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Abdelsattar M, Abdeldaym EA, Alsayied NF, Ahmed E, Abd El-Maksoud RM. Overlapping of copper-nanoparticles with microRNA reveals crippling of heat stress pathway in Solanum lycopersicum: Tomato case study. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108791. [PMID: 38861818 DOI: 10.1016/j.plaphy.2024.108791] [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: 02/20/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Despite the tangible benefits of copper nanoparticles (CuNPs) for plants, the increasing use of CuNPs poses a threat to plants and the environment. Although miRNAs have been shown to mediate heat shock and CuNPs by altering gene expression, no study has investigated how CuNPs in combination with heat shock (HS) affect the miRNA expression profile. Here, we exposed tomato plants to 0.01 CuONPs at 42 °C for 1 h after exposure. It was found that the expression levels of miR156a, miR159a and miR172a and their targets SPL3, MYB33 and AP2a were altered under CuNPs and HS + CuNPs. This alteration accelerated the change of vegetative phase and the process of leaf senescence. The overexpression of miR393 under CuNPs and HS + CuNPs could also be an indicator of the attenuation of leaf morphology. Interestingly, the down-regulation of Cu/ZnSOD1 and Cu/ZnSOD2 as target genes of miR398a, which showed strong abnormal expression, was replaced by FeSOD (FSD1), indicating the influence of CuNPs. In addition, CuNPs triggered the expression of some important genes of heat shock response, including HsFA2, HSP70-9 and HSP90-3, which showed lower expression compared to HS. Thus, CuNPs play an important role in altering the gene expression pathway during heat stress.
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Affiliation(s)
- Mohamed Abdelsattar
- Plant Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
| | - Emad A Abdeldaym
- Department of Vegetable Crops, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Nouf F Alsayied
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makka, Saudi Arabia
| | - Esraa Ahmed
- Plant Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Reem M Abd El-Maksoud
- Nucleic Acid and Protein Chemistry Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
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Liu Y, Yang L, Ma Y, Zhou Y, Zhang S, Liu Q, Ma F, Liu C. The HD-Zip I transcription factor MdHB-7 negatively regulates resistance to Glomerella leaf spot in apple. JOURNAL OF PLANT PHYSIOLOGY 2024; 299:154277. [PMID: 38843655 DOI: 10.1016/j.jplph.2024.154277] [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: 10/27/2023] [Revised: 03/01/2024] [Accepted: 05/29/2024] [Indexed: 06/17/2024]
Abstract
Glomerella leaf spot (GLS), caused by Colletotrichum fructicola (Cf), has been one of the main fungal diseases afflicting apple-producing areas across the world for many years, and it has led to substantial reductions in apple output and quality. HD-Zip transcription factors have been identified in several species, and they are involved in the immune response of plants to various types of biotic stress. In this study, inoculation of MdHB-7 overexpressing (MdHB-7-OE) and interference (MdHB-7-RNAi) transgenic plants with Cf revealed that MdHB-7, which encodes an HD-Zip transcription factor, adversely affects GLS resistance. The SA content and the expression of SA pathway-related genes were lower in MdHB-7-OE plants than in 'GL-3' plants; the content of ABA and the expression of ABA biosynthesis genes were higher in MdHB-7-OE plants than in 'GL-3' plants. Further analysis indicated that the content of phenolics and chitinase and β-1, 3 glucanase activities were lower and H2O2 accumulation was higher in MdHB-7-OE plants than in 'GL-3' plants. The opposite patterns were observed in MdHB-7-RNAi apple plants. Overall, our results indicate that MdHB-7 plays a negative role in regulating defense against GLS in apple, which is likely achieved by altering the content of SA, ABA, polyphenols, the activities of defense-related enzymes, and the content of H2O2.
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Affiliation(s)
- Yuerong Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lulu Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yongxin Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yufei Zhou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shangyu Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qianwei Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Changhai Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Lin J, Ruan S, Guo Q, Zhang Y, Fang M, Li T, Luo G, Tian Z, Zhang Y, Tandayu E, Chen C, Lu J, Ma C, Si H. Comprehensive genome-wide analysis of wheat xylanase inhibitor protein (XIP) genes: unveiling their role in Fusarium head blight resistance and plant immune mechanisms. BMC PLANT BIOLOGY 2024; 24:462. [PMID: 38802731 PMCID: PMC11129392 DOI: 10.1186/s12870-024-05176-4] [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: 03/04/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
In this comprehensive genome-wide study, we identified and classified 83 Xylanase Inhibitor Protein (XIP) genes in wheat, grouped into five distinct categories, to enhance understanding of wheat's resistance to Fusarium head blight (FHB), a significant fungal threat to global wheat production. Our analysis reveals the unique distribution of XIP genes across wheat chromosomes, particularly at terminal regions, suggesting their role in the evolutionary expansion of the gene family. Several XIP genes lack signal peptides, indicating potential alternative secretion pathways that could be pivotal in plant defense against FHB. The study also uncovers the sequence homology between XIPs and chitinases, hinting at a functional diversification within the XIP gene family. Additionally, the research explores the association of XIP genes with plant immune mechanisms, particularly their linkage with plant hormone signaling pathways like abscisic acid and jasmonic acid. XIP-7A3, in particular, demonstrates a significant increase in expression upon FHB infection, highlighting its potential as a key candidate gene for enhancing wheat's resistance to this disease. This research not only enriches our understanding of the XIP gene family in wheat but also provides a foundation for future investigations into their role in developing FHB-resistant wheat cultivars. The findings offer significant implications for wheat genomics and breeding, contributing to the development of more resilient crops against fungal diseases.
