1
|
Yue L, He J, Gan T, Jiu S, Khalil-Ur-Rehman M, Liu K, Bai M, Yang G, Xu Y. Regulatory Mechanism of Proanthocyanidins in Grape Peels Using vvi-miR828a and Its Target Gene VvMYBPA1. PLANTS (BASEL, SWITZERLAND) 2024; 13:1688. [PMID: 38931120 PMCID: PMC11207263 DOI: 10.3390/plants13121688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars 'Italia' and 'Benitaka'. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in 'Italia' at 10 and 11 wpf was significantly higher than that in 'Benitaka'. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in 'Benitaka' was significantly higher than that in 'Italia'; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in 'Italia' and 'Benitaka' peels at 11 wpf demonstrated that the PA content of 'Benitaka' was significantly higher than that of 'Italia'. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1.
Collapse
Affiliation(s)
- Lingqi Yue
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Jingjing He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Tian Gan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | | | - Kunyu Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Guoshun Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| | - Yanshuai Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (L.Y.); (M.B.); (G.Y.)
| |
Collapse
|
2
|
Deng K, Li Z, Huang T, Huang J. Noncoding RNAs in regulation of plant secondary metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108718. [PMID: 38733939 DOI: 10.1016/j.plaphy.2024.108718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Plant secondary metabolites (PSMs) are a large class of structurally diverse molecules, mainly consisting of terpenoids, phenolic compounds, and nitrogen-containing compounds, which play active roles in plant development and stress responses. The biosynthetic processes of PSMs are governed by a sophisticated regulatory network at multiple levels. Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) may serve as post-transcriptional regulators for plant secondary metabolism through acting on genes encoding either transcription factors or participating enzymes in relevant metabolic pathways. High-throughput sequencing technologies have facilitated the large-scale identifications of ncRNAs potentially involved in plant secondary metabolism in model plant species as well as certain species with enriched production of specific types of PSMs. Moreover, a series of miRNA-target modules have been functionally characterized to be responsible for regulating PSM biosynthesis and accumulation in plants under abiotic or biotic stresses. In this review, we will provide an overview of current findings on the ncRNA-mediated regulation of plant secondary metabolism with special attention to its participation in plant stress responses, and discuss possible issues to be addressed in future fundamental research and breeding practice.
Collapse
Affiliation(s)
- Keyin Deng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China
| | - Jianzi Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
| |
Collapse
|
3
|
Zhang L, Fan D, Li H, Chen Q, Zhang Z, Liu M, Liu J, Song Y, He J, Xu W, Song S, Liu H, Ren Y, Ma C. Characterization and identification of grapevine heat stress-responsive microRNAs revealed the positive regulated function of vvi-miR167 in thermostability. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111623. [PMID: 36750140 DOI: 10.1016/j.plantsci.2023.111623] [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: 10/05/2022] [Revised: 12/19/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
High temperature stress is one of the primary abiotic stresses that restrict fruit tree production. Grapevine (Vitis vinifera) with high economic value throughout the world is a cultivated fruit crop, and its growth and development is often influenced by high temperature stress. Studying the heat stress-response mechanism of grapevine has great significance for understanding the acclimation to heat stress. In this study, we identified a series of heat stress responsive miRNAs and analyzed their function during the heat tolerance response. CK (control group, 25 °C) and heat treatment stress (TS, 45 °C) small RNA (sRNA) libraries were constructed and sequenced by high-throughput sequencing in 'Thompson seedless' grapevine. 873 known-miRNAs and 86 novel-miRNAs were identified, of which 88 known and three novel miRNAs were expressed differentially under heat stress. 322 genes were predicted to be targeted by the miRNAs. Eight selected miRNAs and its targets were confirmed by real time quantitative PCR (RT - qPCR), indicating that these "miRNA - target" were responsive to heat stress. In addition, most of the predicted target genes were negatively regulated by corresponding miRNAs. Gene function and pathway analyses indicated that these genes probably play crucial roles in heat stress tolerance. Vvi-miR167b transiently overexpression in grapevine leaves decreased target gene vvARF6, vvARF6-like and vvARF8 expression. The function of vvi-miR167 was verified by ectopic transformation in Arabidopsis thaliana, and the heat tolerance in transgenic lines was enhanced significantly, suggesting that the vvi-miR167 plays a positive regulatory role in grape thermostability. Comparison of miRNA expression patterns between heat treatment stress and CK can help elucidate the heat stress response and resistance mechanisms in grapes. In conclusion, these results gave us useful information to better understand the heat stress-response during domestication as well as for breeding new cultivars with heat stress resistance in fruit trees.
