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Lu L, Chen X, Chen J, Zhang Z, Zhang Z, Sun Y, Wang Y, Xie S, Ma Y, Song Y, Zeng R. MicroRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice. PLANT, CELL & ENVIRONMENT 2024; 47:1452-1470. [PMID: 38233741 DOI: 10.1111/pce.14819] [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: 05/17/2023] [Revised: 11/20/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that play a vital role in plant responses to abiotic and biotic stresses. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stresses, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its target SPL genes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression of miPEP156e led to decreased uptake and accumulation of Cd and reactive oxygen species (ROS) levels in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines. Conversely, miPEP156e mutants displayed sensitivity to Cd stress due to the elevated accumulation of Cd and ROS. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter genes and ROS scavenging genes. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.
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Affiliation(s)
- Long Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Biotechnology of Fujian Higher Education Institutes, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyu Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiaming Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zaoli Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyan Sun
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siwen Xie
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yinuo Ma
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Biotechnology of Fujian Higher Education Institutes, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Biotechnology of Fujian Higher Education Institutes, Fujian Agriculture and Forestry University, Fuzhou, China
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Yan B, Li F, Ma Q, Shen T, Jiang J, Li H. The miR156-SPL4/SPL9 module regulates leaf and lateral branch development in Betula platyphylla. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111869. [PMID: 37827250 DOI: 10.1016/j.plantsci.2023.111869] [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: 06/02/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 10/14/2023]
Abstract
The miR156 gene is known to play an important role in regulating growth and development in plants. This gene is involved in the transition from juvenile to adult stages, leaf morphology, and root development, among other processes. While the function of miR156 is similar in many plants, there are also differences in the function of this gene between herbaceous and native species. We obtained BpmiR156 overexpression transgenic lines in Betula platyphylla, and the transgenic lines exhibited traits such as delayed development, dwarfism, increased leaf epidermal hairs, larger leaf basal angle and altered stem curvature, which were highly consistent with the overexpression miR156 in Arabidopsis, rice and tomato. However, we also observed a lack of apical dominance, increased number of lateral branches and increased diameter of lateral branches in transgenic B. platyphylla, which is different from the effects reported in other plants. Transgenic plants showed changes in the distribution of IAA, GA3, and Zeatin in lateral branches and main stem, and the ratio of the content of the three hormones was significantly higher than in the non-transgenic plants served as control. Additionally, overexpression of BpmiR156 caused down-regulation of BpSPL4 and BpSPL9 expression, as well as differential expression of genes involved in auxin and cytokinin synthesis such as BpARR3, BpARR11 and BpmiR172.
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Affiliation(s)
- Bin Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China
| | - Fangrui Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China
| | - Qing Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China
| | - Tingting Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China.
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Chandra T, Jaiswal S, Iquebal MA, Singh R, Gautam RK, Rai A, Kumar D. Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107933. [PMID: 37549574 DOI: 10.1016/j.plaphy.2023.107933] [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: 02/06/2023] [Revised: 07/04/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.
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Affiliation(s)
- Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India.
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - R K Gautam
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India; Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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4
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Chen G, Wang Y, Liu X, Duan S, Jiang S, Zhu J, Zhang Y, Hou H. The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis. Int J Mol Sci 2023; 24:ijms24076049. [PMID: 37047020 PMCID: PMC10094179 DOI: 10.3390/ijms24076049] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana.
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Affiliation(s)
- Guo Chen
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Yaping Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Xueli Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Siyue Duan
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Shenghui Jiang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Jun Zhu
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Yugang Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongmin Hou
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Qingdao Agricultural University, Qingdao 266109, China
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A Novel miRNA in Rice Associated with the Low Seed Setting Rate Symptom of Rice Stripe Virus. Int J Mol Sci 2023; 24:ijms24043675. [PMID: 36835087 PMCID: PMC9967548 DOI: 10.3390/ijms24043675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
MicroRNAs play key regulatory roles in plant development. The changed pattern of miRNA expression is involved in the production of viral symptoms. Here, we showed that a small RNA, Seq119, a putative novel microRNA, is associated with the low seed setting rate, a viral symptom of rice stripe virus (RSV)-infected rice. The expression of Seq 119 was downregulated in RSV-infected rice. The overexpression of Seq119 in transgenic rice plants did not cause any obvious phenotypic changes in plant development. When the expression of Seq119 was suppressed in rice plants either by expressing a mimic target or by CRISPR/Cas editing, seed setting rates were extremely low, similar to the effects of RSV infection. The putative targets of Seq119 were then predicted. The overexpression of the target of Seq119 in rice caused a low seed setting rate, similar to that in Seq119-suppressed or edited rice plants. Consistently, the expression of the target was upregulated in Seq119-suppressed and edited rice plants. These results suggest that downregulated Seq119 is associated with the low seed setting rate symptom of the RSV in rice.
