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Guo Y, He S, Wang HL, Lin H, Zhang Y, Zhao Y. MicroRNA257 promotes secondary growth in hybrid poplar. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108870. [PMID: 38914038 DOI: 10.1016/j.plaphy.2024.108870] [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: 10/12/2023] [Revised: 04/30/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Populus, a significant fast-growing tree species with global afforestation and energy potential, holds considerable economic value. The abundant production of secondary xylem by trees, which serves as a vital resource for industrial purposes and human sustenance, necessitates the orchestration of various regulatory mechanisms, encompassing transcriptional regulators and microRNAs (miRNAs). Nevertheless, the investigation of microRNA-mediated regulation of poplar secondary growth remains limited. In this study, we successfully isolated a novel microRNA (Pag-miR257) from 84 K poplar and subsequently integrated it into the 35 S overexpression vector. The overexpression of Pag-miR257 resulted in notable increases in plant height, stem diameter, and fresh weight. Additionally, the overexpression of Pag-miR257 demonstrated a significant enhancement in net photosynthetic rate. The findings from the examination of cell wall autofluorescence indicated a substantial increase in both xylem area and the number of vessels in poplar plants overexpressing Pag-miR257. Furthermore, the cell wall of the Pag-miR257 overexpressing plants exhibited thickening as observed through transmission electron microscopy. Moreover, the Fourier Transforms Infrared (FTIR) analysis and phloroglucinol-HCl staining revealed an elevation in lignin content in Pag-miR257 overexpressing poplar plants. The findings of this study suggest that microRNA257 may play a role in the control of secondary growth in poplar stems, thereby potentially enhancing the development of wood engineering techniques for improved material and energy production.
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Affiliation(s)
- Yayu Guo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuhang He
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; Dongguan No.1 Senior High School, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongxia Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuqian Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuanyuan Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China; National Engineering Research Center for Tree Breeding and Ecological Restoration, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
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Madhu, Sharma A, Kaur A, Singh K, Upadhyay SK. Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111902. [PMID: 37879539 DOI: 10.1016/j.plantsci.2023.111902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/23/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their clustering into three groups, which are also related to the subcellular localization in the peroxisome matrix, peroxisome membrane, and chloroplast. Each TaMDHAR protein consisted of two conserved domains; Pyr_redox and Pyr_redox_2 of the pyridine nucleotide disulfide oxidoreductase family. The occurrence of diverse groups of cis-regulatory elements in the promoter region and their interaction with numerous transcription factors suggest assorted functions of TaMDHARs in growth and development and in light, phytohormones, and stress responses. Expression analysis in various tissues further revealed their importance in vegetative and reproductive development. In addition, the differential gene expression and enhanced enzyme activity during drought, heat, and salt treatments exposed their role in abiotic stress response. Interaction of MDHARs with various antioxidant enzymes and biochemicals related to the ascorbate-glutathione cycle exposed their synchronized functioning. Interaction with auxin indicated the probability of cross-talk between antioxidants and auxin signaling. The miR168a, miR169, miR172 and others interaction with various TaMDHARs further directed their association with developmental processes and stress responses. The current study provides extensive information about the importance of TaMDHARs, moreover, the precise role of each gene needs to be established in future studies.
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Affiliation(s)
- Madhu
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
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Yang L, Ping T, Lu W, Song S, Wang J, Wang Q, Chai G, Bai Y, Chen Y. Genome-wide identification of auxin-responsive microRNAs in the poplar stem. Genes Genomics 2023; 45:1073-1083. [PMID: 37336805 DOI: 10.1007/s13258-023-01385-7] [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: 09/27/2022] [Accepted: 04/01/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. OBJECTIVE This report was designed to identify auxin-responsive miRNAs during wood formation. METHODS Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. RESULTS In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. CONCLUSIONS Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.
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Affiliation(s)
- Lihua Yang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tao Ping
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenjin Lu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sangfa Song
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qiao Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
| | - Yue Bai
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
| | - Yan Chen
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China.