Collapse
Affiliation(s)
- Lipeng Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Dongying Fan
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiuju Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271000, China
| | - Zhen Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Minying Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingjing Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Yue Song
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan He
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenping Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiren Song
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, Xinjiang, China
| | - Yi Ren
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chao Ma
- Shanghai Collaborative Innovation Center of Agri-Seeds/Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
4
|
He M, Kong X, Jiang Y, Qu H, Zhu H. MicroRNAs: emerging regulators in horticultural crops. TRENDS IN PLANT SCIENCE 2022; 27:936-951. [PMID: 35466027 DOI: 10.1016/j.tplants.2022.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 05/24/2023]
Abstract
Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.
Collapse
Affiliation(s)
- Meiying He
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjin Kong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
5
|
Liu J, Li H, Zhang L, Song Y, He J, Xu W, Ma C, Ren Y, Liu H. Integrative Investigation of Root-Related mRNAs, lncRNAs and circRNAs of “Muscat Hamburg” (Vitis vinifera L.) Grapevine in Response to Root Restriction through Transcriptomic Analyses. Genes (Basel) 2022; 13:genes13091547. [PMID: 36140715 PMCID: PMC9498474 DOI: 10.3390/genes13091547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/21/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
Root restriction is a physical and ecological cultivation mode which restricts plant roots into a limited container to regulate vegetative and reproduction growth by reshaping root architecture. However, little is known about related molecular mechanisms. To uncover the root-related regulatory network of endogenous RNAs under root restriction cultivation (referred to RR), transcriptome-wide analyses of mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) involved in root development were performed. During root development, RR treatment had a positive effect on root weight, typically, young roots were significantly higher than conventional cultivation (referred to NR) treatment, suggesting that root architecture reconstruction under RR was attributed to the vigorous induction into lateral roots. Furthermore, a total of 26,588 mRNAs, 1971 lncRNAs, and 2615 circRNAs were identified in root of annual “Muscat Hamburg” grapevine by the transcriptomic analyses. The expression profile of mRNAs, lncRNAs and circRNA were further confirmed by the quantitative real-time PCR (RT-qPCR). Gene ontology enrichment analysis showed that a majority of the differentially expressed mRNAs, lncRNAs and circRNAs were enriched into the categories of cellular process, metabolic process, cell part, binding, and catalytic activity. In addition, the regulatory network of endogenous RNAs was then constructed by the prediction of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA network, implying that these RNAs play significant regulatory roles for root architecture shaping in response to root restriction. Our results, for the first time, the regulatory network of competitive endogenous RNAs (ceRNAs) functions of lncRNA and circRNA was integrated, and a basis for studying the potential functions of non-coding RNAs (ncRNAs) during root development of grapevine was provided.
Collapse
Affiliation(s)
- Jingjing Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
| | - Hui Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lipeng Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
| | - Yue Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan He
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Ren
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (Y.R.); (H.L.)
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
- Correspondence: (Y.R.); (H.L.)
| |
Collapse
|
6
|
Wu Y, Huang X, Zhang S, Zhang C, Yang H, Lyu L, Li W, Wu W. Small RNA and degradome sequencing reveal the role of blackberry miRNAs in flavonoid and anthocyanin synthesis during fruit ripening. Int J Biol Macromol 2022; 213:892-901. [PMID: 35691433 DOI: 10.1016/j.ijbiomac.2022.06.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022]
Abstract
Blackberry shrubs are economically important for their production of small, pulped fruits. This species has attracted much attention because of the unique flavor of its fruits and their rich nutritional and medicinal value. In this study, microRNAs (miRNAs) and their target genes related to flavonoids and anthocyanins in blackberry fruits during ripening were analyzed and identified by small RNA and degradome sequencing technology, and the expression levels of key miRNAs in unripe and ripe blackberry fruits were verified via the RT-qPCR. A total of 258 known miRNAs were identified. Eighty differentially expressed miRNAs (DEMs) were detected in the fruits of the ripe group compared with those of the unripe group. Differentially expressed miR828-x/miR828-z and unigene0086056 (unknown function) were coexpressed. Moreover, miR858 had the most target genes for the synthesis of flavonoids and anthocyanins. Taken together, these results provide important value for improving the quality of blackberry fruits and breeding blackberry plants that produce high-flavonoid fruits for the pharmaceutical industry.