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Yang Z, Yuan L, Zhu H, Jiang J, Yang H, Li L. Small RNA profiling reveals the involvement of microRNA-mediated gene regulation in response to symbiosis in raspberry. Front Microbiol 2022; 13:1082494. [PMID: 36620006 PMCID: PMC9810812 DOI: 10.3389/fmicb.2022.1082494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Dark septate endophytes (DSEs) can form reciprocal symbioses with most terrestrial plants, providing them with mineral nutrients in exchange for photosynthetic products. Although the mechanism of plant-DSEs is well understood at the transcriptional level, little is known about their post-transcriptional regulation, and microRNAs (miRNAs) for the symbiotic process of DSE infestation of raspberry have not been identified. In this study, we comprehensively identified the miRNAs of DSE-infested raspberry symbiosis using Illumina sequencing. A total of 361 known miRNAs and 95 novel miRNAs were identified in the roots. Similar to other dicotyledons, most of the identified raspberry miRNAs were 21 nt in length. Thirty-seven miRNAs were differentially expressed during colonization after inoculation with Phialocephala fortinii F5, suggesting a possible role for these miRNAs in the symbiotic process. Notably, two miRNAs (miR171h and miR396) previously reported to be responsive to symbiotic processes in alfalfa also had altered expression during raspberry symbiosis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggests that miRNAs are mainly involved in regulatory mechanisms, such as biological processes, cellular metabolic processes, biosynthesis of secondary metabolites, plant-pathogen interactions, and phytohormone signaling pathways. This study revealed the potential conservation of miRNA-mediated post-transcriptional regulation in symbiotic processes among plants and provides some novel miRNAs for understanding the regulatory mechanisms of DSE-raspberry symbiosis.
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Affiliation(s)
- Zhiyu Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Lianmei Yuan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Haifeng Zhu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongyi Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China,*Correspondence: Hongyi Yang,
| | - Lili Li
- Institute of Forestry Science of Heilongjiang Province, Harbin, China,Lili Li,
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Yu Y, Zhang T, Sun J, Jing T, Shen Y, Zhang K, Chen Y, Ding D, Wang G, Yang J, Tang J, Shi Z, Wang D, Gou M. Evolutionary characterization of miR396s in Poaceae exemplified by their genetic effects in wheat and maize. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111465. [PMID: 36155239 DOI: 10.1016/j.plantsci.2022.111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 09/01/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
MiR396s play important roles in regulating plant growth and stress response, and great potential for crop yield promotion was anticipated. For more comprehensive and precise understanding of miR396s in Poaceae, we analyzed the phylogenetic linkage, gene expression, and chromosomal distribution of miR396s in this study. Although the mature miR396s' sequences were mostly conserved, differential expression patterns and chromosomal distribution were found among Poaceae species including the major cereal crops rice, wheat, and maize. Consistently, in comparison with rice, wheat and maize plants transformed with the target mimicry construct of miR396 (MIM396) exhibited differential effects on grain size and disease resistance. While the TaMIM396 plants showed increased grain size, panicle length and sensitivity to B. graminis, the ZmMIM396 plants didn't show obvious changes in grain size and disease resistance. In Addition, several GROWTH-REGULATING FACTOR (GRF) genes in wheat and maize were repressed by miR396s, which could be reversed by MIM396, confirming the conserved regulatory roles of miR396 on GRFs. While providing new solution to enhance grain yield in wheat and revealing potential regulatory variations of miR396s in controlling grain size and disease resistance in different crops, this study gives clues to further explore miR396s' functions in other Poaceae species.
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Affiliation(s)
- Yanwen Yu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Tongxiang Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingfan Sun
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Teng Jing
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanjie Shen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kunpu Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yan Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Ding
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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Li Y, He Y, Liu Z, Qin T, Wang L, Chen Z, Zhang B, Zhang H, Li H, Liu L, Zhang J, Yuan W. OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1167-1182. [PMID: 35765202 DOI: 10.1111/tpj.15884] [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: 01/12/2022] [Revised: 06/16/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizhou He
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Zhixin Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Tian Qin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Lei Wang
- Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhihui Chen
- Huazhong Agricultural University, Wuhan, 430070, China
| | - Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Haitao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
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Zhou Q, Shi J, Li Z, Zhang S, Zhang S, Zhang J, Bao M, Liu G. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia. PLANT & CELL PHYSIOLOGY 2021; 62:839-857. [PMID: 33768247 DOI: 10.1093/pcp/pcab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhineng Li
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan 430081, China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
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10
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Yan Y, Wei M, Li Y, Tao H, Wu H, Chen Z, Li C, Xu JH. MiR529a controls plant height, tiller number, panicle architecture and grain size by regulating SPL target genes in rice (Oryza sativa L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110728. [PMID: 33288029 DOI: 10.1016/j.plantsci.2020.110728] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 05/02/2023]
Abstract
Rice is one of the most important food crops in the world. Breeding high-yield, multi-resistant and high-quality varieties has always been the goal of rice breeding. Rice tiller, panicle architecture and grain size are the constituent factors of yield, which are regulated by both genetic and environmental factors, including miRNAs, transcription factors, and downstream target genes. Previous studies have shown that SPL (SQUAMOSA PROMOTER BINDING-LIKE) transcription factors can control rice tiller, panicle architecture and grain size, which were regulated by miR156, miR529 and miR535. In this study, we obtained miR529a target mimicry (miR529a-MIMIC) transgenic plants to investigate plant phenotypes, physiological and molecular characteristics together with miR529a overexpression (miR529a-OE) and wild type (WT) to explore the function of miR529a and its SPL target genes in rice. We found that OsSPL2, OsSPL17 and OsSPL18 at seedling stage were regulated by miR529a, but there had complicated mechanism to control plant height. OsSPL2, OsSPL16, OsSPL17 and SPL18 at tillering stage were regulated by miR529a to control plant height and tiller number. And panicle architecture and grain size were controlled by miR529a through altering the expression of all five target genes OsSPL2, OsSPL7, OsSPL14, OsSPL16, OsSPL17 and OsSPL18. Our study suggested that miR529a might control rice growth and development by regulating different SPL target genes at different stages, which could provide a new method to improve rice yield by regulating miR529a and its SPL target genes.
