAA), Av. Universidad, #940, Ciudad Universitaria, Aguascalientes 20100, Mexico; (M.A.M.-M.); (C.G.-P.)
| |
Collapse
|
18
|
Haider MZ, Sami A, Shafiq M, Anwar W, Ali S, Ali Q, Muhammad S, Manzoor I, Shahid MA, Ali D, Alarifi S. Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1269995. [PMID: 37954992 PMCID: PMC10634354 DOI: 10.3389/fpls.2023.1269995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023]
Abstract
Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.
Collapse
Affiliation(s)
- Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Waheed Anwar
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sajid Ali
- Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sher Muhammad
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Sciences Department, University of Florida/Institute of Food and Agricultural Sciences (IFAS), North Florida Research and Education Center, Quincy, FL, United States
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
19
|
Wang X, Zhou R, Zhao S, Niu S. An Integrated Analysis of microRNAs and the Transcriptome Reveals the Molecular Mechanisms Underlying the Regulation of Leaf Development in Xinyang Maojian Green Tea ( Camellia sinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3665. [PMID: 37960023 PMCID: PMC10649745 DOI: 10.3390/plants12213665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Xinyang Maojian (XYMJ) tea is one of the world's most popular green teas; the development of new sprouts directly affects the yield and quality of tea products, especially for XYMJ, which has hairy tips. Here, we used transcriptome and small RNA sequencing to identify mRNAs and miRNAs, respectively, involved in regulating leaf development in different plant tissues (bud, leaf, and stem). We identified a total of 381 conserved miRNAs. Given that no genomic data for XYMJ green tea are available, we compared the sequencing data for XYMJ green tea with genomic data from a closely related species (Tieguanyin) and the Camellia sinensis var. sinensis database; we identified a total of 506 and 485 novel miRNAs, respectively. We also identified 11 sequence-identical novel miRNAs in the tissues of XYMJ tea plants. Correlation analyses revealed 97 miRNA-mRNA pairs involved in leaf growth and development; the csn-miR319-2/csnTCP2 and miR159-csnMYB modules were found to be involved in leaf development in XYMJ green tea. Quantitative real-time PCR was used to validate the expression levels of the miRNAs and mRNAs. The miRNAs and target genes identified in this study might shed new light on the molecular mechanisms underlying the regulation of leaf development in tea plants.
Collapse
Affiliation(s)
- Xianyou Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Ruijin Zhou
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Shanshan Zhao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shengyang Niu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| |
Collapse
|
20
|
Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [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: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
Collapse
Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| |
Collapse
|
21
|
Wong GY, Millar AA. Target Landscape of Conserved Plant MicroRNAs and the Complexities of Their Ancient MicroRNA-Binding Sites. PLANT & CELL PHYSIOLOGY 2023; 64:604-621. [PMID: 36943747 DOI: 10.1093/pcp/pcad019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/02/2023] [Accepted: 03/19/2023] [Indexed: 06/16/2023]
Abstract
In plants, microRNA (miRNA)-target interactions (MTIs) require high complementarity, a feature from which bioinformatic programs have predicted numerous and diverse targets for any given miRNA, promoting the idea of complex miRNA networks. Opposing this is a hypothesis of constrained miRNA specificity, in which functional MTIs are restricted to the few targets whose required expression output is compatible with the expression of the miRNA. To explore these opposing views, the bioinformatic pipeline Targets Ranked Using Experimental Evidence was applied to strongly conserved miRNAs to identity their high-evidence (HE) targets across species. For each miRNA family, HE targets predominantly consisted of homologs from one conserved target gene family (primary family). These primary families corresponded to the known canonical miRNA-target families, validating the approach. Very few additional HE target families were identified (secondary family), and if so, they were likely functionally related to the primary family. Many primary target families contained highly conserved nucleotide sequences flanking their miRNA-binding sites that were enriched in HE homologs across species. A number of these flanking sequences are predicted to form conserved RNA secondary structures that preferentially base pair with the miRNA-binding site, implying that these sites are highly structured. Our findings support a target landscape view that is dominated by the conserved primary target families, with a minority of either secondary target families or non-conserved targets. This is consistent with the constrained hypothesis of functional miRNA specificity, which potentially in part is being facilitated by features beyond complementarity.
Collapse
Affiliation(s)
- Gigi Y Wong
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
22
|
Xu C, Li J, Wang H, Liu H, Yu Z, Zhao Z. Whole-Transcriptome Sequencing Reveals a ceRNA Regulatory Network Associated with the Process of Periodic Albinism under Low Temperature in Baiye No. 1 ( Camellia sinensis). Int J Mol Sci 2023; 24:ijms24087162. [PMID: 37108322 PMCID: PMC10138444 DOI: 10.3390/ijms24087162] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The young shoots of the tea plant Baiye No. 1 display an albino phenotype in the early spring under low environmental temperatures, and the leaves re-green like those of common tea cultivars during the warm season. Periodic albinism is precisely regulated by a complex gene network that leads to metabolic differences and enhances the nutritional value of tea leaves. Here, we identified messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) to construct competing endogenous RNA (ceRNA) regulatory networks. We performed whole-transcriptome sequencing of 12 samples from four periods (Bud, leaves not expanded; Alb, albino leaves; Med, re-greening leaves; and Gre, green leaves) and identified a total of 6325 differentially expressed mRNAs (DEmRNAs), 667 differentially expressed miRNAs (DEmiRNAs), 1702 differentially expressed lncRNAs (DElncRNAs), and 122 differentially expressed circRNAs (DEcircRNAs). Furthermore, we constructed ceRNA networks on the basis of co-differential expression analyses which comprised 112, 35, 38, and 15 DEmRNAs, DEmiRNAs, DElncRNAs, and DEcircRNAs, respectively. Based on the regulatory networks, we identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs during periodic albinism, including the ceRNA regulatory network centered on miR5021x, the GAMYB-miR159-lncRNA regulatory network, and the NAC035-miR319x-circRNA regulatory network. These regulatory networks might be involved in the response to cold stress, photosynthesis, chlorophyll synthesis, amino acid synthesis, and flavonoid accumulation. Our findings provide novel insights into ceRNA regulatory mechanisms involved in Baiye No. 1 during periodic albinism and will aid future studies of the molecular mechanisms underlying albinism mutants.