Collapse
Affiliation(s)
- Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Xin Huang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Shanshan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Chunhong Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Haiyan Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China.
| |
Collapse
|
7
|
Chen B, Ding Z, Zhou X, Wang Y, Huang F, Sun J, Chen J, Han W. Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove ( Sonneratia apetala Buch.-Ham.). Front Genet 2022; 13:932832. [PMID: 35899202 PMCID: PMC9310009 DOI: 10.3389/fgene.2022.932832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that serve as key players in plant stress responses. Although stress-regulated miRNAs have been explored in various plants, they are not well studied in mangroves. Herein, we combined PacBio isoform sequencing (Iso-Seq) with BGISEQ short-read RNA-seq to probe the role of miRNAs in the salt stress response of the mangrove plant, Sonneratia apetala Buch.-Ham. A total of 1,702,463 circular consensus sequencing reads were generated that produced 295,501 nonredundant full-length transcripts from the leaves of a 1-year-old S. apetala. After sequencing nine small RNA libraries constructed from control and 1- and 28-day 300 mM NaCl treatments, we identified 143 miRNAs (114 known and 29 novel) from a total of >261 million short reads. With the criteria of |log2FC| ≥ 1 and q-value < 0.05, 42 and 70 miRNAs were differentially accumulated after 1- and 28-day salt treatments, respectively. These differential accumulated miRNAs potentially targeted salt-responsive genes encoding transcription factors, ion homeostasis, osmotic protection, and detoxificant-related proteins, reminiscent of their responsibility for salinity adaptation in S. apetala. Particularly, 62 miRNAs were Sonneratia specific under salt stress, of which 34 were co-expressed with their 131 predicted targets, thus producing 140 miRNA-target interactions. Of these, 82 miRNA-target pairs exhibited negative correlations. Eighteen miRNA targets were categorized for the 'environmental information processing' during KEGG analysis and were related to plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), and ABC transporters (ko02010). These results underscored miRNAs as possible contributors to mangrove success in severe environments and offer insights into an miRNA-mediated regulatory mechanism of salt response in S. apetala.
Collapse
Affiliation(s)
- Beibei Chen
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Zeyi Ding
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Xiang Zhou
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Yue Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fei Huang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jiaxin Sun
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Weidong Han
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| |
Collapse
|
8
|
Zahid MS, Li D, Javed HU, Sabir IA, Wang L, Jiu S, Song S, Ma C, Wang D, Zhang C, Zhou X, Xu W, Wang S. Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines. BMC Microbiol 2021; 21:317. [PMID: 34784893 PMCID: PMC8594160 DOI: 10.1186/s12866-021-02376-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced reproductive development of grapevines. Fungal interactions and diversity in grapevines are well established; however, our knowledge about fungal diversity under the root-zone restriction technique is still unexplored. To provide insights into the role of mycobiota in the regulation of growth and fruit quality of grapevine under root-zone restriction, DNA from rhizosphere and plant compartments, including white roots (new roots), leaves, flowers, and berries of root-zone restricted (treatment) and conventionally grown plants (control), was extracted at three growth stages (full bloom, veraison, and maturity). RESULTS Diversity analysis based on the ITS1 region was performed using QIIME2. We observed that the root-zone restriction technique primarily affected the fungal communities of the soil and plant compartments at different growth stages. Interestingly, Fusarium, Ilyonectria, Cladosporium and Aspergillus spp observed in the rhizosphere overlapped with the phyllosphere at all phenological stages, having distinctive abundance in grapevine habitats. Peak richness and diversity were observed in the rhizosphere at the full bloom stage of control plants, white roots at the veraison stage of treatment, leaves at the maturity stage of treatment, flowers at the full bloom stage and berries at the veraison stage of control plants. Except for white roots, the diversity of soil and plant compartments of treated plants tended to increase until maturity. At the maturity stage of the treated and control plants, the abundance of Aspergillus spp. was 25.99 and 29.48%, respectively. Moreover, the total soluble sugar content of berries was 19.03 obrix and 16 obrix in treated and control plants, respectively, at the maturity stage. CONCLUSIONS This is the first elucidative study targeting the fungal diversity of conventional and root-restricted cultivation techniques in a single vineyard. Species richness and diversity are affected by stressful cultivation known as root zone restriction. There is an association between the abundance of Aspergillus spp. and fruit quality because despite causing stress to the grapevine, superior quality of fruit is retrieved in root-zone restricted plants.
