1
|
Xu P, Li Q, Liang W, Hu Y, Chen R, Lou K, Zhan L, Wu X, Pu J. A tissue-specific profile of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia lactiflora Pall. by transcriptome, small RNAs and degradome sequencing. PLoS One 2023; 18:e0279992. [PMID: 36701382 PMCID: PMC9879538 DOI: 10.1371/journal.pone.0279992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Paeonia lactiflora Pall. (Paeonia) has aroused many concerns due to its extensive medicinal value, in which monoterpene glucoside paeoniflorin and its derivatives are the active chemical components. However, little is known in the molecular mechanism of monoterpenoids biosynthesis, and the regulation network between small RNAs and mRNAs in monoterpenoids biosynthesis has not been investigated yet. Herein, we attempted to reveal the tissue-specific regulation network of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia by combining mRNA and miRNA expression data with degradome analysis. In all, 289 miRNAs and 30177 unigenes were identified, of which nine miRNAs from seven miRNA families including miR396, miR393, miR835, miR1144, miR3638, miR5794 and miR9555 were verified as monoterpenoids biosynthesis-related miRNAs by degradome sequencing. Moreover, the co-expression network analysis showed that four monoterpenoids-regulating TFs, namely AP2, MYBC1, SPL12 and TCP2, were putatively regulated by five miRNAs including miR172, miR828, miR858, miR156 and miR319, respectively. The present study will improve our knowledge of the molecular mechanisms of the paeoniaflorin and monoterpenoids biosynthesis mediated by miRNA to a new level, and provide a valuable resource for further study on Paeonia.
Collapse
Affiliation(s)
- Pan Xu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Quanqing Li
- Department of Pharmacy, Zhejiang Xiaoshan Hospital, Hangzhou, Zhejiang Province, China
| | - Weiqing Liang
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Yijuan Hu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Rubing Chen
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Kelang Lou
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Lianghui Zhan
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Xiaojun Wu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
| | - Jinbao Pu
- Center for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Research and Development of Chinese Medicine of Zhejiang Province, Hangzhou, Zhejiang Province, China
- * E-mail:
| |
Collapse
|
2
|
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
|
3
|
Zhang T, Tang Y, Luan Y, Cheng Z, Wang X, Tao J, Zhao D. Herbaceous peony AP2/ERF transcription factor binds the promoter of the tryptophan decarboxylase gene to enhance high-temperature stress tolerance. PLANT, CELL & ENVIRONMENT 2022; 45:2729-2743. [PMID: 35590461 DOI: 10.1111/pce.14357] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Global warming has multifarious adverse effects on plant growth and productivity. Nonetheless, the effects of endogenous phytomelatonin on the high-temperature resistance of plants and the underlying genetic mechanisms remain unclear. Here, herbaceous peony (Paeonia lactiflora Pall.) tryptophan decarboxylase (TDC) gene involved in phytomelatonin biosynthesis was shown to respond to high-temperature stress at the transcriptional level, and its transcript level was positively correlated with phytomelatonin production. Moreover, overexpression of PlTDC enhanced phytomelatonin production and high-temperature stress tolerance in transgenic tobacco, while silencing PlTDC expression decreased these parameters in P. lactiflora. In addition, a 2402 bp promoter fragment of PlTDC was isolated, and DNA pull-down assay revealed that one APETALA2/ethylene-responsive element-binding factor (AP2/ERF) transcription factor, PlTOE3, could specifically activate the PlTDC promoter, which was further verified by yeast one-hybrid assay and luciferase reporter assay. PlTOE3 was a nucleus-localized protein, and its transcript level responded to high-temperature stress. Additionally, transgenic tobacco overexpressing PlTOE3 showed enhanced phytomelatonin production and high-temperature stress tolerance, while silencing PlTDC expression obtained the opposite results. These results illustrated that PlTOE3 bound the PlTDC promoter to enhance high-temperature stress tolerance by increasing phytomelatonin production in P. lactiflora.
Collapse
Affiliation(s)
- Tingting Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuhan Tang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuting Luan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhuoya Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoxiao Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jun Tao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Daqiu Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| |
Collapse
|
4
|
Wu F, Xu J, Gao T, Huang D, Jin W. Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection. BMC PLANT BIOLOGY 2021; 21:496. [PMID: 34706648 PMCID: PMC8555085 DOI: 10.1186/s12870-021-03203-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. RESULTS First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. CONCLUSIONS Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.
Collapse
Affiliation(s)
- Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Tiantian Gao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Diao Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
| |
Collapse
|
5
|
Li C, Wang M, Qiu X, Zhou H, Lu S. Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production. Curr Pharm Biotechnol 2021; 22:341-359. [PMID: 32469697 DOI: 10.2174/1389201021666200529101942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field. OBJECTIVE This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production. RESULTS So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production. CONCLUSION The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.