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Affiliation(s)
- Yan Yan
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Mingxiao Wei
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Yu Li
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Hua Tao
- Henan Agricultural Radio and Television School, Zhengzhou, 450008, China
| | - Haoyu Wu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Zhufeng Chen
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China
| | - Can Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jian-Hong Xu
- Institute of Crop Science, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
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11
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Cui Y, Cheng J, Ruan S, Qi P, Liu W, Bian H, Ye L, Zhang Y, Hu J, Dong G, Guo L, Zhang Y, Qian Q, Hu X. The heterochronic gene Oryza sativa LIKE HETEROCHROMATIN PROTEIN 1 modulates miR156b/c/i/e levels. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:1839-1852. [PMID: 32644250 DOI: 10.1111/jipb.12991] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
The juvenile-to-adult transition in plants involves changes in vegetative growth and plant architecture; the timing of this transition has important implications for agriculture. The microRNA miR156 regulates this transition and shoot maturation in plants. In Arabidopsis thaliana, deposition of histone H3 trimethylation on lysine 27 (H3K27me3, a repressive mark) at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1 (PRC1) or PRC2, depending on the developmental stage. The levels of miR156 progressively decline during shoot maturation. The amount of H3K27me3 at MIR156A/C loci affects miR156 levels; however, whether this epigenetic regulation is conserved remains unclear. Here, we found that in rice (Oryza sativa), the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1 (OsLHP1), with the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module, affects developmental phase transitions. Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E, phenocopy of miR156 overexpression, and reduced H3k27me3 levels at MIR156B/C/I/E. This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1. Genetic and transcriptome analyses of wild-type, miR156b/c-overexpression, and Oslhp1-2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile-to-adult transition. Therefore, modifying the OsLHP1-miR156-SPL pathway may enable alteration of the vegetative period and plant architecture.
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Affiliation(s)
- Yongtao Cui
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jingfei Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shuang Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peipei Qi
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuping Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
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12
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Jerome Jeyakumar JM, Ali A, Wang WM, Thiruvengadam M. Characterizing the Role of the miR156-SPL Network in Plant Development and Stress Response. PLANTS 2020; 9:plants9091206. [PMID: 32942558 PMCID: PMC7570127 DOI: 10.3390/plants9091206] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/27/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023]
Abstract
MicroRNA (miRNA) is a short, single-stranded, non-coding RNA found in eukaryotic cells that can regulate the expression of many genes at the post-transcriptional level. Among various plant miRNAs with diverse functions, miR156 plays a key role in biological processes, including developmental regulation, immune response, metabolic regulation, and abiotic stress. MiRNAs have become the regulatory center for plant growth and development. MicroRNA156 (miR156) is a highly conserved and emerging tool for the improvement of plant traits, including crop productivity and stress tolerance. Fine-tuning of squamosa promoter biding-like (SPL) gene expression might be a useful strategy for crop improvement. Here, we studied the regulation of the miR156 module and its interaction with SPL factors to understand the developmental transition of various plant species. Furthermore, this review provides a strong background for plant biotechnology and is an important source of information for further molecular breeding to optimize farming productivity.
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Affiliation(s)
- John Martin Jerome Jeyakumar
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Asif Ali
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
| | - Wen-Ming Wang
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China; (J.M.J.J.); (A.A.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Institute of Rice Research, Sichuan Agricultural University, Wenjiang, Chengdu 625014, China
- Correspondence:
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Sciences, Konkuk University, Seoul 05029, Korea;
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13
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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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14
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Xu L, Yuan K, Yuan M, Meng X, Chen M, Wu J, Li J, Qi Y. Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements. MOLECULAR PLANT 2020; 13:851-863. [PMID: 32087371 DOI: 10.1016/j.molp.2020.02.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 05/24/2023]
Abstract
Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.