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Affiliation(s)
- Juan Lin
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Shuang Ruan
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Qi Guo
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Yonglin Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Mengyuan Fang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Tiantian Li
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Gan Luo
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Zhuangbo Tian
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Yi Zhang
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Erwin Tandayu
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, 2480, Australia
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, 230036, China.
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Shang K, Wang R, Cao W, Wang X, Wang Y, Shi Z, Liu H, Zhou S, Zhu X, Zhu C. Abscisic-acid-responsive StlncRNA13558 induces StPRL expression to increase potato resistance to Phytophthora infestans infection. FRONTIERS IN PLANT SCIENCE 2024; 15:1338062. [PMID: 38504894 PMCID: PMC10948444 DOI: 10.3389/fpls.2024.1338062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Late blight, caused by Phytophthora infestans, is one of the most serious diseases affecting potatoes (Solanum tuberosum L.). Long non-coding RNAs (lncRNAs) are transcripts with a length of more than 200 nucleotides that have no protein-coding potential. Few studies have been conducted on lncRNAs related to plant immune regulation in plants, and the molecular mechanisms involved in this regulation require further investigation. We identified and screened an lncRNA that specifically responds to P. infestans infection, namely, StlncRNA13558. P. infestans infection activates the abscisic acid (ABA) pathway, and ABA induces StlncRNA13558 to enhance potato resistance to P. infestans. StlncRNA13558 positively regulates the expression of its co-expressed PR-related gene StPRL. StPRL promotes the accumulation of reactive oxygen species and transmits a resistance response by affecting the salicylic acid hormone pathway, thereby enhancing potato resistance to P. infestans. In summary, we identified the potato late blight resistance lncRNA StlncRNA13558 and revealed its upstream and downstream regulatory relationship of StlncRNA13558. These results improve our understanding of plant-pathogen interactions' immune mechanism and elucidate the response mechanism of lncRNA-target genes regulating potato resistance to P. infestans infection.
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Affiliation(s)
- Kaijie Shang
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
- College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong, China
| | - Ruolin Wang
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Weilin Cao
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, Shandong, China
| | - Xipan Wang
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Yubo Wang
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Zhenting Shi
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Hongmei Liu
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Shumei Zhou
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong, China
| | - Changxiang Zhu
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, China
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5
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Wu Q, He Y, Cui C, Tao X, Zhang D, Zhang Y, Ying T, Li L. Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7469-7483. [PMID: 37421609 DOI: 10.1002/jsfa.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/17/2023] [Accepted: 07/08/2023] [Indexed: 07/10/2023]
Abstract
BACKGROUND To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction. RESULTS Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups. CONCLUSION ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qiong Wu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Yanan He
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Chunxiao Cui
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Xiaoya Tao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Dongdong Zhang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Yurong Zhang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
| | - Tiejin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Li Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
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Han H, Wang C, Yang X, Wang L, Ye J, Xu F, Liao Y, Zhang W. Role of bZIP transcription factors in the regulation of plant secondary metabolism. PLANTA 2023; 258:13. [PMID: 37300575 DOI: 10.1007/s00425-023-04174-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION This study provides an overview of the structure, classification, regulatory mechanisms, and biological functions of the basic (region) leucine zipper transcription factors and their molecular mechanisms in flavonoid, terpenoid, alkaloid, phenolic acid, and lignin biosynthesis. Basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. The bZIP TFs are widely distributed in plants and play important roles in plant growth and development, photomorphogenesis, signal transduction, resistance to pathogenic microbes, biotic and abiotic stress, and secondary metabolism. Moreover, the expression of bZIP TFs not only promotes or inhibits the accumulation of secondary metabolites in medicinal plants, but also affects the stress response of plants to the external adverse environment. This paper describes the structure, classification, biological function, and regulatory mechanisms of bZIP TFs. In addition, the molecular mechanism of bZIP TFs regulating the biosynthesis of flavonoids, terpenoids, alkaloids, phenolic acids, and lignin are also elaborated. This review provides a summary for in-depth study of the molecular mechanism of bZIP TFs regulating the synthesis pathway of secondary metabolites and plant molecular breeding, which is of significance for the generation of beneficial secondary metabolites and the improvement of plant varieties.
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Affiliation(s)
- Huan Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Caini Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaoyan Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lina Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China
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Li Q, Shen H, Yuan S, Dai X, Yang C. miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses. FRONTIERS IN PLANT SCIENCE 2023; 13:1094459. [PMID: 36714724 PMCID: PMC9875070 DOI: 10.3389/fpls.2022.1094459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.