Collapse
Affiliation(s)
- Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Hong Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| |
Collapse
|
6
|
UPLC-ESI-MS/MS Analysis and Evaluation of Antioxidant Activity of Total Flavonoid Extract from Paeonia lactiflora Seed Peel and Optimization by Response Surface Methodology (RSM). BIOMED RESEARCH INTERNATIONAL 2021; 2021:7304107. [PMID: 33681378 PMCID: PMC7906810 DOI: 10.1155/2021/7304107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 01/08/2023]
Abstract
In this study, the ultrasound-assisted extraction (UAE) of flavonoid from Paeonia lactiflora seed peel was optimized by response surface methodology (RSM). Single-factor experiments and a three-factor three-level Box-Behnken design (BBD) were performed to explore the effects of the following parameters on flavonoid extraction: ethanol concentration (X1), liquid-solid ratio (X2), and ultrasonic time (X3). The results showed that the optimal flavonoid yield (10.9045 mg RE/g) was as follows: ethanol concentration 62.93%, ultrasonic time 64.56 min, and liquid-solid ratio 24.86 mL/g. The optimized extract of P. lactiflora seed shell was further analyzed by UPLC-ESI-MS/MS, and 20 main flavonoids were identified and quantified, among which protocatechuic acid, vanillic acid, 4-hydroxybenzoic acid, and 3,4-dihydroxybenzaldehyde had the highest content. Furthermore, the results of the antioxidant test showed that the P. lactiflora seed peel extract obtained under optimized UAE conditions exhibited good antioxidant activity. The experimental results showed that ultrasound-assisted extraction was a fast, efficient, and simple method for extracting active ingredients from P. lactiflora seed peel, thereby making this byproduct a promising source of compounds in food and healthcare sectors.
Collapse
|
7
|
Gao X, Zhang Q, Zhao Y, Yang J, He H, Jia G. The lre-miR159a-LrGAMYB pathway mediates resistance to grey mould infection in Lilium regale. MOLECULAR PLANT PATHOLOGY 2020; 21:749-760. [PMID: 32319186 PMCID: PMC7214475 DOI: 10.1111/mpp.12923] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
Grey mould is one of the most determinative factors of lily growth and plays a major role in limiting lily productivity. MicroRNA159 (miR159) is a highly conserved microRNA in plants, and participates in the regulation of plant development and stress responses. Our previous studies revealed that lre-miR159a participates in the response of Lilium regale to Botrytis elliptica according to deep sequencing analyses; however, the response mechanism remains unknown. Here, lre-miR159a and its target LrGAMYB gene were isolated from L. regale. Transgenic Arabidopsis overexpressing lre-MIR159a exhibited larger leaves and smaller necrotic spots on inoculation with Botrytis than those of wild-type and overexpressing LrGAMYB plants. The lre-MIR159a overexpression also led to repressed expression of two targets of miR159, AtMYB33 and AtMYB65, and enhanced accumulation of hormone-related genes, including AtPR1, AtPR2, AtNPR1, AtPDF1.2, and AtLOX for both the jasmonic acid and salicylic acid pathways. Moreover, lower levels of H2 O2 and O2- were observed in lre-MIR159a transgenic Arabidopsis, which reduced the damage from reactive oxygen species accumulation. Taken together, these results indicate that lre-miR159a positively regulates resistance to grey mould by repressing the expression of its target LrGAMYB gene and activating a defence response.
Collapse
Affiliation(s)
- Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Qian Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Yu‐Qian Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Jie Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Heng‐Bin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Gui‐Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| |
Collapse
|
8
|
Fan Y, Wang Q, Dong Z, Yin Y, Teixeira da Silva JA, Yu X. Advances in molecular biology of Paeonia L. PLANTA 2019; 251:23. [PMID: 31784828 DOI: 10.1007/s00425-019-03299-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
Molecular biology can serve as a tool to solve the limitations of traditional breeding and cultivation techniques related to flower patterns, the improvement of flower color, and the regulation of flowering and stress resistance. These characteristics of molecular biology ensured its significant role in improving the efficiency of breeding and germplasm amelioration of Paeonia. This review describes the advances in molecular biology of Paeonia, including: (1) the application of molecular markers; (2) genomics, transcriptomics, proteomics, metabolomics, and microRNA studies; (3) studies of functional genes; and (4) molecular biology techniques. This review also points out select limitations in current molecular biology, analyzes the direction of Paeonia molecular biology research, and provides advice for future research objectives.