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Wang L, Hou J, Xu H, Zhang Y, Huang R, Wang D, He XQ. The PtoTCP20-miR396d-PtoGRF15 module regulates secondary vascular development in Populus. PLANT COMMUNICATIONS 2023; 4:100494. [PMID: 36419363 PMCID: PMC10030372 DOI: 10.1016/j.xplc.2022.100494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/07/2022] [Accepted: 11/18/2022] [Indexed: 05/04/2023]
Abstract
Secondary vascular development is a key biological characteristic of woody plants and the basis of wood formation. Our understanding of gene expression regulation and dynamic changes in microRNAs (miRNAs) during secondary vascular development is still limited. Here we present an integrated analysis of the miRNA and mRNA transcriptome of six phase-specific tissues-the shoot apex, procambium, primary vascular tissue, cambium, secondary phloem, and secondary xylem-in Populus tomentosa. Several novel regulatory modules, including the PtoTCP20-miR396d-PtoGRF15 module, were identified during secondary vascular development in Populus. A series of biochemical and molecular experiments confirmed that PtoTCP20 activated transcription of the miR396d precursor gene and that miR396d targeted PtoGRF15 to downregulate its expression. Plants overexpressing miR396d (35S:miR396d) showed enhanced secondary growth and increased xylem production. Conversely, during the transition from primary to secondary vascular development, plants with downregulated PtoTCP20expression (PtoTCP20-SRDX), downregulated miR396 expression (35S:STTM396), and PtoGRF15 overexpression (35S:PtoGRF15) showed delayed secondary growth. Novel regulatory modules were identified by integrated analysis of the miRNA and mRNA transcriptome, and the regulatory role of the PtoTCP20-miR396d-PtoGRF15 signaling cascade in secondary vascular development was validated in Populus, providing information to support improvements in forest cultivation and wood properties.
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Affiliation(s)
- Lingyan Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jie Hou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Huimin Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yufei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Runzhou Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Donghui Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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Shi Q, Tian D, Wang J, Chen A, Miao Y, Chen Y, Li J, Wu X, Zheng B, Guo W, Shi X. Overexpression of miR390b promotes stem elongation and height growth in Populus. HORTICULTURE RESEARCH 2023; 10:uhac258. [PMID: 36778185 PMCID: PMC9907050 DOI: 10.1093/hr/uhac258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/18/2022] [Indexed: 06/18/2023]
Abstract
MicroRNA390 (miR390) is involved in plant growth and development by down-regulating the expression of the downstream genes trans-acting short interfering RNA3 (TAS3) and AUXIN RESPONSE FACTORs (ARFs). There is a scarcity of research on the involvement of the miR390-TAS3-ARFs pathway in the stem development of Populus. Here, differentially expressed miRNAs during poplar stem development were screened by small RNA sequencing analysis, and a novel function of miR390b in stem development was revealed. Overexpression of miR390b (OE-miR390b) resulted in a large increase in the number of xylem fiber cells and a slight decrease in the cell length at the longitudinal axis. Overall increases in stem elongation and plant height were observed in the OE-miR390b plants. According to transcriptome sequencing results and transient co-expression analysis, TAS3.1 and TAS3.2 were identified as the target genes of miR390 in poplar and were negatively regulated by miR390 in the apex. The transcription levels of ARF3.2 and ARF4 were significantly repressed in OE-miR390b plants and strongly negatively correlated with the number of xylem fiber cells along the longitudinal axis. These findings indicate that the conserved miR390-TAS3-ARFs pathway in poplar is involved in stem elongation and plant height growth.