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Affiliation(s)
- Qian Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Heng Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Shoujuan Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xigang Dai
- School of Life Sciences, Jianghan University/Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Zhang A, Zhang S, Wang F, Meng X, Ma Y, Guan J, Zhang F. The roles of microRNAs in horticultural plant disease resistance. Front Genet 2023; 14:1137471. [PMID: 36923786 PMCID: PMC10009157 DOI: 10.3389/fgene.2023.1137471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 03/03/2023] Open
Abstract
The development of the horticultural industry is largely limited by disease and excessive pesticide application. MicroRNAs constitute a major portion of the transcriptomes of eukaryotes. Various microRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycle of plants. Recently, small RNA sequencing has been applied to study gene regulation in horticultural plants. In this review, we summarize the current understanding of the biogenesis and contributions of microRNAs in horticultural plant disease resistance. These microRNAs may potentially be used as genetic resources for improving disease resistance and for molecular breeding. The challenges in understanding horticultural plant microRNA biology and the possibilities to make better use of these horticultural plant gene resources in the future are discussed in this review.
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Affiliation(s)
- Aiai Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shunshun Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xianmin Meng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feng Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2022; 13:7890. [PMID: 36550095 PMCID: PMC9780251 DOI: 10.1038/s41467-022-35452-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
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Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
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Wai AH, Rahman MM, Waseem M, Cho LH, Naing AH, Jeon JS, Lee DJ, Kim CK, Chung MY. Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of PLATZ Gene Family Members in Solanum Lycopersicum L. under Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223112. [PMID: 36432841 PMCID: PMC9697139 DOI: 10.3390/plants11223112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 05/29/2023]
Abstract
PLATZ (plant AT-rich sequence and zinc-binding) family proteins with two conserved zinc-dependent DNA-binding motifs are transcription factors specific to the plant kingdom. The functions of PLATZ proteins in growth, development, and adaptation to multiple abiotic stresses have been investigated in various plant species, but their role in tomato has not been explored yet. In the present work, 20 non-redundant Solanum lycopersicum PLATZ (SlPLATZ) genes with three segmentally duplicated gene pairs and four tandemly duplicated gene pairs were identified on eight tomato chromosomes. The comparative modeling and gene ontology (GO) annotations of tomato PLATZ proteins indicated their probable roles in defense response, transcriptional regulation, and protein metabolic processes as well as their binding affinity for various ligands, including nucleic acids, peptides, and zinc. SlPLATZ10 and SlPLATZ17 were only expressed in 1 cm fruits and flowers, respectively, indicating their preferential involvement in the development of these organs. The expression of SlPLATZ1, SlPLATZ12, and SlPLATZ19 was up- or down-regulated following exposure to various abiotic stresses, whereas that of SlPLATZ11 was induced under temperature stresses (i.e., cold and heat stress), revealing their probable function in the abiotic stress tolerance of tomato. Weighted gene co-expression network analysis corroborated the aforementioned findings by spotlighting the co-expression of several stress-associated genes with SlPLATZ genes. Confocal fluorescence microscopy revealed the localization of SlPLATZ−GFP fusion proteins in the nucleus, hinting at their functions as transcription factors. These findings provide a foundation for a better understanding of the structure and function of PLATZ genes and should assist in the selection of potential candidate genes involved in the development and abiotic stress adaptation in tomato.
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Affiliation(s)
- Antt Htet Wai
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
- Department of Biology, Yangon University of Education, Kamayut Township 11041, Yangon Region, Myanmar
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51600, Pakistan
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si 50463, Gyeongsangnam-do, Republic of Korea
| | - Aung Htay Naing
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Do-jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon 57922, Republic of Korea
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11
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Miao S, Li F, Han Y, Yao Z, Xu Z, Chen X, Liu J, Zhang Y, Wang A. Identification of OSCA gene family in Solanum habrochaites and its function analysis under stress. BMC Genomics 2022; 23:547. [PMID: 35915415 PMCID: PMC9341080 DOI: 10.1186/s12864-022-08675-6] [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: 04/24/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
Background OSCA (hyperosmolality-gated calcium-permeable channel) is a calcium permeable cation channel protein that plays an important role in regulating plant signal transduction. It is involved in sensing changes in extracellular osmotic potential and an increase in Ca2+ concentration. S. habrochaites is a good genetic material for crop improvement against cold, late blight, planthopper and other diseases. Till date, there is no report on OSCA in S. habrochaites. Thus, in this study, we performed a genome-wide screen to identify OSCA genes in S. habrochaites and characterized their responses to biotic and abiotic stresses. Results A total of 11 ShOSCA genes distributed on 8 chromosomes were identified. Subcellular localization analysis showed that all members of ShOSCA localized on the plasma membrane and contained multiple stress-related cis acting elements. We observed that genome-wide duplication (WGD) occurred in the genetic evolution of ShOSCA5 (Solhab04g250600) and ShOSCA11 (Solhab12g051500). In addition, repeat events play an important role in the expansion of OSCA gene family. OSCA gene family of S. habrochaites used the time lines of expression studies by qRT-PCR, do indicate OSCAs responded to biotic stress (Botrytis cinerea) and abiotic stress (drought, low temperature and abscisic acid (ABA)). Among them, the expression of ShOSCAs changed significantly under four stresses. The resistance of silencing ShOSCA3 plants to the four stresses was reduced. Conclusion This study identified the OSCA gene family of S. habrochaites for the first time and analyzed ShOSCA3 has stronger resistance to low temperature, ABA and Botrytis cinerea stress. This study provides a theoretical basis for clarifying the biological function of OSCA, and lays a foundation for tomato crop improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08675-6.