Collapse
Affiliation(s)
- Cunbin Xu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Jinling Li
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Hualei Wang
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Huijuan Liu
- College of Life Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| | - Zhihai Yu
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Zhi Zhao
- Guizhou Key Laboratory of Propagation and Cultivation on Medicinal Plants, Guizhou University, Guiyang 550025, China
| |
Collapse
|
23
|
New method for microRNA detection based on multimerization. Anal Biochem 2023; 664:115049. [PMID: 36639117 DOI: 10.1016/j.ab.2023.115049] [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: 11/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Detection of specific microRNA (miRNA) is of great demand due to their essential role in genes regulation, stress response and development of diseases. However, mature miRNAs are small molecules that make it difficult to use routine amplification-based methods. Here, we report an approach for detection of miRNA based on a new type of isothermal amplification, namely, multimerization. The proposed technique is simple and versatile, excludes a reverse transcription step, and requires two conventional primers only and no additional stem-loop or fluorogenic probes. Only mature miRNAs can initiate multimerization, thereby, pri- or pre-miRNA are excluded from analysis, ensuring high accuracy of the assay. The approach was approved on miRNA from common wheat Triticum aestivum; the increase of Tae-miRNA159 level for plants affected by Stagonospora nodorum Berk infection was demonstrated. The obtained results allow to perform quantitative analysis, providing determination of specific targets with high reliability (detection limit of about 20 pM).
Collapse
|
24
|
Guo L, Li Y, Zhang C, Wang Z, Carlson JE, Yin W, Zhang X, Hou X. Integrated analysis of miRNAome transcriptome and degradome reveals miRNA-target modules governing floral florescence development and senescence across early- and late-flowering genotypes in tree peony. FRONTIERS IN PLANT SCIENCE 2022; 13:1082415. [PMID: 36589111 PMCID: PMC9795019 DOI: 10.3389/fpls.2022.1082415] [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: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
As a candidate national flower of China, tree peony has extremely high ornamental, medicinal and oil value. However, the short florescence and rarity of early-flowering and late-flowering varieties restrict further improvement of the economic value of tree peony. Specific miRNAs and their target genes engaged in tree peony floral florescence, development and senescence remain unknown. This report presents the integrated analysis of the miRNAome, transcriptome and degradome of tree peony petals collected from blooming, initial flowering, full blooming and decay stages in early-flowering variety Paeonia ostii 'Fengdan', an early-flowering mutant line of Paeonia ostii 'Fengdan' and late-flowering variety Paeonia suffruticosa 'Lianhe'. Transcriptome analysis revealed a transcript ('psu.G.00014095') which was annotated as a xyloglucan endotransglycosylase/hydrolase precursor XTH-25 and found to be differentially expressed across flower developmental stages in Paeonia ostii 'Fengdan' and Paeonia suffruticosa 'Lianhe'. The miRNA-mRNA modules were presented significant enrichment in various pathways such as plant hormone signal transduction, indole alkaloid biosynthesis, arachidonic acid metabolism, folate biosynthesis, fatty acid elongation, and the MAPK signaling pathway. Multiple miRNA-mRNA-TF modules demonstrated the potential functions of MYB-related, bHLH, Trihelix, NAC, GRAS and HD-ZIP TF families in floral florescence, development, and senescence of tree peony. Comparative spatio-temporal expression investigation of eight floral-favored miRNA-target modules suggested that transcript 'psu.T.00024044' and microRNA mtr-miR166g-5p are involved in the floral florescence, development and senescence associated agronomic traits of tree peony. The results might accelerate the understanding of the potential regulation mechanism in regards to floral florescence, development and abscission, and supply guidance for tree peony breeding of varieties with later and longer florescence characteristics.
Collapse
Affiliation(s)
- Lili Guo
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Yuying Li
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Chenjie Zhang
- College of Tree Peony, Henan University of Science and Technology, Luoyang, Henan, China
| | - Zhanying Wang
- Department of Horticulture, Luoyang Academy of Agricultural and Forestry Sciences, Luoyang, Henan, China
| | - John E. Carlson
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States
| | - Weinlun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiuxin Zhang
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| | - Xiaogai Hou
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China
| |
Collapse
|
25
|
What Do We Know about Barley miRNAs? Int J Mol Sci 2022; 23:ijms232314755. [PMID: 36499082 PMCID: PMC9740008 DOI: 10.3390/ijms232314755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.