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Affiliation(s)
- Qiaofang Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongdong Tian
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jieyu Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Aoli Chen
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing Miao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Chen
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Li
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Poplar Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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Kaur A, Sharma A, Dixit S, Singh K, Upadhyay SK. OSCA Genes in Bread Wheat: Molecular Characterization, Expression Profiling, and Interaction Analyses Indicated Their Diverse Roles during Development and Stress Response. Int J Mol Sci 2022; 23:ijms232314867. [PMID: 36499199 PMCID: PMC9737358 DOI: 10.3390/ijms232314867] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
The hyperosmolality-gated calcium-permeable channels (OSCA) are pore-forming transmembrane proteins that function as osmosensors during various plant developmental processes and stress responses. In our analysis, through in silico approaches, a total of 42 OSCA genes are identified in the Triticum aestivum genome. A phylogenetic analysis reveals the close clustering of the OSCA proteins of Arabidopsis thaliana, Oryza sativa, and T. aestivum in all the clades, suggesting their origin before the divergence of dicots and monocots. Furthermore, evolutionary analyses suggest the role of segmental and tandem duplication events (Des) and purifying selection pressure in the expansion of the OSCA gene family in T. aestivum. Expression profiling in various tissue developmental stages and under abiotic and biotic stress treatments reveals the probable functioning of OSCA genes in plant development and the stress response in T. aestivum. In addition, protein-protein and protein-chemical interactions reveal that OSCA proteins might play a putative role in Ca2+-mediated developmental processes and adaptive responses. The miRNA interaction analysis strengthens the evidence for their functioning in various biological processes and stress-induced signaling cascades. The current study could provide a foundation for the functional characterization of TaOSCA genes in future studies.
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Affiliation(s)
- Amandeep Kaur
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Alok Sharma
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Sameer Dixit
- Department of Biology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Santosh Kumar Upadhyay
- Department of Botany, Panjab University, Chandigarh 160014, India
- Correspondence: or ; Tel.: +91-172-2534001; Fax: +91-172-2779510
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Ding C, Shen T, Ran N, Zhang H, Pan H, Su X, Xu M. Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar. Int J Mol Sci 2022; 23:ijms23094537. [PMID: 35562928 PMCID: PMC9100975 DOI: 10.3390/ijms23094537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/27/2022] [Accepted: 04/14/2022] [Indexed: 02/04/2023] Open
Abstract
Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation.
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Affiliation(s)
- Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Na Ran
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Heng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Huixin Pan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; (T.S.); (N.R.); (H.Z.); (H.P.)
- Correspondence: (X.S.); (M.X.); Tel.: +86-136-4130-7199 (X.S.); +86-150-9430-7586 (M.X.)
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Pawełkowicz ME, Skarzyńska A, Koter MD, Turek S, Pląder W. miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2022; 23:ijms23084317. [PMID: 35457133 PMCID: PMC9031375 DOI: 10.3390/ijms23084317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA's target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants' somaclonal variation.
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Luo X, Luo S, Fu Y, Kong C, Wang K, Sun D, Li M, Yan Z, Shi Q, Zhang Y. Genome-Wide Identification and Comparative Profiling of MicroRNAs Reveal Flavonoid Biosynthesis in Two Contrasting Flower Color Cultivars of Tree Peony. FRONTIERS IN PLANT SCIENCE 2022; 12:797799. [PMID: 35058956 PMCID: PMC8763678 DOI: 10.3389/fpls.2021.797799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/19/2021] [Indexed: 05/08/2023]
Abstract
MicroRNA (miRNA)-mediated gene regulation is involved in various physiological processes in plants. Flower color is one of the vital ornamental traits of tree peony (Paeonia suffruticosa Andr.). However, the yellow-flowered tree peony cultivars are particularly rare. To elucidate the miRNA-mediated gene regulatory mechanism underlying yellow pigmentation in tree peony, we combined pigment assessment, miRNA identification, expression analysis, and gene functional verification in two contrasting flower color cultivars "High Noon" and "Roufurong." Flavones/flavonols and anthocyanins were found to be the main contributors to the coloration of "High Noon" and "Roufurong" petals, respectively. Subsequently, miRNA analysis based on available genome data identified 9 differentially expressed miRNAs and 12 relevant target genes implicated in flavonoid biosynthesis. Their dynamic expression patterns determined the key role of mdm-miR156b-PsSPL2 module in yellow pigmentation of tree peony flowers. The sequence analysis and subcellular localization validated that PsSPL2 might function as a nuclear-localized transcription factor. Overexpression of PsSPL2 in tobacco resulted in a decrease of anthocyanin content and down-regulation of NtF3'H and NtDFR transcripts. PsSPL2-silenced petals exhibited lighter yellow color, and the contents of THC, Ap, and Ch decreased significantly. Meanwhile, expression levels of PsCHS, PsCHI, and PsF3H were significantly decreased in the petals with PsSPL2 silencing, while those of PsF3'H and PsDFR were remarkably increased. This study offers a novel insight into yellow pigmentation-related miRNA regulation network in tree peony, and further provides the valuable information on physiological changes during yellow coloring process of tree peony.