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Affiliation(s)
- Le Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kun Yuan
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Yuan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiangbing Meng
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayang Li
- Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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15
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Xing M, Su H, Liu X, Yang L, Zhang Y, Wang Y, Fang Z, Lv H. Morphological, transcriptomics and phytohormone analysis shed light on the development of a novel dwarf mutant of cabbage (Brassica oleracea). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110283. [PMID: 31779912 DOI: 10.1016/j.plantsci.2019.110283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/10/2019] [Accepted: 09/23/2019] [Indexed: 05/28/2023]
Abstract
Plant dwarf mutants generally exhibit delayed growth, delayed development, short internodes, and abnormal leaves and flowers and are ideal materials to explore the molecular mechanism of plant growth and development. In the current study, we first discovered a spontaneous cabbage (Brassica oleracea) dwarf mutant 99-198dw, which exhibits a dwarf stature, wrinkled leaves, non-heading, and substantially reduced self-fertility compared with the wild-type 99-198; however, the underlying molecular mechanism of its dwarfism is unknown. Here, we performed comparative phenotype, transcriptome and phytohormone analyses between 99-198 and 99-198dw. Cytological analysis showed that an increase in cell size, a reduction in cell layers, chloroplast degradation and a reduction in mitochondria were observed in 99-198dw. RNA-Seq showed that a total of 3801 differentially expressed genes (DEGs) were identified, including 2203 upregulated and 1598 downregulated genes in the dwarf mutant. Key genes in stress-resistant pathways were mostly upregulated, including salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), ethylene (ET), etc., while the DEGs reported to be related to plant height, such as those involved in the gibberellin (GA), brassinolide (BR), indole-3-acetic acid (IAA), and strigolactone (SL) pathways were mostly downregulated. In addition, the DEGs in the cell division pathway were all downregulated, which is consistent with the cytokinesis defects detected by cytological analysis. The changes in the GA4, JA, ET, SA and ABA contents measured by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) absolute quantification were consistent with the transcriptome analysis. Further hormone treatment tests showed that the exogenous application of GA, BR, 6BA, paclobutrazol (PC), etc. did not rescue the phenotype, implying that the change in phytohormones is due to but not the cause of the dwarf trait. It was speculated that mutation of certain DEG related to cell division or participating in signalling pathway of phytohormones like GA, BR, IAA, and SL were the cause of dwarf. These results are informative for the elucidation of the underlying regulatory network in 99-198dw and enrich our understanding of plant dwarf traits at the molecular level.
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Affiliation(s)
- Miaomiao Xing
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Henan Su
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Xing Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China.
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16
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MicroRNAs and their targeted genes associated with phase changes of stem explants during tissue culture of tea plant. Sci Rep 2019; 9:20239. [PMID: 31882926 PMCID: PMC6934718 DOI: 10.1038/s41598-019-56686-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022] Open
Abstract
Elucidation of the molecular mechanism related to the dedifferentiation and redifferentiation during tissue culture will be useful for optimizing regeneration system of tea plant. In this study, an integrated sRNAome and transcriptome analyses were carried out during phase changes of the stem explant culture. Among 198 miRNAs and 8001 predicted target genes, 178 differentially expressed miRNAs and 4264 potential targets were screened out from explants, primary calli, as well as regenerated roots and shoots. According to KEGG analysis of the potential targets, pathway of "aminoacyl-tRNA biosynthesis", "proteasome" and "glutathione metabolism" was of great significance during the dedifferentiation, and pathway of "porphyrin and chlorophyll metabolism", "mRNA surveillance pathway", "nucleotide excision repair" was indispensable for redifferentiation of the calli. Expression pattern of 12 miRNAs, including csn-micR390e, csn-miR156b-5p, csn-miR157d-5p, csn-miR156, csn-miR166a-3p, csn-miR166e, csn-miR167d, csn-miR393c-3p, csn-miR394, csn-miR396a-3p, csn-miR396 and csn-miR396e-3p, was validated by qRT-PCR among 57 differentially expressed phase-specific miRNAs. Validation also confirmed that regulatory module of csn-miR167d/ERF3, csn-miR156/SPB1, csn-miR166a-3p/ATHB15, csn-miR396/AIP15A, csn-miR157d-5p/GST and csn-miR393c-3p/ATG18b might play important roles in regulating the phase changes during tissue culture of stem explants.
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17
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Pirrò S, Matic I, Guidi A, Zanella L, Gismondi A, Cicconi R, Bernardini R, Colizzi V, Canini A, Mattei M, Galgani A. Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus. Sci Rep 2019; 9:15145. [PMID: 31641153 PMCID: PMC6805943 DOI: 10.1038/s41598-019-51100-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 01/30/2023] Open
Abstract
MicroRNAs, a class of small, non-coding RNAs, play important roles in plant growth, development and stress response by negatively regulating gene expression. Moringa oleifera Lam. plant has many medical and nutritional uses; however, little attention has been dedicated to its potential for the bio production of active compounds. In this study, 431 conserved and 392 novel microRNA families were identified and 9 novel small RNA libraries constructed from leaf, and cold stress treated callus, using high-throughput sequencing technology. Based on the M. oleifera genome, the microRNA repertoire of the seed was re-evaluated. qRT-PCR analysis confirmed the expression pattern of 11 conserved microRNAs in all groups. MicroRNA159 was found to be the most abundant conserved microRNA in leaf and callus, while microRNA393 was most abundantly expressed in the seed. The majority of predicted microRNA target genes were transcriptional factors involved in plant reproduction, growth/development and abiotic/biotic stress response. In conclusion, this is the first comprehensive analysis of microRNAs in M. oleifera leaf and callus which represents an important addition to the existing M. oleifera seed microRNA database and allows for possible exploitation of plant microRNAs induced with abiotic stress, as a tool for bio-enrichment with pharmacologically important phytochemicals.
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Affiliation(s)
- Stefano Pirrò
- Mir-Nat s.r.l., Rome, 00133, Italy
- Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University London, London, EC1M 6BQ, UK
| | - Ivana Matic
- Mir-Nat s.r.l., Rome, 00133, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Letizia Zanella
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Angelo Gismondi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Vittorio Colizzi
- Mir-Nat s.r.l., Rome, 00133, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Antonella Canini
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Andrea Galgani
- Mir-Nat s.r.l., Rome, 00133, Italy.