Collapse
|
26
|
Biswal AK, Alakonya AE, Mottaleb KA, Hearne SJ, Sonder K, Molnar TL, Jones AM, Pixley KV, Prasanna BM. Maize Lethal Necrosis disease: review of molecular and genetic resistance mechanisms, socio-economic impacts, and mitigation strategies in sub-Saharan Africa. BMC PLANT BIOLOGY 2022; 22:542. [PMID: 36418954 PMCID: PMC9686106 DOI: 10.1186/s12870-022-03932-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Maize lethal necrosis (MLN) disease is a significant constraint for maize producers in sub-Saharan Africa (SSA). The disease decimates the maize crop, in some cases, causing total crop failure with far-reaching impacts on regional food security. RESULTS In this review, we analyze the impacts of MLN in Africa, finding that resource-poor farmers and consumers are the most vulnerable populations. We examine the molecular mechanism of MLN virus transmission, role of vectors and host plant resistance identifying a range of potential opportunities for genetic and phytosanitary interventions to control MLN. We discuss the likely exacerbating effects of climate change on the MLN menace and describe a sobering example of negative genetic association between tolerance to heat/drought and susceptibility to viral infection. We also review role of microRNAs in host plant response to MLN causing viruses as well as heat/drought stress that can be carefully engineered to develop resistant varieties using novel molecular techniques. CONCLUSIONS With the dual drivers of increased crop loss due to MLN and increased demand of maize for food, the development and deployment of simple and safe technologies, like resistant cultivars developed through accelerated breeding or emerging gene editing technologies, will have substantial positive impact on livelihoods in the region. We have summarized the available genetic resources and identified a few large-effect QTLs that can be further exploited to accelerate conversion of existing farmer-preferred varieties into resistant cultivars.
Collapse
Affiliation(s)
- Akshaya Kumar Biswal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico.
| | - Amos Emitati Alakonya
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Khondokar Abdul Mottaleb
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | - Kai Sonder
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | | | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kevin Vail Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico-Veracruz, El Batan, Texcoco, C.P. 56237, Mexico
| | | |
Collapse
|
27
|
Huang LZ, Zhou M, Ding YF, Zhu C. Gene Networks Involved in Plant Heat Stress Response and Tolerance. Int J Mol Sci 2022; 23:ijms231911970. [PMID: 36233272 PMCID: PMC9569452 DOI: 10.3390/ijms231911970] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 12/03/2022] Open
Abstract
Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca2+ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.
Collapse
Affiliation(s)
| | | | - Yan-Fei Ding
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
| | - Cheng Zhu
- Correspondence: (Y.-F.D.); (C.Z.); Tel.: +86-571-8683-6090 (C.Z.)
| |
Collapse
|
28
|
Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review. Curr Issues Mol Biol 2022; 44:3695-3710. [PMID: 36005149 PMCID: PMC9406886 DOI: 10.3390/cimb44080253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.
Collapse
|
29
|
Genome-Wide Analysis of miR159 Gene Family and Predicted Target Genes Associated with Environmental Stress in Dendrobium officinale: A Bioinformatics Study. Genes (Basel) 2022; 13:genes13071221. [PMID: 35886004 PMCID: PMC9320484 DOI: 10.3390/genes13071221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/26/2022] Open
Abstract
Dendrobium officinale (D. officinale) is a widely used traditional Chinese medicine with high economic value. MicroR159 (miR159) is an ancient and conserved microRNA (miRNA) family in land plants, playing roles in the progress of growth and development, as well as the stress response. In order to find out functions of miR159 in D. officinale, multiple bioinformatic approaches were employed and 10 MIR159 genes were found, localizing on seven chromosomes and an unanchored segment of the D. officinale genome. All of the precursor sequences of Dof-miR159 could form a stable stem-loop structure. The phylogenetic analysis revealed that the MIR159 genes of D. officinale were divided into five clades. Furthermore, the conservation analysis suggested that the 2 to 20 nt region of miR159 mature sequences were highly conserved among family members. The promoter analysis of MIR159s showed that the majority of the predicted cis-elements were related to environmental stress or hormones. In total, five classes of genes were predicted to be the target genes of Dof-miR159s, including GAMYB transcription factors, which had been confirmed in many other land plants. The expression patterns of predicted target genes revealed their potential roles in the growth and development of D. officinale, as well as in cold and drought stress responses. In conclusion, our results illustrated the stress-related miR159-targeted genes in D. officinale, which could provide candidate genes for resistance breeding in the future.
Collapse
|
30
|
Qing Y, Zheng Y, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y, Fei Z. Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1536-1550. [PMID: 35514123 DOI: 10.1111/tpj.15798] [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: 12/20/2021] [Revised: 04/23/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
Collapse
Affiliation(s)
- You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Heather N Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| |
Collapse
|
31
|
Zhao P, Wang F, Deng Y, Zhong F, Tian P, Lin D, Deng J, Zhang Y, Huang T. Sly-miR159 regulates fruit morphology by modulating GA biosynthesis in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:833-845. [PMID: 34882929 PMCID: PMC9055814 DOI: 10.1111/pbi.13762] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/28/2021] [Indexed: 05/29/2023]
Abstract
Fruit morphology is an important agronomical trait of many crops. Here, we identify Sly-miR159 as an important regulator of fruit morphology in tomato, a model species of fleshy-fruit development. We show that Sly-miR159 functions through its target SlGAMYB2 to control fruit growth. Suppression of Sly-miR159 and overexpression of SlGAMYB2 result in larger fruits with a reduced length/width ratio, while loss of function of SlGAMYB2 leads to the formation of smaller and more elongated fruits. Gibberellin (GA) is a major phytohormone that regulates fruit development in tomato. We show the Sly-miR159-SlGAMYB2 pathway controls fruit morphology by modulating GA biosynthesis. In particular, we demonstrate that Sly-miR159 promotes GA biosynthesis largely through the direct repression of the GA biosynthetic gene SlGA3ox2 by SlGAMYB2. Together, our findings reveal the action of Sly-miR159 on GA biosynthesis as a previously unidentified mechanism that controls fruit morphology in tomato. Modulating this pathway may have potential applications in tomato breeding for manipulating fruit growth and facilitating the process of fruit improvement.