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Affiliation(s)
- Xiaoning Luo
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Sha Luo
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Yaqi Fu
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Chen Kong
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Kai Wang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Daoyang Sun
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Mengchen Li
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Zhenguo Yan
- Academy of Agricultural Planning and Engineering, MARA, Beijing, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
| | - Yanlong Zhang
- College of Landscape Architecture and Art, Northwest A&F University, Yangling, China
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Xu J, Xian Q, Zhang N, Wang K, Zhou X, Li Y, Dong J, Chen X. Identification of miRNA-Target Gene Pairs Responsive to Fusarium Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles. Biomolecules 2021; 11:1620. [PMID: 34827618 PMCID: PMC8615934 DOI: 10.3390/biom11111620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium wilt (FW) of cucumber (Cucumis sativus L.) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to FW remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar 'Rijiecheng', which is resistant to FW. The integrated analysis identified FW-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that JRL3 (Csa2G362470), which is targeted by miR319a, and BEE1 (Csa1G024150), DAHP1 (Csa2G369040), and PERK2 (Csa4G642480), which are targeted by miR6300, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that miR319a-JRL3, miR6300-BEE1, miR6300-DAHP1 and miR6300-PERK2 regulate cucumber defenses against FW, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to FW.
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Affiliation(s)
- Jun Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Qianqian Xian
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Ningyuan Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Ke Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Xin Zhou
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Yansong Li
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Jingping Dong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (Q.X.); (N.Z.); (K.W.); (X.Z.); (Y.L.); (J.D.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300192, China
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11
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Wang J, Zhou H, Zhao Y, Jiang C, Li J, Tang F, Liu Y, Zhao S, Hu J, Song X, Lu MZ. PagGRF12a interacts with PagGIF1b to regulate secondary xylem development through modulating PagXND1a expression in Populus alba × P. glandulosa. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1683-1694. [PMID: 33913591 DOI: 10.1111/jipb.13102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Growth-regulating factors (GRFs) are important regulators of plant development and growth, but their possible roles in xylem development in woody plants remain unclear. Here, we report that Populus alba × Papulus glandulosa PagGRF12a negatively regulates xylem development in poplar. PagGRF12a is expressed in vascular tissues. Compared to non-transgenic control plants, transgenic poplar plants overexpressing PagGRF12a exhibited reduced xylem width and plants with repressed expression of PagGRF12a exhibited increased xylem width. Xylem NAC domain 1 (XND1) encodes a NAC domain transcription factor that regulates xylem development and transcriptional analyses revealed that PagXND1a is highly upregulated in PagGRF12a-overexpressing plants and downregulated in PagGRF12a-suppressed plants, indicating that PagGRF12a may regulate xylem development through PagXND1a. Transient transcriptional assays and chromatin immunoprecipitation-polymerase chain reaction assays confirmed that PagGRF12a directly upregulates PagXND1a. In addition, PagGRF12a interacts with the GRF-Interacting Factor (GIF) PagGIF1b, and this interaction enhances the effects of PagGRF12a on PagXND1a. Our results indicate that PagGRF12a inhibits xylem development by upregulating the expression of PagXND1a.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jihong Li
- Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yingli Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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12
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Chu L, He X, Shu W, Wang L, Tang F. Knockdown of miR393 Promotes the Growth and Biomass Production in Poplar. FRONTIERS IN PLANT SCIENCE 2021; 12:714907. [PMID: 34335671 PMCID: PMC8317616 DOI: 10.3389/fpls.2021.714907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Short tandem target mimic (STTM), which is composed of two short sequences mimicking small RNA target sites, separated by a linker of optimal size, can block the functions of all members in a miRNA family. microRNA393 (miR393), which is one of the conserved miRNA families in plants, can regulate plant root growth, leaf development, plant architecture, and stress resistance. In order to verify the role of miR393 in the secondary growth of trees, we created its STTM transgenic poplar lines (STTM393). The expression of miR393 in STTM393 lines was reduced by over 10 times compared with the control plants. STTM393 lines showed promoted growth with about 20% higher, 15% thicker, and 2-4 more internodes than the control plants after 3 months of growth. The cross-section of the stems showed that STTM393 lines had wider phloem, xylem, and more cambium cell layers than control plants, and the lignin content in STTM393 lines was also higher as revealed by staining and chemical determination. Based on the transcriptome analysis, the genes related to the auxin signaling pathway, cell cyclin, cell expansion, and lignin synthesis had higher expression in STTM393 lines than that in control plants. The higher expression levels of FBL family members suggested that the auxin signaling pathway was strengthened in STTM393 lines to promote plant growth. Therefore, the knockdown of miR393 using the STTM approach provides a way to improve poplar growth and biomass production.