- CIMETA, University of Rome Tor Vergata, Rome, Italy.
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18
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Joint RNA-Seq and miRNA Profiling Analyses to Reveal Molecular Mechanisms in Regulating Thickness of Pod Canopy in Brassica napus. Genes (Basel) 2019; 10:genes10080591. [PMID: 31387302 PMCID: PMC6722711 DOI: 10.3390/genes10080591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 07/31/2019] [Indexed: 12/14/2022] Open
Abstract
Oilseed rape (Brassica napus) is the second largest oilseed crop worldwide. As an architecture component of B. napus, thickness of pod canopy (TPC) plays an important role in yield formation, especially under high-density cultivation conditions. However, the mechanisms underlying the regulation of TPC remain unclear. RNA and microRNA (miRNA) profiling of two groups of B. napus lines with significantly different TPC at the bolting with a tiny bud stage revealed differential expressions of numerous genes involved in nitrogen-related pathways. Expression of several nitrogen-related response genes, including ASP5, ASP2, ASN3, ATCYSC1, PAL2, APT2, CRTISO, and COX15, was dramatically changed in the thick TPC lines compared to those in the thin TPC lines. Differentially expressed miRNAs also included many involved in nitrogen-related pathways. Expression of most target genes was negatively associated with corresponding miRNAs, such as miR159, miR6029, and miR827. In addition, 12 (including miR319, miR845, and miR158) differentially expressed miRNAs between two plant tissues sampled (stem apex and flower bud) were identified, implying that they might have roles in determining overall plant architecture. These results suggest that nitrogen signaling may play a pivotal role in regulating TPC in B. napus.
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19
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Peng T, Teotia S, Tang G, Zhao Q. MicroRNAs meet with quantitative trait loci: Small powerful players in regulating quantitative yield traits in rice. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1556. [DOI: 10.1002/wrna.1556] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Ting Peng
- Collaborative Innovation Center of Henan Grain Crops Henan Agricultural University Zhengzhou China
- Research Center for Rice Engineering in Henan Province Henan Agricultural University Zhengzhou China
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain Crops Henan Agricultural University Zhengzhou China
- Department of Biological Sciences Michigan Technological University Houghton Michigan
| | - Guiliang Tang
- Collaborative Innovation Center of Henan Grain Crops Henan Agricultural University Zhengzhou China
- Department of Biological Sciences Michigan Technological University Houghton Michigan
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops Henan Agricultural University Zhengzhou China
- Research Center for Rice Engineering in Henan Province Henan Agricultural University Zhengzhou China
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20
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Dai Z, Wang J, Yang X, Lu H, Miao X, Shi Z. Modulation of plant architecture by the miR156f-OsSPL7-OsGH3.8 pathway in rice. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5117-5130. [PMID: 30053063 PMCID: PMC6184515 DOI: 10.1093/jxb/ery273] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/16/2018] [Indexed: 05/18/2023]
Abstract
Tiller number and plant height are two of the main features of plant architecture that directly influence rice yield. Auxin and miR156, an extensively studied small RNA (smRNA), are both broadly involved in plant development and physiology, suggesting a possible relationship between the two. In this study, we identified a rice T-DNA insertion cluster and dwarf (cd) mutant that has an increased tiller number and reduced plant height. The T-DNA insertion was in close proximity to the miR156f gene and was associated with its up-regulation. Plants overexpressing miR156f resembled the cd mutant. In contrast, plants overexpressing an miR156f target mimic (MIM156fOE) had a reduced tiller number and increased height. Genetic analysis showed that OsSPL7 is a target of miR156f that regulates plant architecture. Plants overexpressing OsSPL7 had a reduced tiller number, while OsSPL7 RNAi plants had an increased tiller number and a reduced height. We also found that OsSPL7 binds directly to the OsGH3.8 promoter to regulate its transcription. Overexpression of OsGH3.8 and OsGH3.8 RNAi partially complemented the MIM156fOE and cd mutant phenotypes, respectively. Our combined data show that the miR156f-OsSPL7-OsGH3.8 pathway regulates tiller number and plant height in rice, and this pathway may allow crosstalk between miR156 and auxin.