Collapse
Affiliation(s)
- Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Fengpan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Yinjiao Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Fanjia Zhong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Juhui Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| |
Collapse
|
32
|
Zhu M, Wang X, Zhou Y, Tan J, Zhou Y, Gao F. Small RNA Sequencing Revealed that miR4415, a Legume-Specific miRNA, was Involved in the Cold Acclimation of Ammopiptanthus nanus by Targeting an L-Ascorbate Oxidase Gene and Regulating the Redox State of Apoplast. Front Genet 2022; 13:870446. [PMID: 35444684 PMCID: PMC9013972 DOI: 10.3389/fgene.2022.870446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous single-stranded RNAs that regulate plant growth, development, and environmental stress response posttranscriptionally. Ammopiptanthus nanus, a rare evergreen broad-leaved shrub in the temperate area of Central Asia, can tolerate freezing stress as low as -30 degrees centigrade in winter, and miRNA might be involved in the cold acclimation which enables A. nanus to obtain tolerance to freezing stress. Systematic identification and functional analysis of the miRNAs involved in the cold acclimation in A. nanus may promote understanding of the miRNA-mediated gene regulation network underlying cold acclimation. Here, based on small RNA and degradome sequencing, 256 miRNAs and 1,808 miRNA-target pairs were identified in A. nanus. A total of 39 cold-responsive miRNAs were identified, of which 29 were upregulated and ten were downregulated. These cold-responsive miRNAs may participate in the cold acclimation by regulating redox homeostasis (miR398, miR4415, and miR408), calcium signaling (miR5225 and miR5211), growth and development (miR159 and miR390), and small RNA-mediated gene silencing (miR168 and miR1515). We found that miR4415, a legume-specific miRNA, is involved in the cold acclimation of A. nanus by targeting an L-ascorbate oxidase gene and then regulating the redox state of the apoplast. Our study provides important data for understanding the regulatory role of miRNA in the cold acclimation of A. nanus.
Collapse
Affiliation(s)
- Ming Zhu
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Xue Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yanqiu Zhou
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jinhua Tan
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yijun Zhou
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Fei Gao
- Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics, National Ethnic Affairs Commission, Minzu University of China, Beijing, China.,College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| |
Collapse
|
33
|
Ma X, Zhao F, Zhou B. The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2022; 23:ijms23084124. [PMID: 35456943 PMCID: PMC9032736 DOI: 10.3390/ijms23084124] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.
Collapse
Affiliation(s)
- Xu Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
| | - Bo Zhou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
| |
Collapse
|
34
|
Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
Collapse
Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
35
|
Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
Collapse
Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
36
|
Ashraf MA, Feng X, Hu X, Ashraf F, Shen L, Iqbal MS, Zhang S. In silico identification of sugarcane (Saccharum officinarum L.) genome encoded microRNAs targeting sugarcane bacilliform virus. PLoS One 2022; 17:e0261807. [PMID: 35051194 PMCID: PMC8775236 DOI: 10.1371/journal.pone.0261807] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Sugarcane bacilliform virus (SCBV) is considered one of the most economically damaging pathogens for sugarcane production worldwide. Three open reading frames (ORFs) are characterized in the circular, ds-DNA genome of the SCBV; these encode for a hypothetical protein (ORF1), a DNA binding protein (ORF2), and a polyprotein (ORF3). A comprehensive evaluation of sugarcane (Saccharum officinarum L.) miRNAs for the silencing of the SCBV genome using in silico algorithms were carried out in the present study using mature sugarcane miRNAs. miRNAs of sugarcane are retrieved from the miRBase database and assessed in terms of hybridization with the SCBV genome. A total of 14 potential candidate miRNAs from sugarcane were screened out by all used algorithms used for the silencing of SCBV. The consensus of three algorithms predicted the hybridization site of sof-miR159e at common locus 5534. miRNA-mRNA interactions were estimated by computing the free-energy of the miRNA-mRNA duplex using the RNAcofold algorithm. A regulatory network of predicted candidate miRNAs of sugarcane with SCBV-ORFs, generated using Circos-is used to identify novel targets. The predicted data provide useful information for the development of SCBV-resistant sugarcane plants.