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Affiliation(s)
- Shuang Miao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fengshuo Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Han
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zhongtong Yao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Zeqian Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Jiayin Liu
- College of Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Yao Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China. .,College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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12
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Fan R, Tao XY, Xia ZQ, Sim S, Hu LS, Wu BD, Wang QH, Hao CY. Comparative Transcriptome and Metabolome Analysis of Resistant and Susceptible Piper Species Upon Infection by the Oomycete Phytophthora Capsici. FRONTIERS IN PLANT SCIENCE 2022; 13:864927. [PMID: 35845707 PMCID: PMC9278165 DOI: 10.3389/fpls.2022.864927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/16/2022] [Indexed: 06/04/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen that causes devastating disease in black pepper, resulting in a significant decline in yield and economic losses. Piper nigrum (black pepper) is documented as susceptible to P. capsici, whereas its close relative Piper flaviflorum is known to be resistant. However, the molecular mechanism underlying the resistance of P. flaviflorum remains obscure. In this study, we conducted a comparative transcriptome and metabolome analysis between P. flaviflorum and P. nigrum upon P. capsici infection and found substantial differences in their gene expression profiles, with altered genes being significantly enriched in terms relating to plant-pathogen interaction, phytohormone signal transduction, and secondary metabolic pathways, including phenylpropanoid biosynthesis. Further metabolome analysis revealed the resistant P. flaviflorum to have a high background endogenous ABA reservoir and time-course-dependent accumulation of ABA and SA upon P. capsici inoculation, while the susceptible P. nigrum had a high background endogenous IAA reservoir and time-course-dependent accumulation of JA-Ile, the active form of JA. Investigation of the phenylpropanoid biosynthesis metabolome further indicated the resistant P. flaviflorum to have more accumulation of lignin precursors than the susceptible P. nigrum, resulting in a higher accumulation after inoculation. This study provides an overall characterization of biologically important pathways underlying the resistance of P. flaviflorum, which theoretically explains the advantage of using this species as rootstock for the management of oomycete pathogen in black pepper production.
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Affiliation(s)
- Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
| | - Xiao-yuan Tao
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | - Soonliang Sim
- Academy of Sciences Malaysia, Kuala Lumpur, Malaysia
| | - Li-song Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
| | - Bao-duo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, China
| | - Qing-huang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
| | - Chao-yun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
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13
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Ascophyllum nodosum Extract and Mycorrhizal Colonization Synergistically Trigger Immune Responses in Pea Plants against Rhizoctonia Root Rot, and Enhance Plant Growth and Productivity. J Fungi (Basel) 2022; 8:jof8030268. [PMID: 35330270 PMCID: PMC8953849 DOI: 10.3390/jof8030268] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Rhizoctonia root rot is one of the most destructive diseases affecting pea crops, resulting in up to 75% loss. In this study, the biocontrol activity of seaweed (Ascophyllum nodosum) extract at 1, 2, and 3% and/or mycorrhization of pea roots was investigated against Rhizoctonia root rot under greenhouse conditions. In addition, their effects on the transcriptional, physiological, ultrastructural, and growth status of pea plants were also studied. The results showed that the mycorrhizal colonization of pea roots and the application of the seaweed extract at 3% synergistically overexpressed the responsive factor (JERF3) recording 18.2-fold, and the defense-related genes peroxidase (23.2-fold) and chitinase II (31.8-fold). In addition, this treatment improved the activity of the antioxidant enzymes POD and PPO, increased the phenolic content in pea roots, and triggered multiple hypersensitivity reactions at the ultrastructural level of the cell, leading to a 73.1% reduction in disease severity. Moreover, a synergistic growth-promoting effect on pea plants was also observed. The photosynthetic pigments in pea leaves were enhanced in response to this dual treatment, which significantly improved their yield (24 g/plant). The inducing effect of mycorrhizal colonization on plant resistance and growth has been extensively studied. However, developing improved and synergistically acting biological agents for plant disease control and growth promotion as alternatives to the chemical fungicides is crucial for safety and food security. Based on these results, it can be concluded that the mycorrhizal colonization of pea roots and soaking their seeds in the A. nodosum extract at 3% have a promising and improved biocontrol activity against R. solani, and a growth-promoting effect on pea plants. However, field applications should be evaluated prior to any use recommendations.