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Affiliation(s)
- Liwei Chu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xuejiao He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wenbo Shu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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13
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Wang J, Zhou H, Zhao Y, Sun P, Tang F, Song X, Lu MZ. Characterization of poplar growth-regulating factors and analysis of their function in leaf size control. BMC PLANT BIOLOGY 2020; 20:509. [PMID: 33153427 PMCID: PMC7643314 DOI: 10.1186/s12870-020-02699-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/13/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Growth-regulating factors (GRFs) are plant-specific transcription factors that control organ size. Nineteen GRF genes were identified in the Populus trichocarpa genome and one was reported to control leaf size mainly by regulating cell expansion. In this study, we further characterize the roles of the other poplar GRFs in leaf size control in a similar manner. RESULTS The 19 poplar GRF genes were clustered into six groups according to their phylogenetic relationship with Arabidopsis GRFs. Bioinformatic analysis, degradome, and transient transcription assays showed that 18 poplar GRFs were regulated by miR396, with GRF12b the only exception. The functions of PagGRF6b (Pag, Populus alba × P. glandulosa), PagGRF7a, PagGRF12a, and PagGRF12b, representing three different groups, were investigated. The results show that PagGRF6b may have no function on leaf size control, while PagGRF7a functions as a negative regulator of leaf size by regulating cell expansion. By contrast, PagGRF12a and PagGRF12b may function as positive regulators of leaf size control by regulating both cell proliferation and expansion, primarily cell proliferation. CONCLUSIONS The diversity of poplar GRFs in leaf size control may facilitate the specific, coordinated regulation of poplar leaf development through fine adjustment of cell proliferation and expansion.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Ludong University, Yantai, 264025, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Pengbo Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
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14
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Li H, Huang X, Li W, Lu Y, Dai X, Zhou Z, Li Q. MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation. PLANT CELL REPORTS 2020; 39:1199-1217. [PMID: 32577818 DOI: 10.1007/s00299-020-02559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/12/2020] [Indexed: 05/22/2023]
Abstract
MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.
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Affiliation(s)
- Hui Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanfeng Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Zaizhi Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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15
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Fan D, Li C, Fan C, Hu J, Li J, Yao S, Lu W, Yan Y, Luo K. MicroRNA6443-mediated regulation of FERULATE 5-HYDROXYLASE gene alters lignin composition and enhances saccharification in Populus tomentosa. THE NEW PHYTOLOGIST 2020; 226:410-425. [PMID: 31849071 DOI: 10.1111/nph.16379] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/01/2019] [Indexed: 05/22/2023]
Abstract
Ferulate 5-hydroxylase (F5H) is a limiting enzyme involved in biosynthesizing sinapyl (S) monolignol in angiosperms. Genetic regulation of F5H can influence S monolignol synthesis and therefore improve saccharification efficiency and biofuel production. To date, little is known about whether F5H is post-transcriptionally regulated by endogenous microRNAs (miRNAs) in woody plants. Here, we report that a microRNA, miR6443, specifically regulates S lignin biosynthesis during stem development in Populus tomentosa. In situ hybridization showed that miR6443 is preferentially expressed in vascular tissues. We further identified that F5H2 is the direct target of miR6443. Overexpression of miR6443 decreased the transcript level of F5H2 in transgenic plants, resulting in a significant reduction in S lignin content. Conversely, reduced miR6443 expression by short tandem target mimics (STTM) elevated F5H2 transcripts, therefore increasing S lignin composition. Introduction of a miR6443-resistant form of F5H2 into miR6443-overexpression plants restored lignin ectopic composition, supporting that miR6443 specifically regulated S lignin biosynthesis by repressing F5H2 in P. tomentosa. Furthermore, saccharification assays revealed decreased hexose yields by 7.5-24.5% in miR6443-overexpression plants compared with the wild-type control, and increased hexoses yields by 13.2-14.6% in STTM6443-overexpression plants. Collectively, we demonstrate that miR6443 modulates S lignin biosynthesis by specially regulating F5H2 in P. tomentosa.