Collapse
Affiliation(s)
- Muhammad Aleem Ashraf
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Department of Bioscience and Technology, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
- * E-mail: (MAA); (SZ)
| | - Xiaoyan Feng
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaowen Hu
- Zhanjiang Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Fakiha Ashraf
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Linbo Shen
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | | | - Shuzhen Zhang
- Institute of Tropical Bioscience and Biotechnology, Sugarcane Research Centre of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (MAA); (SZ)
| |
Collapse
|
37
|
Palakolanu SR, Gupta S, Yeshvekar RK, Chakravartty N, Kaliamoorthy S, Shankhapal AR, Vempati AS, Kuriakose B, Lekkala SP, Philip M, Perumal RC, Lachagari VBR, Bhatnagar-Mathur P. Genome-wide miRNAs profiles of pearl millet under contrasting high vapor pressure deficit reveal their functional roles in drought stress adaptations. PHYSIOLOGIA PLANTARUM 2022; 174:e13521. [PMID: 34392545 DOI: 10.1111/ppl.13521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Pearl millet (Pennisetum glaucum [L.] R. Br.) is an important crop capable of growing in harsh and marginal environments, with the highest degree of tolerance to drought and heat stresses among cereals. Diverse germplasm of pearl millet shows a significant phenotypic variation in response to abiotic stresses, making it a unique model to study the mechanisms responsible for stress mitigation. The present study focuses on identifying the physiological response of two pearl millet high-resolution cross (HRC) genotypes, ICMR 1122 and ICMR 1152, in response to low and high vapor pressure deficit (VPD). Under high VPD conditions, ICMR 1152 exhibited a lower transpiration rate (Tr), higher transpiration efficiency, and lower root sap exudation than ICMR 1122. Further, Pg-miRNAs expressed in the contrasting genotypes under low and high VPD conditions were identified by deep sequencing analysis. A total of 116 known and 61 novel Pg-miRNAs were identified from ICMR 1152, while 26 known and six novel Pg-miRNAs were identified from ICMR 1122 genotypes, respectively. While Pg-miR165, 168, 170, and 319 families exhibited significant differential expression under low and high VPD conditions in both genotypes, ICMR 1152 showed abundant expression of Pg-miR167, Pg-miR172, Pg-miR396 Pg-miR399, Pg-miR862, Pg-miR868, Pg-miR950, Pg-miR5054, and Pg-miR7527 indicating their direct and indirect role in root physiology and abiotic stress responses. Drought responsive Pg-miRNA targets showed upregulation in response to high VPD stress, further narrowing down the miRNAs involved in regulation of drought tolerance in pearl millet.
Collapse
Affiliation(s)
- Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | - Saurabh Gupta
- AgriGenome Labs Pvt. Ltd, Hyderabad, Telangana, India
| | - Richa K Yeshvekar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
- Centre for Plant Sciences, School of Biology, University of Leeds, Leeds, UK
| | | | - Sivasakthi Kaliamoorthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | | | - Ashwini Soumya Vempati
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| | | | | | | | | | | | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, India
| |
Collapse
|
38
|
An L, Zhang S, Guo P, Song L, Xie C, Guo H, Fang R, Jia Y. RIR1 represses plant immunity by interacting with mitochondrial complex I subunit in rice. MOLECULAR PLANT PATHOLOGY 2022; 23:92-103. [PMID: 34628712 PMCID: PMC8659553 DOI: 10.1111/mpp.13145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
We previously observed decreased expression of rice OsmiR159a.1 on infection with the bacterial blight-causing pathogen Xanthomonas oryzae pv. oryzae (Xoo), and identified the OsLRR_RLK (leucine-rich repeat_ receptor like kinase) gene as an authentic target of OsmiR159a.1. Here, we found that a Tos17 insertion mutant of LRR_RLK displayed increasing temporal resistance to Xoo, whereas the LRR_RLK overexpression lines were susceptible to the pathogen early on in the infection, indicating that LRR_RLK encodes a repressor of rice resistance to Xoo infection, and it was renamed as RIR1 (Rice Immunity Repressor 1). RIR1 overexpression plants were more susceptible to Xoo at late growth stage, suggesting that RIR1 mRNA levels are negatively correlated with the resistance of rice against Xoo. We discovered that OsmiR159a.1 repression in Xoo-infected plants was largely dependent on the pathogen's type III secretion system. Co-immunoprecipitation, bimolecular fluoresence complementation, and pull-down assays indicated that RIR1 interacted with the NADH-ubiquinone oxidoreductase (NUO) 51-kDa subunit of the mitochondrial complex I through its kinase domain. Notably, impairment of RIR1 or overexpression of NUO resulted in reactive oxygen species accumulation and enhanced expression of pathogen-resistance genes, including jasmonic acid pathway genes. We propose that pathogens may inhibit OsmiR159 to interfere with the RIR1-NUO interaction, and subsequently depression of rice immune signalling pathways. The resistance genes manipulated by Xoo can be a probe to explore the regulatory network during host-pathogen interactions.