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14
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The Mulberry SPL Gene Family and the Response of MnSPL7 to Silkworm Herbivory through Activating the Transcription of MnTT2L2 in the Catechin Biosynthesis Pathway. Int J Mol Sci 2022; 23:ijms23031141. [PMID: 35163065 PMCID: PMC8835075 DOI: 10.3390/ijms23031141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/15/2022] Open
Abstract
SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, as unique plant transcription factors, play important roles in plant developmental regulation and stress response adaptation. Although mulberry is a commercially valuable tree species, there have been few systematic studies on SPL genes. In this work, we identified 15 full-length SPL genes in the mulberry genome, which were distributed on 4 Morus notabilis chromosomes. Phylogenetic analysis clustered the SPL genes from five plants (Malus × domestica Borkh, Populus trichocarpa, M. notabilis, Arabidopsis thaliana, and Oryza sativa) into five groups. Two zinc fingers (Zn1 and Zn2) were found in the conserved SBP domain in all of the MnSPLs. Comparative analyses of gene structures and conserved motifs revealed the conservation of MnSPLs within a group, whereas there were significant structure differences among groups. Gene quantitative analysis showed that the expression of MnSPLs had tissue specificity, and MnSPLs had much higher expression levels in older mulberry leaves. Furthermore, transcriptome data showed that the expression levels of MnSPL7 and MnSPL14 were significantly increased under silkworm herbivory. Molecular experiments revealed that MnSPL7 responded to herbivory treatment through promoting the transcription of MnTT2L2 and further upregulating the expression levels of catechin synthesis genes (F3′H, DFR, and LAR).
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15
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Tahmasebi A, Khahani B, Tavakol E, Afsharifar A, Shahid MS. Microarray analysis of Arabidopsis thaliana exposed to single and mixed infections with Cucumber mosaic virus and turnip viruses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:11-27. [PMID: 33627959 PMCID: PMC7873207 DOI: 10.1007/s12298-021-00925-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 01/03/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Cucumber mosaic virus (CMV), Turnip mosaic virus (TuMV) and Turnip crinkle virus (TCV) are important plant infecting viruses. In the present study, whole transcriptome alteration of Arabidopsis thaliana in response to CMV, TuMV and TCV, individual as well as mixed infections of CMV and TuMV/CMV and TCV were investigated using microarray data. In response to CMV, TuMV and TCV infections, a total of 2517, 3985 and 277 specific differentially expressed genes (DEGs) were up-regulated, while 2615, 3620 and 243 specific DEGs were down-regulated, respectively. The number of 1222 and 30 common DEGs were up-regulated during CMV and TuMV as well as CMV and TCV infections, while 914 and 24 common DEGs were respectively down-regulated. Genes encoding immune response mediators, signal transducer activity, signaling and stress response functions were among the most significantly upregulated genes during CMV and TuMV or CMV and TCV mixed infections. The NAC, C3H, C2H2, WRKY and bZIP were the most commonly presented transcription factor (TF) families in CMV and TuMV infection, while AP2-EREBP and C3H were the TF families involved in CMV and TCV infections. Moreover, analysis of miRNAs during CMV and TuMV and CMV and TCV infections have demonstrated the role of miRNAs in the down regulation of host genes in response to viral infections. These results identified the commonly expressed virus-responsive genes and pathways during plant-virus interaction which might develop novel antiviral strategies for improving plant resistance to mixed viral infections. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00925-3.
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Affiliation(s)
- Aminallah Tahmasebi
- Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, 7916193145 Iran
- Plant Protection Research Group, University of Hormozgan, Bandar Abbas, Iran
| | - Bahman Khahani
- Department of Plant Genetics and Production, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Elahe Tavakol
- Department of Plant Genetics and Production, College of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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16
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Wall associated kinases (WAKs) gene family in tomato (Solanum lycopersicum): Insights into plant immunity. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Sun X, Wang M, Leng X, Zhang K, Liu G, Fang J. Characterization of the regulation mechanism of grapevine microRNA172 family members during flower development. BMC PLANT BIOLOGY 2020; 20:409. [PMID: 32883203 PMCID: PMC7650276 DOI: 10.1186/s12870-020-02627-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Grapevine (Vitis vinifera L.), which has important nutritional values and health benefits, is one of the most economically important fruit crops cultivated worldwide. Several studies showed a large number of microRNAs (VvmiRNAs) involved in the modulation of grape growth and development, and many VvmiRNA families have multiple members. However, the way by which various members from the same miRNA family work is unclear, particularly in grapes. RESULTS In this study, an important conserved VvmiR172 family (VvmiR172s) and their targets were set as a good example for elucidating the interaction degree, mechanism, and spatio-temporal traits of diverse members from the same miRNA family. miR-RACE and Stem-loop RT-PCR were used to identify the spatio-temporal expressions of various members of VvmiR172s; together with RLM-RACE, PPM-RACE, Western blot, transgenic technologies, their interaction degree, and regulation mechanism were further validated. The expression of VvmiR172c was significantly higher than that of VvmiR172a, b, and d and showed a positive correlation with the abundance of VvAP2 cleavage products. These findings indicated that VvmiR172c might be one of the main action factors of the VvmiR172 family in flower development. The ability of VvmiR172c to cleave target genes differed due to divergence in complementary degree with VvAP2 and expression levels of various members. In VvmiR172 transgenic lines, we observed that 35S::VvmiR172c resulted in the earliest and abundant flowering, indicating the strong function of VvmiR172c. In contrast, the non-significant phenotypic changes were detected in the VvAP2 transgenic lines. The qRT-PCR and Western bolt results demonstrated that VvmiR172c plays a major role in targeting VvAP2. CONCLUSIONS VvmiR172 up-regulated the expression of NtFT and decreased the expression of NtFLC. The up/down regulation of VvmiR172c was the most pronounced. The functions of four VvmiR172 members in grape differed, and miR172c had the strongest regulation on AP2.