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Affiliation(s)
- Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chaofeng Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chunfen Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Jian Hu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jianqiu Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shu Yao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wanxiang Lu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yangyang Yan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
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16
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Identification of Grafting-Responsive MicroRNAs Associated with Growth Regulation in Pecan [Carya illinoinensis (Wangenh.) K. Koch]. FORESTS 2020. [DOI: 10.3390/f11020196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pecan [Carya illinoinensis (Wangenh.) K. Koch] is an economically important nut tree and grafting is often used for clonal propagation of cultivars. However, there is a lack of research on the effects of rootstocks on scions, which are meaningful targets for directed breeding of pecan grafts. MicroRNAs (miRNAs) play an important role in many biological processes, but the mechanism underlying the involvement of miRNAs in grafting-conferred physiological changes is unclear. To identify the grafting-responsive miRNAs that may be involved in the regulation of growth in grafted pecan, six small RNA libraries were constructed from the phloem of two groups of grafts with significantly different growth performance on short and tall rootstocks. A total of 441 conserved miRNAs belonging to 42 miRNA families and 603 novel miRNAs were identified. Among the identified miRNAs, 24 (seven conserved and 17 novel) were significantly differentially expressed by the different grafts, implying that they might be responsive to grafting and potentially involved in the regulation of graft growth. Ninety-five target genes were predicted for the differentially expressed miRNAs; gene annotation was available for 33 of these. Analysis of their targets suggested that the miRNAs may regulate auxin transport, cell activity, and inorganic phosphate (Pi) acquisition, and thereby, mediate pecan graft growth. Use of the recently-published pecan genome enabled identification of a substantial population of miRNAs, which are now available for further research. We also identified the grafting-responsive miRNAs and their potential roles in pecan graft growth, providing a basis for research on long-distance regulation in grafted pecan.
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17
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Chhetri HB, Furches A, Macaya-Sanz D, Walker AR, Kainer D, Jones P, Harman-Ware AE, Tschaplinski TJ, Jacobson D, Tuskan GA, DiFazio SP. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2020; 11:545748. [PMID: 33013968 PMCID: PMC7509168 DOI: 10.3389/fpls.2020.545748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/21/2020] [Indexed: 05/04/2023]
Abstract
To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the distribution range in western North America. Using GEMMA mixed model analysis, we tested for the association of 25 phenotypic traits and nine multitrait combinations with 6.741 million SNPs covering the entire genome. Broad-sense trait heritabilities ranged from 0.117 to 0.477. Most traits were significantly correlated with geoclimatic variables suggesting a role of climate and geography in shaping the variation of this species. Fifty-seven SNPs from single trait GWAS and 11 SNPs from multitrait GWAS passed an FDR threshold of 0.05, leading to the identification of eight and seven nearby candidate genes, respectively. The percentage of phenotypic variance explained (PVE) by the significant SNPs for both single and multitrait GWAS ranged from 0.01% to 6.18%. To further evaluate the potential roles of candidate genes, we used a multi-omic network containing five additional data sets, including leaf and wood metabolite GWAS layers and coexpression and comethylation networks. We also performed a functional enrichment analysis on coexpression nearest neighbors for each gene model identified by the wood anatomical and morphological trait GWAS analyses. Genes affecting cell wall composition and transport related genes were enriched in wood anatomy and stomatal density trait networks. Signaling and metabolism related genes were also common in networks for stomatal density. For leaf morphology traits (leaf dry and wet weight) the networks were significantly enriched for GO terms related to photosynthetic processes as well as cellular homeostasis. The identified genes provide further insights into the genetic control of these traits, which are important determinants of the suitability and sustainability of improved genotypes for lignocellulosic biofuel production.