Collapse
Affiliation(s)
- Lin An
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Siyuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ping Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liyang Song
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chuanmiao Xie
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - Hongyan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| | - Yantao Jia
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, China
| |
Collapse
|
39
|
Roy D, Adhikari S, Adhikari A, Ghosh S, Azahar I, Basuli D, Hossain Z. Impact of CuO nanoparticles on maize: Comparison with CuO bulk particles with special reference to oxidative stress damages and antioxidant defense status. CHEMOSPHERE 2022; 287:131911. [PMID: 34461334 DOI: 10.1016/j.chemosphere.2021.131911] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/20/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
The present study aimed to systematically investigate the particle size effects of copper (II) oxide [CuO nanoparticles (<50 nm) and CuO bulk particles (<10 μm)] on maize (Zea mays L.). Bioaccumulation of Cu, in vivo ROS generation, membrane damage, transcriptional modulation of antioxidant genes, cellular redox status of glutathione and ascorbate pool, expression patterns of COPPER TRANSPORTER 4 and stress responsive miRNAs (miR398a, miR171b, miR159f-3p) with their targets were investigated for better understanding of the underlying mechanisms and the extent of CuO nanoparticles and CuO bulk particles induced oxidative stress damages. More restricted seedling growth, comparatively higher membrane injury, marked decline in the levels of chlorophylls and carotenoids and severe oxidative burst were evident in CuO bulk particles challenged leaves. Dihydroethidium and CM-H2DCFDA staining further supported elevated reactive oxygen species generation in CuO bulk particles stressed roots. CuO bulk particles exposed seedlings accumulated much higher amount of Cu in roots as compared to CuO nanoparticles stressed plants with low root-to-shoot Cu translocation. Moderately high GR expression with maintenance of a steady GSH-GSSG ratio in CuO nanoparticles challenged leaves might be accountable for their rather improved performance under stressed condition. miR171b-mediated enhanced expression of SCARECROW 6 might participate in the marked decline of chlorophyll content in CuO bulk particles exposed leaves. Ineffective recycling of AsA pool is another decisive feature of inadequate performance of CuO bulk particles stressed seedlings in combating oxidative stress damages. Taken together, our findings revealed that toxicity of CuO bulk particles was higher than CuO nanoparticles and the adverse effects of CuO bulk particles on maize seedlings might be due to higher Cu ions dissolution.
Collapse
Affiliation(s)
- Doyel Roy
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Sinchan Adhikari
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Ayan Adhikari
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Supriya Ghosh
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Ikbal Azahar
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Debapriya Basuli
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India
| | - Zahed Hossain
- Plant Stress and Molecular Biology Laboratory, Department of Botany, University of Kalyani, Kalyani, 741235, West Bengal, India.
| |
Collapse
|
40
|
Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
Collapse
Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
| |
Collapse
|
41
|
Lei P, Qi N, Zhou Y, Wang Y, Zhu X, Xuan Y, Liu X, Fan H, Chen L, Duan Y. Soybean miR159 -GmMYB33 Regulatory Network Involved in Gibberellin-Modulated Resistance to Heterodera glycines. Int J Mol Sci 2021; 22:13172. [PMID: 34884977 PMCID: PMC8658632 DOI: 10.3390/ijms222313172] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is an obligate sedentary biotroph that poses major threats to soybean production globally. Recently, multiple miRNAome studies revealed that miRNAs participate in complicated soybean-SCN interactions by regulating their target genes. However, the functional roles of miRNA and target genes regulatory network are still poorly understood. In present study, we firstly investigated the expression patterns of miR159 and targeted GmMYB33 genes. The results showed miR159-3p downregulation during SCN infection; conversely, GmMYB33 genes upregulated. Furthermore, miR159 overexpressing and silencing soybean hairy roots exhibited strong resistance and susceptibility to H. glycines, respectively. In particular, miR159-GAMYB genes are reported to be involve in GA signaling and metabolism. Therefore, we then investigated the effects of GA application on the expression of miR159-GAMYB module and the development of H. glycines. We found that GA directly controls the miR159-GAMYB module, and exogenous GA application enhanced endogenous biologically active GA1 and GA3, the abundance of miR159, lowered the expression of GmMYB33 genes and delayed the development of H. glycines. Moreover, SCN infection also results in endogenous GA content decreased in soybean roots. In summary, the soybean miR159-GmMYB33 module was directly involved in the GA-modulated soybean resistance to H. glycines.
Collapse
Affiliation(s)
- Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nawei Qi
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuan Zhou
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (N.Q.); (Y.Z.); (Y.W.); (X.Z.); (Y.X.); (X.L.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| |
Collapse
|
42
|
Hu H, Guo Z, Yang J, Cui J, Zhang Y, Xu J. Transcriptome and microRNA Sequencing Identified miRNAs and Target Genes in Different Developmental Stages of the Vascular Cambium in Cryptomeria fortunei Hooibrenk. FRONTIERS IN PLANT SCIENCE 2021; 12:751771. [PMID: 34868137 PMCID: PMC8638621 DOI: 10.3389/fpls.2021.751771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/28/2021] [Indexed: 05/15/2023]
Abstract
Cryptomeria fortunei Hooibrenk is an important fast-growing coniferous timber species that is widely used in landscaping. Recently, research on timber quality has gained substantial attention in the field of tree breeding. Wood is the secondary xylem formed by the continuous inward division and differentiation of the vascular cambium; therefore, the development of the vascular cambium is particularly important for wood quality. In this study, we analyzed the transcriptomes of the cambial zone in C. fortunei during different developmental stages using Illumina HiSeq sequencing, focusing on general transcriptome and microRNA (miRNA) data. We performed functional annotation of the differentially expressed genes (DEGs) in the different stages identified by transcriptome sequencing and generated 15 miRNA libraries yielding 4.73 Gb of clean reads. The most common length of the filtered miRNAs was 21nt, accounting for 33.1% of the total filtered reads. We annotated a total of 32 known miRNA families. Some miRNAs played roles in hormone signal transduction (miR159, miR160, and miR166), growth and development (miR166 and miR396), and the coercion response (miR394 and miR395), and degradome sequencing showed potential cleavage sites between miRNAs and target genes. Differential expression of miRNAs and target genes and functional validation of the obtained transcriptome and miRNA data provide a theoretical basis for further elucidating the molecular mechanisms of cellular growth and differentiation, as well as wood formation in the vascular cambium, which will help improve the wood quality of C. fortunei.