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Affiliation(s)
- Xin Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengqi Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kekun Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gengsen Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Jinggui Fang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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18
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Li T, Gonzalez N, Inzé D, Dubois M. Emerging Connections between Small RNAs and Phytohormones. TRENDS IN PLANT SCIENCE 2020; 25:912-929. [PMID: 32381482 DOI: 10.1016/j.tplants.2020.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 05/20/2023]
Abstract
Small RNAs (sRNAs), mainly including miRNAs and siRNAs, are ubiquitous in eukaryotes. sRNAs mostly negatively regulate gene expression via (post-)transcriptional gene silencing through DNA methylation, mRNA cleavage, or translation inhibition. The mechanisms of sRNA biogenesis and function in diverse biological processes, as well as the interactions between sRNAs and environmental factors, like (a)biotic stress, have been deeply explored. Phytohormones are central in the plant's response to stress, and multiple recent studies highlight an emerging role for sRNAs in the direct response to, or the regulation of, plant hormonal pathways. In this review, we discuss recent progress on the unraveling of crossregulation between sRNAs and nine plant hormones.
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Affiliation(s)
- Ting Li
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, F-33882 Villenave d'Ornon cedex, France
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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19
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Luan W, Dai Y, Li XY, Wang Y, Tao X, Li CX, Mao P, Ma XR. Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid. BMC PLANT BIOLOGY 2020; 20:320. [PMID: 32635887 PMCID: PMC7339384 DOI: 10.1186/s12870-020-02528-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/26/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. RESULTS Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5'terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. CONCLUSIONS Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
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Affiliation(s)
- Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Yu Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
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Qiu L, Chen R, Fan Y, Huang X, Luo H, Xiong F, Liu J, Zhang R, Lei J, Zhou H, Wu J, Li Y. Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.). BMC Genomics 2019; 20:817. [PMID: 31699032 PMCID: PMC6836457 DOI: 10.1186/s12864-019-6201-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.
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Affiliation(s)
- Lihang Qiu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Hanmin Luo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Faqian Xiong
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Junxian Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Ronghua Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jingchao Lei
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jianming Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
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21
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Wang Y, Li W, Chang H, Zhou J, Luo Y, Zhang K, Wang B. Sweet cherry fruit miRNAs and effect of high CO 2 on the profile associated with ripening. PLANTA 2019; 249:1799-1810. [PMID: 30840178 DOI: 10.1007/s00425-019-03110-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/12/2019] [Indexed: 05/11/2023]
Abstract
157 known and 55 novel miRNAs were found in sweet cherry fruit. MiRNA target genes involved in fruit ripening and the differentially expressed miRNAs under CO2 treatment were identified. MicroRNAs (miRNAs) are short non-coding RNAs and play important functions in many biological processes, including fruit ripening and senescence. In the current study, the high-throughput sequencing and bioinformatics methods were implemented to decipher the miRNAs landscape in sweet cherry fruit. A total of 157 known miRNAs belonging to 50 families and 55 putative novel miRNAs were found. Target genes of the miRNAs were predicted and genes involved in fruit ripening were found, including F-box proteins and TFs such as SPL, TCP, NAC, MYB, ARF and AP2/ERF. And these target genes were further confirmed by degradome sequencing. A regulatory network model was constructed to uncover the miRNAs and their targets involved in fruit ripening and senescence. Importantly, elevated carbon dioxide can significantly postpone the ripening and senescence of sweet cherry fruit and the differentially expressed miRNAs exposed to CO2 were identified. These miRNAs included miR482j, miR6275, miR164, miR166, miR171, miR393, miR858, miR3627a, miR6284, miR6289 and miR7122b, and some of their functions were linked to fruit ripening. This study was the first report to profile miRNAs in sweet cherry fruit and it would provide more information for further study of miRNA roles in the ripening processes and their regulation mechanism underlying the effects of high carbon dioxide treatment on fruit ripening.
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Affiliation(s)
- Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Wensheng Li
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Hong Chang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Jiahua Zhou
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National R&D Center For Fruit Processing, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
| | - Yunbo Luo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kaichun Zhang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
- National R&D Center For Fruit Processing, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China.