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Affiliation(s)
- Hari B. Chhetri
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Anna Furches
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Alejandro R. Walker
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - David Kainer
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Piet Jones
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Anne E. Harman-Ware
- Biosciences Center, and National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel Jacobson
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
- *Correspondence: Stephen P. DiFazio,
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18
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Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing. Biomolecules 2019; 9:biom9090483. [PMID: 31547414 PMCID: PMC6769560 DOI: 10.3390/biom9090483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA-mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.
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Tang F, Chu L, Shu W, He X, Wang L, Lu M. Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar. PLANT METHODS 2019; 15:35. [PMID: 30996729 PMCID: PMC6451301 DOI: 10.1186/s13007-019-0420-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a rapid and sensitive approach to identify miRNA and protein-coding gene expression in plants. However, because of the specially designated reverse transcription and shorter PCR products, very few reference genes have been identified for the quantitative analysis of miRNA expression in plants, and different internal reference genes are needed to normalize the expression of miRNAs and mRNA genes respectively. Therefore, it is particularly important to select the suitable common reference genes for normalization of quantitative PCR of miRNA and mRNA. RESULTS In this study, a modified reverse transcription PCR protocol was adopted for selecting and validating universal internal reference genes of mRNAs and miRNAs. Eight commonly used reference genes, four stably expressed novel genes in Populus tremula, three small noncoding RNAs and three conserved miRNAs were selected as candidate genes, and the stability of their expression was examined across a set of 38 tissue samples from four developmental stages of poplar clone 84K (Populus alba × Populus glandulosa). The expression stability of these candidate genes was evaluated systematically by four algorithms: geNorm, NormFinder, Bestkeeper and DeltaCt. The results showed that Eukaryotic initiation factor 4A III (EIF4A) and U6-2 were suitable for samples of the callus stage; U6-1 and U6-2 were best for the seedling stage; Protein phosphatase 2A-2 (PP2A-2) and U6-1 were best for the plant stage; and Protein phosphatase 2A-2 (PP2A-2) and Oligouridylate binding protein 1B (UBP) were the best reference genes in the adventitious root (AR) regeneration stage. CONCLUSIONS The purpose of this study was to identify the most appropriate reference genes for qRT-PCR of miRNAs and mRNAs in different tissues at several developmental stages in poplar. U6-1, EIF4A and PP2A-2 were the three most appropriate reference genes for qRT-PCR normalization of miRNAs and mRNAs during the plant regeneration process, and PP2A-2 and UBP represent the best reference genes in the AR regeneration stage of poplar. This work will benefit future studies of expression and function analysis of miRNAs and their target genes in poplar.
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Affiliation(s)
- Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Liwei Chu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Wenbo Shu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuejiao He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Lijuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
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Zhou H, Song X, Wei K, Zhao Y, Jiang C, Wang J, Tang F, Lu M. Growth-regulating factor 15 is required for leaf size control in Populus. TREE PHYSIOLOGY 2019; 39:381-390. [PMID: 30307572 DOI: 10.1093/treephys/tpy107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/09/2018] [Accepted: 09/05/2018] [Indexed: 05/14/2023]
Abstract
Growth-regulating factors (GRFs) are involved in various developmental events, particularly leaf development. However, the functions of GRFs in woody plants remain elusive. In this study, functional characterization of GRF15 in Populus was performed. Most GRFs are preferentially expressed in young leaves. As GRF15 was expressed at the highest level and with highest ratio in Populus species with large leaves, this gene was investigated through transgenic analyses. Promotor-β-glucuronidase analysis revealed expression of GRF15 at the leaf expansion zone. Additionally, GRF15 was found to be localized in the nucleus and regulated by miR396. Leaf size and palisade cell size were significantly increased and decreased in GRF15-overexpressing and dominant repression lines, respectively. Consistently, expression of EXPA11a, a homolog of cell-expansion marker EXPA11 in Arabidopsis, was strongly upregulated and downregulated in the GRF15-overexpressing and dominant repression lines, respectively, which was further manifested by activation of EXPA11a by GRF15 in transactivation assays. Therefore, GRF15 is required for leaf size control and primarily modulates cell expansion during leaf development in Populus.