Collapse
Affiliation(s)
- Muhammad Salman Zahid
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dongmei Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hafiz Umer Javed
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Dapeng Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xuhui Zhou
- Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241 China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China
| |
Collapse
|
9
|
Fang L, Wang Y. MicroRNAs in Woody Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:686831. [PMID: 34531880 PMCID: PMC8438446 DOI: 10.3389/fpls.2021.686831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 08/03/2021] [Indexed: 05/05/2023]
Abstract
MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.
Collapse
Affiliation(s)
- Lisha Fang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yanmei Wang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| |
Collapse
|
10
|
Chen Q, Wang J, Danzeng P, Danzeng C, Song S, Wang L, Zhao L, Xu W, Zhang C, Ma C, Wang S. VvMYB114 mediated by miR828 negatively regulates trichome development of Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110936. [PMID: 34134843 DOI: 10.1016/j.plantsci.2021.110936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Trichome is a specialized structure differentiated during the morphogenesis of plant leaf epidermal cells. In recent years, with the continuous researches on trichome development of Arabidopsis and other plants, more and more genes related to trichome morphogenesis have been discovered, including R2R3-type MYB genes. In this study, we cloned a R2R3-type MYB family gene from grape, VvMYB114, a target gene of vvi-miR828. qRT-PCR showed that VvMYB114 mRNA accumulated during grape fruit ripening, and VvMYB114 protein had transcriptional activation activity. Heterologous overexpression of VvMYB114 in Arabidopsis reduced the number of trichome on leaves and stems. Mutating the miR828-binding site in VvMYB114 without altering amino-acid sequence had no effect on trichome development in Arabidopsis. The results showed a different role of the regulation of miR828 to VvMYB114 in Arabidopsis from in grape, which indicated the functional divergence of miRNA targeting homoeologous genes in different species played an important roles in evolution and useful trait selection.
Collapse
Affiliation(s)
- Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pingcuo Danzeng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ciren Danzeng
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Institute of Agro-food Science and Technology/Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| |
Collapse
|
11
|
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
|
12
|
Zhang Y, Rahmani RS, Yang X, Chen J, Shi T. Integrative expression network analysis of microRNA and gene isoforms in sacred lotus. BMC Genomics 2020; 21:429. [PMID: 32586276 PMCID: PMC7315500 DOI: 10.1186/s12864-020-06853-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/19/2020] [Indexed: 01/29/2023] Open
Abstract
Background Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Results Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
Collapse
Affiliation(s)
- Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
13
|
Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine ( Vitis vinifera L.). Int J Mol Sci 2020; 21:ijms21103513. [PMID: 32429227 PMCID: PMC7278995 DOI: 10.3390/ijms21103513] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/16/2022] Open
Abstract
Root restriction cultivation (RRC) can influence plant root architecture, but its root phenotypic changes and molecular mechanisms are still unknown. In this study, phenotype observations of grapevine root under RRC and control cultivation (nRC) at 12 time points were conducted, and the root phenotype showed an increase of adventitious and lateral root numbers and root tip degeneration after RRC cultivation from 70 days after planting (DAP). The 70 and 125 DAP sampling of two different cultivations, named nR70, RR70, nR125, and RR125, were selected for small RNA sequencing. A total of 153 known miRNAs and 119 predicted novel miRNAs were obtained. Furthermore, BLAST was used to predict the novel miRNAs with miRBase databases using the default parameters; 96 of the 119 predicted novel miRNAs were similar to other species, and the remaining 23 grapevine-specific novel miRNAs were obtained. There were 26, 33, 26, and 32 miRNAs that were differentially expressed in different comparison groups (RR70 vs. nR70, RR125 vs. nR125, nR125 vs. nR70 and RR125 vs. RR70). Target genes prediction of differentially expressed miRNAs was annotated on a variety of biological processes, and 24 participated in root development. Moreover, multiple miRNAs were found to jointly regulate lateral root development under root restriction conditions. The miRNA expression pattern comparison between RRC and nRC may provide a framework for the future analysis of miRNAs associated with root development in grapevine.
Collapse
|