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China.
| | - Baogang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
- National R&D Center For Fruit Processing, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China.
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China.
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22
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Goel S, Goswami K, Pandey VK, Pandey M, Sanan-Mishra N. Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress. Funct Integr Genomics 2019; 19:867-888. [PMID: 31127449 DOI: 10.1007/s10142-019-00673-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.
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Affiliation(s)
- Shikha Goel
- Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi, 110068, India.,Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kavita Goswami
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Vimal K Pandey
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Maneesha Pandey
- Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi, 110068, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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23
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Yang X, Liu F, Zhang Y, Wang L, Cheng YF. Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum. BMC Genomics 2017; 18:1000. [PMID: 29287583 PMCID: PMC5747154 DOI: 10.1186/s12864-017-4341-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance. Results Here, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association. Conclusions In summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Lu Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu-Fu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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24
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Pan C, Ye L, Zheng Y, Wang Y, Yang D, Liu X, Chen L, Zhang Y, Fei Z, Lu G. Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato. BMC Genomics 2017; 18:843. [PMID: 29096602 PMCID: PMC5668977 DOI: 10.1186/s12864-017-4238-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 10/25/2017] [Indexed: 12/18/2022] Open
Abstract
Background Autogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Numerous small RNAs (sRNAs) have been shown to play significant roles in plant development and stress responses, however, none of them have been studied with respect to stamen and pistil development under high-temperature conditions. We investigated the associations between stigma exsertion and small RNAs using high-throughput sequencing technology and molecular biology approaches. Results Sixteen sRNA libraries of Micro-Tom were constructed from plants stamen and pistil samples and sequenced after 2 d and 12 d of exposure to heat stress, respectively, from which a total of 110 known and 84 novel miRNAs were identified. Under heat stress conditions, 34 known and 35 novel miRNAs were differentially expressed in stamens, and 20 known and 10 novel miRNAs were differentially expressed in pistils. GO and KEGG pathway analysis showed that the predicted target genes of differentially expressed miRNAs were significantly enriched in metabolic pathways in both stamen and pistil libraries. Potential miRNA-target cleavage cascades that correlated with the regulation of stigma exsertion under heat stress conditions were found and validated through qRT-PCR and RLM-5′ RACE. Conclusion Overall, a global spectrum of known and novel miRNAs involved in tomato stigma exsertion and induced by high temperatures were identified using high-throughput sequencing and molecular biology approaches, laying a foundation for revealing the miRNA-mediated regulatory network involved in the development of tomato stamens and pistils under high-temperature conditions. Electronic supplementary material The online version of this article (10.1186/s12864-017-4238-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Changtian Pan
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Lei Ye
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yan Wang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Dandan Yang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Xue Liu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Lifei Chen
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Youwei Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Gang Lu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China. .,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310085, China.
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25
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Wang Y, Wang Q, Gao L, Zhu B, Luo Y, Deng Z, Zuo J. Integrative analysis of circRNAs acting as ceRNAs involved in ethylene pathway in tomato. PHYSIOLOGIA PLANTARUM 2017; 161:311-321. [PMID: 28664538 DOI: 10.1111/ppl.12600] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/22/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Circular RNAs (circRNAs) are a large class of non-coding endogenous RNAs that could act as competing endogenous RNAs (ceRNAs) to terminate the mRNA targets' suppression of miRNAs. To elucidate the intricate regulatory roles of circRNAs in the ethylene pathway in tomato fruit, deep sequencing and bioinformatics methods were performed. After strict screening, a total of 318 circRNAs were identified. Among these circRNAs, 282 were significantly differentially expressed among wild-type and sense-/antisense-LeERF1 transgenic tomato fruits. Besides, 1254 target genes were identified and a large amount of them were found to be involved in ethylene pathway. In addition, a sophisticated regulatory model consisting of circRNAs, target genes and ethylene was set up. Importantly, 61 circRNAs were found to be potential ceRNAs to combine with miRNAs and some of the miRNAs had been revealed to participate in the ethylene signaling pathway. This research further raised the possibility that the ethylene pathway in tomato fruit may be under the regulation of various circRNAs and provided a new perspective of the roles of circRNAs.
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Affiliation(s)
- Yunxiang Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Zhiping Deng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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26
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Van Gijsegem F, Pédron J, Patrit O, Simond-Côte E, Maia-Grondard A, Pétriacq P, Gonzalez R, Blottière L, Kraepiel Y. Manipulation of ABA Content in Arabidopsis thaliana Modifies Sensitivity and Oxidative Stress Response to Dickeya dadantii and Influences Peroxidase Activity. FRONTIERS IN PLANT SCIENCE 2017; 8:456. [PMID: 28421092 PMCID: PMC5376553 DOI: 10.3389/fpls.2017.00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/15/2017] [Indexed: 05/06/2023]
Abstract
The production of reactive oxygen species (ROS) is one of the first defense reactions induced in Arabidopsis in response to infection by the pectinolytic enterobacterium Dickeya dadantii. Previous results also suggest that abscisic acid (ABA) favors D. dadantii multiplication and spread into its hosts. Here, we confirm this hypothesis using ABA-deficient and ABA-overproducer Arabidopsis plants. We investigated the relationships between ABA status and ROS production in Arabidopsis after D. dadantii infection and showed that ABA status modulates the capacity of the plant to produce ROS in response to infection by decreasing the production of class III peroxidases. This mechanism takes place independently of the well-described oxidative stress related to the RBOHD NADPH oxidase. In addition to this weakening of plant defense, ABA content in the plant correlates positively with the production of some bacterial virulence factors during the first stages of infection. Both processes should enhance disease progression in presence of high ABA content. Given that infection increases transcript abundance for the ABA biosynthesis genes AAO3 and ABA3 and triggers ABA accumulation in leaves, we propose that D. dadantii manipulates ABA homeostasis as part of its virulence strategy.