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Affiliation(s)
- Zhengyan Dai
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiang Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China
| | - Xiaofang Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences
| | - Huan Lu
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Correspondence:
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Wei C, Zhu L, Wen J, Yi B, Ma C, Tu J, Shen J, Fu T. Morphological, transcriptomics and biochemical characterization of new dwarf mutant of Brassica napus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:97-113. [PMID: 29576090 DOI: 10.1016/j.plantsci.2018.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
Plant height is a key trait of plant architecture, and is responsible for both yield and lodging resistance in Brassica napus. A dwarf mutant line (bnaC.dwf) was obtained by chemical mutagenesis of an inbred line T6. However, the molecular mechanisms and changed biological processes of the dwarf mutant remain to be determined. In this study, a comparative transcriptome analysis between bnaC.dwf and T6 plants was performed to identify genome-wide differentially expressed genes (DEGs) and possible biological processes that may explain the phenotype variations in bnaC.dwf. As a result of this analysis, 60,134,746-60,301,384 clean reads were aligned to 60,074 genes in the B. napus genome, and accounted for 60.03% of the annotated genes. In total, 819 differentially expressed genes were used for GO (Gene Ontology) term and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses with a FDR (false discovery rate) criterion of <0.001, |log2Ratio| ≥ 1. We focused on plant hormone signal transduction pathways, plant-pathogen interaction pathway, protein phosphorylation and degradation pathways and sugar metabolism pathways. Taken together, the decrease in local auxin (IAA) levels, the variation in BnTCH4, BnKAN1, BnERF109, COI1-JAZ9-MYC2, auxin response genes (BnGH3.11, BnSAUR78, and AUX/IAA19), and ABA (abscisic acid) signaling genes (BnADP5, BnSnRK2.1, BnABF3.1) partially accounted for variations of cell proliferation in internodes, shoot and root apical meristem maintenance, abiotic and biotic stress resistance, and pre-harvest sprouting. As a comprehensive consequence of the cross-talk between plant hormones, sugar metabolism, plant-pathogen interactions and protein metabolism, bnaC.dwf presents distinct phenotypes from T6. These results will be helpful for shedding light on molecular mechanisms in the dwarf mutant, and give insight into further molecular breeding of semi-dwarf B. napus.
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Affiliation(s)
- Chao Wei
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Lixia Zhu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jing Wen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Bin Yi
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Chaozhi Ma
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxing Tu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Jinxiong Shen
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
| | - Tingdong Fu
- Tingdong Fu National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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Srivastava S, Sharma A. Study of microRNA mediated gene regulation in Striga hermonthica through in-silico approach. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.aggene.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Zhao D, Xia X, Wei M, Sun J, Meng J, Tao J. Overexpression of herbaceous peony miR156e-3p improves anthocyanin accumulation in transgenic Arabidopsis thaliana lateral branches. 3 Biotech 2017; 7:379. [PMID: 29071176 DOI: 10.1007/s13205-017-1011-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/14/2017] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) play critical regulatory roles in plant growth and development. In the present study, the function of herbaceous peony (Paeonia lactiflora Pall.) miR156e-3p in the regulation of color formation has been investigated. Firstly, P. lactiflora miR156e-3p precursor sequence (pre-miR156e-3p) was isolated. Subsequently, the overexpression vector of pre-miR156e-3p was constructed and transformed into Arabidopsis thaliana. Moreover, the medium screening, GUS staining, polymerase chain reaction (PCR) of the GUS region and real-time quantitative PCR (qRT-PCR) of miR156e-3p all confirmed that the purpose gene had been successfully transferred into Arabidopsis plants and expressed, which resulted in apparent purple lateral branches. And this change in color was caused by the improved anthocyanin accumulation. In addition, expression analysis had shown that the level of miR156e-3p transcript was increased, while transcription level of target gene squamosa promoter binding protein-like gene (SPL1), encoding SPL transcription factor that negatively regulated anthocyanin accumulation, was repressed in miR156e-3p-overexpressing transgenic plants, and its downstream gene dihydroflavonol 4-reductase gene (DFR) that was directly involved in anthocyanin biosynthesis was strongly expressed, which resulted in anthocyanin accumulation of Arabidopsis lateral branches. These findings would improve the understanding of miRNAs regulation of color formation in P. lactiflora.
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Affiliation(s)
- Daqiu Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Xing Xia
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Mengran Wei
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jing Sun
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jiasong Meng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
| | - Jun Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 People's Republic of China
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Singh I, Smita S, Mishra DC, Kumar S, Singh BK, Rai A. Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea. FRONTIERS IN PLANT SCIENCE 2017; 8:1943. [PMID: 29209340 PMCID: PMC5702422 DOI: 10.3389/fpls.2017.01943] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/30/2017] [Indexed: 05/30/2023]
Abstract
Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shuchi Smita
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dwijesh C. Mishra
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Binay K. Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Liu M, Yu H, Zhao G, Huang Q, Lu Y, Ouyang B. Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 2017; 18:481. [PMID: 28651543 PMCID: PMC5485680 DOI: 10.1186/s12864-017-3869-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/19/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Abiotic stresses cause severe loss of crop production. Among them, drought is one of the most frequent environmental stresses, which limits crop growth, development and productivity. Plant drought tolerance is fine-tuned by a complex gene regulatory network. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success to improve plant yield and quality. Recent studies have demonstrated that microRNAs play critical roles in plant drought tolerance. However, little is known about the microRNA in drought response of the model plant tomato. Here, we described the profiling of drought-responsive microRNA and mRNA in tomato using high-throughput next-generation sequencing. RESULTS Drought stress was applied on the seedlings of M82, a drought-sensitive cultivated tomato genotype, and IL9-1, a drought-tolerant introgression line derived from the stress-resistant wild species Solanum pennellii LA0716 and M82. Under drought, IL9-1 performed superior than M82 regarding survival rate, H2O2 elimination and leaf turgor maintenance. A total of four small RNA and eight mRNA libraries were constructed and sequenced using Illumina sequencing technology. 105 conserved and 179 novel microRNAs were identified, among them, 54 and 98 were differentially expressed upon drought stress, respectively. The majority of the differentially-expressed conserved microRNAs was up-regulated in IL9-1 whereas down-regulated in M82. Under drought stress, 2714 and 1161 genes were found to be differentially expressed in M82 and IL9-1, respectively, and many of their homologues are involved in plant stress, such as genes encoding transcription factor and protein kinase. Various pathways involved in abiotic stress were revealed by Gene Ontology and pathway analysis. The mRNA sequencing results indicated that most of the target genes were regulated by their corresponding microRNAs, which suggested that microRNAs may play essential roles in the drought tolerance of tomato. CONCLUSION In this study, numerous microRNAs and mRNAs involved in the drought response of tomato were identified using high-throughput sequencing, which will provide new insights into the complex regulatory network of plant adaption to drought stress. This work will also help to exploit new players functioning in plant drought-stress tolerance.