Collapse
Affiliation(s)
- Hailiang Hu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhenhao Guo
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yingting Zhang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jin Xu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
43
|
Bhadresha K, Patel M, Brahmbhatt J, Jain N, Rawal R. Targeting Bone Metastases Signaling Pathway Using Moringa oleifera Seed Nutri-miRs: A Cross Kingdom Approach. Nutr Cancer 2021; 74:2522-2539. [PMID: 34751606 DOI: 10.1080/01635581.2021.2001547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Moringa oleifera is a medicinally important plant that has various medical and nutritional uses. Plant miRNAs are a class of non-coding endogenous small RNAs that regulate human-specific mRNA but the mechanistic actions are largely unknown. Here, in this study, we aim to explore the mechanistic action and influence of M. oleifera seed miRNAs on vital human target genes using computer based approaches. The M. oleifera seed miRNAs sequence was taken from published data and identified its human gene targets using a psRNA target analysis server. We identified 94 miRNAs that are able to significantly regulate 47 human target genes, which has enormous biological and functional importance. Out of 47 human targeted genes, 23 genes were found to be associated with PI3K-AKT, RUNX, and MAPK1/MAPK3 signaling pathway which has shown to play key roles in bone metastases during cancer progression. The M. oleifera seed miRNAs hold a strong potential for future research that might uncover the possibility of miRNA-facilitated cross-kingdom regulation and therapeutic targets for bone metastases.
Collapse
Affiliation(s)
- Kinjal Bhadresha
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jpan Brahmbhatt
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Nayan Jain
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh Rawal
- Department of Life Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| |
Collapse
|
44
|
Barrera-Rojas CH, Otoni WC, Nogueira FTS. Shaping the root system: the interplay between miRNA regulatory hubs and phytohormones. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6822-6835. [PMID: 34259838 DOI: 10.1093/jxb/erab299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
The root system commonly lies underground, where it provides anchorage for the aerial organs, as well as nutrients and water. Both endogenous and environmental cues contribute to the establishment of the root system. Among the endogenous cues, microRNAs (miRNAs), transcription factors, and phytohormones modulate root architecture. miRNAs belong to a subset of endogenous hairpin-derived small RNAs that post-transcriptionally control target gene expression, mostly transcription factors, comprising the miRNA regulatory hubs. Phytohormones are signaling molecules involved in most developmental processes. Some miRNAs and targets participate in more than one hormonal pathway, thereby providing new bridges in plant hormonal crosstalk. Unraveling the intricate network of molecular mechanisms underlying the establishment of root systems is a central aspect in the development of novel strategies for plant breeding to increase yield and optimize agricultural land use. In this review, we summarize recent findings describing the molecular mechanisms associated with the interplay between miRNA regulatory hubs and phytohormones to ensure the establishment of a proper root system. We focus on post-embryonic growth and development of primary, lateral, and adventitious roots. In addition, we discuss novel insights for future research on the interaction between miRNAs and phytohormones in root architecture.
Collapse
Affiliation(s)
- Carlos Hernán Barrera-Rojas
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Sao Paulo, Brazil
| | - Wagner Campos Otoni
- Department of Plant Biology, Federal University of Viçosa, Viçosa, MG, Brazil
| | - Fabio Tebaldi Silveira Nogueira
- Laboratory of Molecular Genetics of Plant Development, Department of Biological Sciences, Luiz de Queiroz College of Agriculture, University of Sao Paulo, Piracicaba, Sao Paulo, Brazil
| |
Collapse
|
45
|
The Regulation of Plant Vegetative Phase Transition and Rejuvenation: miRNAs, a Key Regulator. EPIGENOMES 2021; 5:epigenomes5040024. [PMID: 34968248 PMCID: PMC8715473 DOI: 10.3390/epigenomes5040024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
In contrast to animals, adult organs in plants are not formed during embryogenesis but generated from meristematic cells as plants advance through development. Plant development involves a succession of different phenotypic stages and the transition between these stages is termed phase transition. Phase transitions need to be tightly regulated and coordinated to ensure they occur under optimal seasonal, environmental conditions. Polycarpic perennials transition through vegetative stages and the mature, reproductive stage many times during their lifecycles and, in both perennial and annual species, environmental factors and culturing methods can reverse the otherwise unidirectional vector of plant development. Epigenetic factors regulating gene expression in response to internal cues and external (environmental) stimuli influencing the plant’s phenotype and development have been shown to control phase transitions. How developmental and environmental cues interact to epigenetically alter gene expression and influence these transitions is not well understood, and understanding this interaction is important considering the current climate change scenarios, since epigenetic maladaptation could have catastrophic consequences for perennial plants in natural and agricultural ecosystems. Here, we review studies focusing on the epigenetic regulators of the vegetative phase change and highlight how these mechanisms might act in exogenously induced plant rejuvenation and regrowth following stress.