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Affiliation(s)
- Frédérique Van Gijsegem
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
- Institut d’Ecologie et des Sciences de l’Environnement de Paris, Sorbonne Universités, Université Pierre et Marie Curie – Université Paris 06, Diderot Université Paris 07, Université Paris-Est Créteil – Université Paris 12, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le DéveloppementParis, France
| | - Jacques Pédron
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
- Institut d’Ecologie et des Sciences de l’Environnement de Paris, Sorbonne Universités, Université Pierre et Marie Curie – Université Paris 06, Diderot Université Paris 07, Université Paris-Est Créteil – Université Paris 12, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le DéveloppementParis, France
| | - Oriane Patrit
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
| | - Elizabeth Simond-Côte
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
| | - Alessandra Maia-Grondard
- Institut Jean-Pierre Bourgin, AgroParisTech, Institut National de la Recherche AgronomiqueVersailles, France
| | - Pierre Pétriacq
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
| | - Raphaël Gonzalez
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
| | - Lydie Blottière
- Institut d’Ecologie et des Sciences de l’Environnement de Paris, Sorbonne Universités, Université Pierre et Marie Curie – Université Paris 06, Diderot Université Paris 07, Université Paris-Est Créteil – Université Paris 12, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le DéveloppementParis, France
| | - Yvan Kraepiel
- Interactions Plantes-Pathogènes, AgroParisTech, Institut National de la Recherche Agronomique, Université Pierre et Marie Curie – Université Paris 06Paris, France
- Institut d’Ecologie et des Sciences de l’Environnement de Paris, Sorbonne Universités, Université Pierre et Marie Curie – Université Paris 06, Diderot Université Paris 07, Université Paris-Est Créteil – Université Paris 12, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Institut de Recherche pour le DéveloppementParis, France
- *Correspondence: Yvan Kraepiel,
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27
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Samad AFA, Sajad M, Nazaruddin N, Fauzi IA, Murad AMA, Zainal Z, Ismail I. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. FRONTIERS IN PLANT SCIENCE 2017; 8:565. [PMID: 28446918 PMCID: PMC5388764 DOI: 10.3389/fpls.2017.00565] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/29/2017] [Indexed: 05/14/2023]
Abstract
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
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Affiliation(s)
- Abdul F. A. Samad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Muhammad Sajad
- Department of Plant Breeding and Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, PunjabPakistan
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Nazaruddin Nazaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Syiah Kuala University, Darussalam, Banda AcehIndonesia
| | - Izzat A. Fauzi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Abdul M. A. Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
| | - Ismanizan Ismail
- School of Biosciences and Biotechnology, Faculty of Science and Technology, National University of Malaysia, SelangorMalaysia
- Centre of Plant Biotechnology, Institute of Systems Biology, National University of Malaysia, SelangorMalaysia
- *Correspondence: Ismanizan Ismail,
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28
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Wang Y, Wang Q, Gao L, Zhu B, Ju Z, Luo Y, Zuo J. Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato. FRONTIERS IN PLANT SCIENCE 2017; 8:527. [PMID: 28443119 PMCID: PMC5387102 DOI: 10.3389/fpls.2017.00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/24/2017] [Indexed: 05/11/2023]
Abstract
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits. Except for the known miRNAs, 36 putative novel miRNAs, 6 trans-acting short interfering RNAs (ta-siRNAs), and 958 natural antisense small interfering RNAs (nat-siRNAs) were also found in our results, which enriched the tomato small RNAs repository. Among these small RNAs, 9 miRNAs, and 12 nat-siRNAs were differentially expressed between the wild and transgenic tomato fruits significantly. A large amount of target genes of the small RNAs were identified and some of them were involved in ethylene pathway, including AP2 TFs, auxin response factors, F-box proteins, ERF TFs, APETALA2-like protein, and MADS-box TFs. Degradome sequencing further confirmed the targets of miRNAs and six novel targets were also discovered. Furthermore, a regulatory model which reveals the regulation relationships between the small RNAs and their targets involved in ethylene signaling was set up. This work provides basic information for further investigation of the function of small RNAs in ethylene pathway and fruit ripening.
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Affiliation(s)
- Yunxiang Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Zheng Ju
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- *Correspondence: Jinhua Zuo
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