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Bravo-Vázquez LA, García-Ortega M, Medina-Feria S, Srivastava A, Paul S. Identification and expression profiling of microRNAs in leaf tissues of Foeniculum vulgare Mill. under salinity stress. PLANT SIGNALING & BEHAVIOR 2024; 19:2361174. [PMID: 38825852 DOI: 10.1080/15592324.2024.2361174] [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: 04/13/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
Foeniculum vulgare Mill. commonly known as fennel, is a globally recognized aromatic medicinal plant and culinary herb with widespread popularity due to its antimicrobial, antioxidant, carminative, and diuretic properties, among others. Although the phenotypic effects of salinity stress have been previously explored in fennel, the molecular mechanisms underlying responses to elevated salinity in this plant remain elusive. MicroRNAs (miRNAs) are tiny, endogenous, and extensively conserved non-coding RNAs (ncRNAs) typically ranging from 20 to 24 nucleotides (nt) in length that play a major role in a myriad of biological functions. In fact, a number of miRNAs have been extensively associated with responses to abiotic stress in plants. Consequently, employing computational methodologies and rigorous filtering criteria, 40 putative miRNAs belonging to 25 different families were characterized from fennel in this study. Subsequently, employing the psRNATarget tool, a total of 67 different candidate target transcripts for the characterized fennel miRNAs were predicted. Additionally, the expression patterns of six selected fennel miRNAs (i.e. fvu-miR156a, fvu-miR162a-3p, fvu-miR166a-3p, fvu-miR167a-5p, fvu-miR171a-3p, and fvu-miR408-3p) were analyzed under salinity stress conditions via qPCR. This article holds notable significance as it identifies not only 40 putative miRNAs in fennel, a non-model plant, but also pioneers the analysis of their expression under salinity stress conditions.
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Affiliation(s)
| | - Mariana García-Ortega
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
| | - Sara Medina-Feria
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
| | | | - Sujay Paul
- School of Engineering and Sciences, Tecnologico de Monterrey, San Pablo, Queretaro, Mexico
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Liang Y, Yang X, Wang C, Wang Y. miRNAs: Primary modulators of plant drought tolerance. JOURNAL OF PLANT PHYSIOLOGY 2024; 301:154313. [PMID: 38991233 DOI: 10.1016/j.jplph.2024.154313] [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: 11/20/2023] [Revised: 06/17/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024]
Abstract
Drought is a principal environmental factor that affects the growth and development of plants. Accordingly, plants have evolved adaptive mechanisms to cope with adverse environmental conditions. One of the mechanisms is gene regulation mediated by microRNAs (miRNAs). miRNAs are regarded as primary modulators of gene expression at the post-transcriptional level and have been shown to participate in drought stress response, including ABA response, auxin signaling, antioxidant defense, and osmotic regulation through downregulating the corresponding targets. miRNA-based genetic reconstructions have the potential to improve the tolerance of plants to drought. However, there are few precise classification and discussion of miRNAs in specific response behaviors to drought stress and their applications. This review summarized and discussed the specific response behaviors of miRNAs under drought stress and the role of miRNAs as regulators in the response of plants to drought and highlighted that the modification of miRNAs might effectively improve the tolerance of plants to drought.
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Affiliation(s)
- Yanting Liang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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3
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Hao H, Xie B, Zhao D, Kang J, Jiang X, Gai Y. Proteomic insights into adventitious root formation in Larix kaempferi. J Proteomics 2024; 307:105288. [PMID: 39173904 DOI: 10.1016/j.jprot.2024.105288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 08/09/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
The adventitious root formaton (ARF) in excised plant parts is essential for the survival of isolated plant fragments. In this study, we explored the complex mechanisms of ARF in Larix kaempferi by conducting a comprehensive proteomic analysis across three distinct stages: the induction of adventitious root primordia (C1, 0-25 d), the formation of adventitious root primordia (C2, 25-35 d), and the elongation of adventitious roots (C3, 35-45 d). We identified 1976 proteins, with 263 and 156 proteins exhibiting increased abundance in the C2/C1 and C3/C2 transitions, respectively. In contrast, a decrease in the abundance of 106 and 132 proteins suggests a significant demand for metabolic processes during the C2/C1 phase. The abundance of IAA-amino acid hydrolase and S-adenosylmethionine synthase were increased in the C2/C1 phase, underscoring the role of auxin in adventitious root induction. The decrease in abundance of photosynthesis-related proteins during the C2/C1 phase highlights the significance of initial light conditions in adventitious root induction. Moreover, variation in cell wall synthesis and metabolic proteins in the C2/C1 and C3/C2 stages suggests that cell wall metabolism is integral to adventitious root regeneration. Gene Ontology enrichment analysis revealed pathways related to protein modification enzymes, including deubiquitinases and kinases, which are crucial for modulating protein modifications to promote ARF. Furthermore, the increased abundance of antioxidant enzymes, such as peroxidases and glutathione peroxidases, indicates a potential approach for enhancing ARF by supplementing the culture medium with antioxidants. Our study provides insights into metabolic changes during ARF in L. kaempferi, offering strategies to enhance adventitious root regeneration. These findings have the potential to refine plant propagation techniques and expedite breeding processes. SIGNFICANCE: The main challenge in the asexual reproduction technology of Larix kaempferi lies in adventitious root formation (ARF). While numerous studies have concentrated on the efficiency of ARF, proteomic data are currently scarce. In this study, we collected samples from three stages of ARF in L. kaempferi and subsequently performed proteomic analysis. The data generated not only reveal changes in protein abundance but also elucidate key metabolic processes involved in ARF. These insights offer a novel perspective on addressing the challenge of adventurous root regeneration.