Collapse
|
46
|
Kunej U, Jakše J, Radišek S, Štajner N. Identification and Characterization of Verticillium nonalfalfae-Responsive MicroRNAs in the Roots of Resistant and Susceptible Hop Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:1883. [PMID: 34579416 PMCID: PMC8471970 DOI: 10.3390/plants10091883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
MicroRNAs are 21- to 24-nucleotide-long, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They can modulate various biological processes, including plant response and resistance to fungal pathogens. Hops are grown for use in the brewing industry and, recently, also for the pharmaceutical industry. Severe Verticillium wilt caused by the phytopathogenic fungus Verticillium nonalfalfae, is the main factor in yield loss in many crops, including hops (Humulus lupulus L.). In our study, we identified 56 known and 43 novel miRNAs and their expression patterns in the roots of susceptible and resistant hop cultivars after inoculation with V. nonalfalfae. In response to inoculation with V. nonalfalfae, we found five known and two novel miRNAs that are differentially expressed in the susceptible cultivar and six known miRNAs in the resistant cultivar. Differentially expressed miRNAs target 49 transcripts involved in protein localization and pigment synthesis in the susceptible cultivar, whereas they are involved in transcription factor regulation and hormone signalling in the resistant cultivar. The results of our study suggest that the susceptible and resistant hop cultivars respond differently to V. nonalfalfae inoculation at the miRNA level and that miRNAs may contribute to the successful defence of the resistant cultivar.
Collapse
Affiliation(s)
- Urban Kunej
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia;
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.K.); (J.J.)
| |
Collapse
|
47
|
Srivastava S, Suprasanna P. MicroRNAs: Tiny, powerful players of metal stress responses in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:928-938. [PMID: 34246107 DOI: 10.1016/j.plaphy.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/14/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.
Collapse
Affiliation(s)
- Sudhakar Srivastava
- Plant Stress Biology Laboratory, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, Maharashtra, India
| |
Collapse
|
48
|
The Sw5a gene confers resistance to ToLCNDV and triggers an HR response after direct AC4 effector recognition. Proc Natl Acad Sci U S A 2021; 118:2101833118. [PMID: 34385303 DOI: 10.1073/pnas.2101833118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several attempts have been made to identify antiviral genes against Tomato leaf curl New Delhi virus (ToLCNDV) and related viruses. This has led to the recognition of Ty genes (Ty1-Ty6), which have been successful in developing virus-resistant crops to some extent. Owing to the regular appearance of resistance-breaking strains of these viruses, it is important to identify genes related to resistance. In the present study, we identified a ToLCNDV resistance (R) gene, SlSw5a, in a ToLCNDV-resistant tomato cultivar, H-88-78-1, which lacks the known Ty genes. The expression of SlSw5a is controlled by the transcription factor SlMyb33, which in turn is regulated by microRNA159 (sly-miR159). Virus-induced gene silencing of either SlSw5a or SlMyb33 severely increases the disease symptoms and viral titer in leaves of resistant cultivar. Moreover, in SlMyb33-silenced plants, the relative messenger RNA level of SlSw5a was reduced, suggesting SlSw5a is downstream of the sly-miR159-SlMyb33 module. We also demonstrate that SlSw5a interacts physically with ToLCNDV-AC4 (viral suppressor of RNA silencing) to trigger a hypersensitive response (HR) and generate reactive oxygen species at infection sites to limit the spread of the virus. The "RTSK" motif in the AC4 C terminus is important for the interaction, and its mutation completely abolishes the interaction with Sw5a and HR elicitation. Overall, our research reports an R gene against ToLCNDV and establishes a connection between the upstream miR159-Myb33 module and its downstream target Sw5a to activate HR in the tomato, resulting in geminivirus resistance.
Collapse
|
49
|
Regmi R, Newman TE, Kamphuis LG, Derbyshire MC. fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen. BMC PLANT BIOLOGY 2021; 21:366. [PMID: 34380425 PMCID: PMC8356391 DOI: 10.1186/s12870-021-03148-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Small RNAs are short non-coding RNAs that are key gene regulators controlling various biological processes in eukaryotes. Plants may regulate discrete sets of sRNAs in response to pathogen attack. Sclerotinia sclerotiorum is an economically important pathogen affecting hundreds of plant species, including the economically important oilseed B. napus. However, there are limited studies on how regulation of sRNAs occurs in the S. sclerotiorum and B. napus pathosystem. RESULTS We identified different classes of sRNAs from B. napus using high throughput sequencing of replicated mock and infected samples at 24 h post-inoculation (HPI). Overall, 3999 sRNA loci were highly expressed, of which 730 were significantly upregulated during infection. These 730 up-regulated sRNAs targeted 64 genes, including disease resistance proteins and transcriptional regulators. A total of 73 conserved miRNA families were identified in our dataset. Degradome sequencing identified 2124 cleaved mRNA products from these miRNAs from combined mock and infected samples. Among these, 50 genes were specific to infection. Altogether, 20 conserved miRNAs were differentially expressed and 8 transcripts were cleaved by the differentially expressed miRNAs miR159, miR5139, and miR390, suggesting they may have a role in the S. sclerotiorum response. A miR1885-triggered disease resistance gene-derived secondary sRNA locus was also identified and verified with degradome sequencing. We also found further evidence for silencing of a plant immunity related ethylene response factor gene by a novel sRNA using 5'-RACE and RT-qPCR. CONCLUSIONS The findings in this study expand the framework for understanding the molecular mechanisms of the S. sclerotiorum and B. napus pathosystem at the sRNA level.
Collapse
Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia.
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| |
Collapse
|
50
|
|