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Affiliation(s)
- Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
| | - Kaili Wei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
| | - Mengzhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, China
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Qiu Z, He Y, Zhang Y, Guo J, Zhang L. Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes. Gene 2018; 677:32-40. [PMID: 30036657 DOI: 10.1016/j.gene.2018.07.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/23/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, have been shown to play essential roles in the regulation of gene expression at the post-transcriptional level. Although Paulownia tomentosa is an ecologically and economically important timber species due to its rapid growth, few efforts have focused on small RNAs (sRNAs) in the cambial tissues during winter and summer transition. In the present study, we identified 33 known miRNA families and 29 novel miRNAs which include 20 putative novel miRNAs* in P. tomentosa cambial tissues during winter and summer transition. Through differential expression analysis, we showed that 15 known miRNAs and 8 novel miRNAs were preferentially abundant in certain stage of cambial tissues. Based on the P. tomentosa mRNA transcriptome database, 1667 and 78 potential targets were predicted for 29 known and 20 novel miRNAs, respectively and the predicted targets are mostly transcription factors and functional genes. The targets of these miRNAs were enriched in "metabolic process" and "transcription regulation" by using Gene Ontology enrichment analysis. In addition, KEGG pathway analyses revealed the involvement of miRNAs in starch and sucrose metabolism and plant-pathogen interaction metabolism pathways. Noticeably, qRT-PCR expression analysis demonstrated that 9 miRNAs and their targets were existed a negative correlation in P. tomentosa cambial tissues. This study is the first to examine known and novel miRNAs and their potential targets in P. tomentosa cambial tissues during winter and summer transition and identify several candidate genes potentially regulating cambial phase transition, and thus provide a framework for further understanding of miRNAs functions in the regulation of cambial phase transition and wood formation in trees.
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Affiliation(s)
- Zongbo Qiu
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China.
| | - Yanyan He
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Yimeng Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Junli Guo
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
| | - Liang Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, PR China
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Zhao D, Wei M, Shi M, Hao Z, Tao J. Identification and comparative profiling of miRNAs in herbaceous peony (Paeonia lactiflora Pall.) with red/yellow bicoloured flowers. Sci Rep 2017; 7:44926. [PMID: 28317945 PMCID: PMC5357961 DOI: 10.1038/srep44926] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 02/15/2017] [Indexed: 02/05/2023] Open
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) is popular worldwide because of its gorgeous flower colour, and the yellow flower is the rarest. However, its mechanism of yellow formation is still unexplored from the post-translational level. In this study, the anatomy of the petal, cell sap pH and metal elements were investigated in bicoloured flower cultivar 'Jinhui' with red outer-petal and yellow inner-petal, and the yellow formation was influenced by the anatomy of petal, while not by the cell sap pH and metal elements. Subsequently, microRNAs sequencing (miRNA-seq) was used to identify small RNAs (sRNAs). A total of 4,172,810 and 3,565,152 specific unique sRNAs were obtained, 207 and 204 conserved miRNAs and 38 and 42 novel miRNAs were identified from red outer-petal and yellow inner-petal, respectively, which were confirmed by subcloning. Among these miRNAs, 163 conserved and 28 novel miRNAs were differentially expressed in two wheel of petals. And 5 differentially expressed miRNAs and their corresponding target genes related to yellow formation were screened, and their dynamic expression patterns confirmed that the yellow formation might be under the regulation of miR156e-3p-targeted squamosa promoter binding protein-like gene (SPL1). These results improve the understanding of miRNA regulation of the yellow formation in P. lactiflora.
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Affiliation(s)
- Daqiu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R. China
| | - Mengran Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R. China
| | - Min Shi
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R. China
| | - Zhaojun Hao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R. China
| | - Jun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, P.R. China
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