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Affiliation(s)
- Minmin Liu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Gangjun Zhao
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiufeng Huang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Yongen Lu
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology (MOE), Huazhong Agricultural University, Wuhan, 430070 China
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26
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Liu H, Able AJ, Able JA. SMARTER De-Stressed Cereal Breeding. TRENDS IN PLANT SCIENCE 2016; 21:909-925. [PMID: 27514453 DOI: 10.1016/j.tplants.2016.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 05/06/2023]
Abstract
In cereal breeding programs, improved yield potential and stability are ultimate goals when developing new varieties. To facilitate achieving these goals, reproductive success under stressful growing conditions is of the highest priority. In recent times, small RNA (sRNA)-mediated pathways have been associated with the regulation of genes involved in stress adaptation and reproduction in both model plants and several cereals. Reproductive and physiological traits such as flowering time, reproductive branching, and root architecture can be manipulated by sRNA regulatory modules. We review sRNA-mediated pathways that could be exploited to expand crop diversity with adaptive traits and, in particular, the development of high-yielding stress-tolerant cereals: SMARTER cereal breeding through 'Small RNA-Mediated Adaptation of Reproductive Targets in Epigenetic Regulation'.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, University of Adelaide, Waite Research Institute, PMB 1, Glen Osmond, South Australia 5064, Australia.
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Zhou Y, Xu Z, Duan C, Chen Y, Meng Q, Wu J, Hao Z, Wang Z, Li M, Yong H, Zhang D, Zhang S, Weng J, Li X. Dual transcriptome analysis reveals insights into the response to Rice black-streaked dwarf virus in maize. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4593-609. [PMID: 27493226 PMCID: PMC4973738 DOI: 10.1093/jxb/erw244] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Maize rough dwarf disease (MRDD) is a viral infection that results in heavy yield losses in maize worldwide, particularly in the summer maize-growing regions of China. MRDD is caused by the Rice black-streaked dwarf virus (RBSDV). In the present study, analyses of microRNAs (miRNAs), the degradome, and transcriptome sequences were used to elucidate the RBSDV-responsive pathway(s) in maize. Genomic analysis indicated that the expression of three non-conserved and 28 conserved miRNAs, representing 17 known miRNA families and 14 novel miRNAs, were significantly altered in response to RBSDV when maize was inoculated at the V3 (third leaf) stage. A total of 99 target transcripts from 48 genes of 10 known miRNAs were found to be responsive to RBSDV infection. The annotations of these target genes include a SQUAMOSA promoter binding (SPB) protein, a P450 reductase, an oxidoreductase, and a ubiquitin-related gene, among others. Characterization of the entire transcriptome suggested that a total of 28 and 1085 differentially expressed genes (DEGs) were detected at 1.5 and 3.0 d, respectively, after artificial inoculation with RBSDV. The expression patterns of cell wall- and chloroplast-related genes, and disease resistance- and stress-related genes changed significantly in response to RBSDV infection. The negatively regulated genes GRMZM2G069316 and GRMZM2G031169, which are the target genes for miR169i-p5 and miR8155, were identified as a nucleolin and a NAD(P)-binding Rossmann-fold superfamily protein in maize, respectively. The gene ontology term GO:0003824, including GRMZM2G031169 and other 51 DEGs, was designated as responsive to RBSDV.
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Affiliation(s)
- Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Zhennan Xu
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Canxing Duan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Yanping Chen
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Qingchang Meng
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Jirong Wu
- Jiangsu Academy of Agricultural Sciences, Zhongling Street, Xuanwu District, Nanjing, Jiangsu Province 210014, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang Province 150030, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China
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Pandey A, Sharma M, Pandey GK. Emerging Roles of Strigolactones in Plant Responses to Stress and Development. FRONTIERS IN PLANT SCIENCE 2016; 7:434. [PMID: 27092155 PMCID: PMC4821062 DOI: 10.3389/fpls.2016.00434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/21/2016] [Indexed: 05/03/2023]
Abstract
Our environment constantly undergoes changes either natural or manmade affecting growth and development of all the organisms including plants. Plants are sessile in nature and therefore to counter environmental changes such as light, temperature, nutrient and water availability, pathogen, and many others; plants have evolved intricate signaling mechanisms, composed of multiple components including several plant hormones. Research conducted in the last decade has placed Strigolactones (SLs) in the growing list of plant hormones involved in coping with environmental changes. SLs are carotenoid derivatives functioning as both endogenous and exogenous signaling molecules in response to various environmental cues. Initially, SLs were discovered as compounds that are harmful to plants due to their role as stimulants in seed germination of parasitic plants, a more beneficial role in plant growth and development was uncovered much later. SLs are required for maintaining plant architecture by regulating shoot and root growth in response to various external stimuli including arbuscular mycorrhizal fungi, light, nutrients, and temperature. Moreover, a role for SLs has also been recognized during various abiotic and biotic stress conditions making them suitable target for generating genetically engineered crop plants with improved yield. This review discusses the biosynthesis of SLs and their regulatory and physiological roles in various stress conditions. Understanding of detailed signaling mechanisms of SLs will be an important factor for designing genetically modified crops for overcoming the problem of crop loss under stressful conditions.