Collapse
Affiliation(s)
- Yongming Fan
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Qi Wang
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Zhijun Dong
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | - Yijia Yin
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China
| | | | - Xiaonan Yu
- College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, People's Republic of China.
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 100083, People's Republic of China.
| |
Collapse
|
9
|
Sabzehzari M, Naghavi M. Phyto-miRNA: A molecule with beneficial abilities for plant biotechnology. Gene 2019; 683:28-34. [DOI: 10.1016/j.gene.2018.09.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022]
|
10
|
Identification and characterization of known and novel microRNAs in strawberry fruits induced by Botrytis cinerea. Sci Rep 2018; 8:10921. [PMID: 30026481 PMCID: PMC6053406 DOI: 10.1038/s41598-018-29289-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs are endogenous small non-coding RNAs that negatively regulate mRNAs, mainly at the post-transcriptional level, and play an important role in resistance response of plants. To date, there are few reports on resistance response of strawberry miRNAs to pathogens. In this study, using high-throughput sequencing, 134 conserved and 35 novel miRNAs were identified in six libraries within the treatment of Botrytis cinerea. A total 497 potential target genes were predicted using Fragaria vesca genome. Most of the differential expressed miRNAs in strawberry fruits were up-regulated in early libraries and down-regulated in late libraries. PIRL, the target gene of miR5290a, showed the opposite expressed trend compared with miR5290 from T1 to T3 libraries, and functional analysis of the PIRL gene shows that it has obvious resistance to B. cinerea in the strawberry fruits with overexpressed PIRL gene. We speculate that miR5290a negatively regulates its target gene PIRL to increase resistance to pathogen infection, and further analysis of PIRL function is meaningful for studying the plant-pathogen relationship and improving strawberry fruit quality and yield.
Collapse
|
11
|
Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing. Sci Rep 2018; 8:2880. [PMID: 29440670 PMCID: PMC5811567 DOI: 10.1038/s41598-018-21193-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/31/2018] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of Lilium lancifolium Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified. In total, 366 target genes for conserved miRNAs and 415 target genes for novel miRNAs were predicted. The majority of the target genes for conserved miRNAs were transcriptional factors and novel miRNAs targeted mainly protein coding genes. A total of 53 cleavage sites belonging to 6 conserved miRNAs families and 14 novel miRNAs were identified using degradome sequencing. Twenty-three miRNAs were randomly selected, then, their credibility was confirmed using northern blot or stem-loop qRT-PCR. The results from qRT-PCR analysis showed the expression pattern of 4 LL-miRNAs was opposite to their targets. Therefore, our finding provides an important basis to understand the biological functions of miRNAs in Lilium.
Collapse
|
12
|
High throughput sequencing of herbaceous peony small RNAs to screen thermo-tolerance related microRNAs. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0505-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Gao X, Cui Q, Cao QZ, Liu Q, He HB, Zhang DM, Jia GX. Transcriptome-Wide Analysis of Botrytis elliptica Responsive microRNAs and Their Targets in Lilium Regale Wilson by High-Throughput Sequencing and Degradome Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:753. [PMID: 28572808 PMCID: PMC5435993 DOI: 10.3389/fpls.2017.00753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/21/2017] [Indexed: 05/07/2023]
Abstract
MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B. elliptica treatment or B. elliptica infection for 6 and 24 h. By high-throughput sequencing, 71 known miRNAs belonging to 47 conserved families and 24 novel miRNA were identified, of which 18 miRNAs were downreguleted and 13 were upregulated in response to B. elliptica. Moreover, based on the lily mRNA transcriptome, 22 targets for 9 known and 1 novel miRNAs were identified by the degradome sequencing approach. Most target genes for elliptica-responsive miRNAs were involved in metabolic processes, few encoding different transcription factors, including ELONGATION FACTOR 1 ALPHA (EF1a) and TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 2 (TCP2). Furthermore, the expression patterns of a set of elliptica-responsive miRNAs and their targets were validated by quantitative real-time PCR. This study represents the first transcriptome-based analysis of miRNAs responsive to B. elliptica and their targets in lily. The results reveal the possible regulatory roles of miRNAs and their targets in B. elliptica interaction, which will extend our understanding of the mechanisms of this disease in lily.
Collapse
Affiliation(s)
- Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qi Cui
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qin-Zheng Cao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Qiang Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Heng-Bin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Dong-Mei Zhang
- Shanghai Academy of Landscape Architecture Science and PlanningShanghai, China
- Shanghai Engineering Research Center of Landscaping on Challenging Urban SitesShanghai, China
| | - Gui-Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry UniversityBeijing, China
- *Correspondence: Gui-Xia Jia
| |
Collapse
|
15
|
Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing. FORESTS 2016. [DOI: 10.3390/f7120318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|