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Affiliation(s)
- Amita Pandey
- Department of Plant Molecular Biology, University of DelhiNew Delhi, India
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Yang J, Zhang F, Li J, Chen JP, Zhang HM. Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus. PLoS One 2016; 11:e0146946. [PMID: 26799317 PMCID: PMC4723043 DOI: 10.1371/journal.pone.0146946] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022] Open
Abstract
Rice stripe virus (RSV) is one of the most serious rice viruses in East Asia. To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed as a result of RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.
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Affiliation(s)
- Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Jing Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jian-Ping Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- * E-mail: (HZ); (JC)
| | - Heng-Mu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- * E-mail: (HZ); (JC)
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Makhzoum A, Yousefzadi M, Malik S, Gantet P, Tremouillaux-Guiller J. Strigolactone biology: genes, functional genomics, epigenetics and applications. Crit Rev Biotechnol 2015; 37:151-162. [PMID: 26669271 DOI: 10.3109/07388551.2015.1121967] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Strigolactones (SLs) represent an important new plant hormone class marked by their multifunctional role in plant and rhizosphere interactions. These compounds stimulate hyphal branching in arbuscular mycorrhizal fungi (AMF) and seed germination of root parasitic plants. In addition, they are involved in the control of plant architecture by inhibiting bud outgrowth as well as many other morphological and developmental processes together with other plant hormones such as auxins and cytokinins. The biosynthetic pathway of SLs that are derived from carotenoids was partially decrypted based on the identification of mutants from a variety of plant species. Only a few SL biosynthetic and regulated genes and related regulatory transcription factors have been identified. However, functional genomics and epigenetic studies started to give first elements on the modality of the regulation of SLs related genes. Since they control plant architecture and plant-rhizosphere interaction, SLs start to be used for agronomical and biotechnological applications. Furthermore, the genes involved in the SL biosynthetic pathway and genes regulated by SL constitute interesting targets for plant breeding. Therefore, it is necessary to decipher and better understand the genetic determinants of their regulation at different levels.
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Affiliation(s)
- Abdullah Makhzoum
- a Department of Biology , University of Western Ontario , London , Ontario , Canada
| | - Morteza Yousefzadi
- b Department of Marine Biology , Faculty of Marine Sciences and Technology, Hormozgan University , Bandar Abbas , Iran
| | - Sonia Malik
- c Health Sciences Graduate Program, Biological and Health Sciences Centre, Federal University of Maranhão , São Luís, MA , Brazil
| | - Pascal Gantet
- d Faculté des Sciences , Université de Montpellier , UMR DIADE , Montpellier , France , and
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Xu K, Sun F, Chai G, Wang Y, Shi L, Liu S, Xi Y. De novo assembly and transcriptome analysis of two contrary tillering mutants to learn the mechanisms of tillers outgrowth in switchgrass (Panicum virgatum L.). FRONTIERS IN PLANT SCIENCE 2015; 6:749. [PMID: 26442062 PMCID: PMC4584987 DOI: 10.3389/fpls.2015.00749] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/02/2015] [Indexed: 05/20/2023]
Abstract
Tillering is an important trait in monocotyledon plants. The switchgrass (Panicum virgatum), studied usually as a source of biomass for energy production, can produce hundreds of tillers in its lifetime. Studying the tillering of switchgrass also provides information for other monocot crops. High-tillering and low-tillering mutants were produced by ethyl methanesulfonate mutagenesis. Alteration of tillering ability resulted from different tiller buds outgrowth in the two mutants. We sequenced the tiller buds transcriptomes of high-tillering and low-tillering plants using next-generation sequencing technology, and generated 34 G data in total. In the de novo assembly results, 133,828 unigenes were detected with an average length of 1,238 bp, and 5,290 unigenes were differentially expressed between the two mutants, including 3,225 up-regulated genes and 2,065 down-regulated genes. Differentially expressed gene analysis with functional annotations was performed to identify candidate genes involved in tiller bud outgrowth processes using Gene Ontology classification, Cluster of Orthologous Groups of proteins, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. This is the first study to explore the tillering transcriptome in two types of tillering mutants by de novo sequencing.
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Affiliation(s)
- Kaijie Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- Institute of Cotton Research of CAASAnyang, China
| | - Fengli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- *Correspondence: Yajun Xi and Fengli Sun, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, No. 3, Taicheng Road, Yangling, Shaanxi 712100, China, ;
| | - Guaiqiang Chai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Yongfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Lili Shi
- HanDanShi Agriculture Academy of SciencesHandan, China
| | - Shudong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Yajun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F UniversityYangling, China
- *Correspondence: Yajun Xi and Fengli Sun, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, No. 3, Taicheng Road, Yangling, Shaanxi 712100, China, ;
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