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Affiliation(s)
- Haifei Hao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Baohui Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Dadi Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Jiaqi Kang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Xiangning Jiang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China
| | - Ying Gai
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, 100083 Beijing, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, 100083 Beijing, China.
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Nivedha M, Harish S, Angappan K, Karthikeyan G, Kumar KK, Murugan M, Infant Richard J. Profiling of Groundnut bud necrosis orthotospovirus-responsive microRNA and their targets in tomato based on deep sequencing. J Virol Methods 2024; 327:114924. [PMID: 38574773 DOI: 10.1016/j.jviromet.2024.114924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Tomato, an extensively cultivated vegetable crop produces miRNAs in response to infection with Groundnut bud necrosis orthotospovirus, a viral pathogen causing significant economic losses. High-throughput miRNA sequencing was performed on tomato leaves inoculated with GBNV and mock-inoculated leaves as controls. Analysis revealed 73 known miRNAs belonging to 24 miRNA families, with variable expression levels. Interestingly, 39 miRNAs were upregulated, and 34 were downregulated in response to GBNV infection. Stem-loop quantitative reverse transcription PCR validated the differential expression of selected miRNAs. Additionally, 30 miRNA encoded proteins were identified to be involved in disease resistance and susceptibility. The miRNA-target interactions were found to play significant roles in cellular and metabolic activities, as well as modulating signaling pathways during the plant-virus interaction. The findings shed light on the intricate regulatory network of miRNAs in tomato response to viral infection and may contribute to developing strategies for improving crop protection against viral diseases.
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Affiliation(s)
- M Nivedha
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - S Harish
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India.
| | - K Angappan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - K K Kumar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - M Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - J Infant Richard
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
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Luo H, Li T, Guan Y, Zhang Z, Zhang Z, Zhang Z, Li H. FvemiR160-FveARF18A-FveAP1/FveFUL module regulates flowering time in woodland strawberry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1130-1147. [PMID: 37967025 DOI: 10.1111/tpj.16544] [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: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
Flowering is an indicator of plant transformation from vegetative to reproductive growth. miR160 has been shown to have a significant effect on the growth and development of fruits, leaves, and roots of plants or their stress response to environment, but the participation of miR160 in regulating flowering time in plants is unclear. In this study, we found that two FvemiR160s (FvemiR160a/FvemiR160b) mature sequences in strawberry (Fragaria vesca) were consistent. It was displayed that the miR160 mature sequence is highly conserved in various species, and the miR160 mature sequence formed by the 5' arm of the MIR160 precursor was more conserved. Three FveARFs in woodland strawberry were negatively regulated by FvemiR160a, among which FveARF18A was the most significant. Phylogenetic analysis indicated that FvemiR160 is closely related to apple (Malus domestica), grape (Vitis vinifera), and Arabidopsis thaliana, while FveARF18A is closely related to RcARF18. Subsequently, we demonstrated that FvemiR160a can target cutting FveARF18A to negatively regulate its expression by RLM-5' RACE, cleavage site mutation, and GFP fluorescence assay. Moreover, we observed that FveMIR160a overexpressed plants have advanced flowering, while mFveARF18A overexpressed plants have delayed flowering. We also verified that FveARF18A negatively regulates the expression of FveAP1 and FveFUL by binding their promoters by yeast one-hybrid, LUC, and GUS assay, and FveAP1 and FveFUL transgenic Arabidopsis showed early flowering phenotype. In addition, the expression level of FvemiR160a was decreased obviously while that of FveARF18A was increased obviously by MeJA, GA and IAA. In conclusion, our study reveals the important role of the FvemiR160-FveARF18A-FveAP1/FveFUL module in the flowering process of woodland strawberry and provides a new pathway for studying flowering.
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Affiliation(s)
- He Luo
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tianyu Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuhan Guan
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhuo Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zihui Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
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Jha UC, Nayyar H, Roychowdhury R, Prasad PVV, Parida SK, Siddique KHM. Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108164. [PMID: 38008006 DOI: 10.1016/j.plaphy.2023.108164] [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: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/28/2023]
Abstract
Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.
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Affiliation(s)
- Uday Chand Jha
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India.
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - The Volcani Institute, Rishon Lezion 7505101, Israel
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA
| | - Swarup K Parida
- National Institute of Plant Genomic Research, New Delhi, 110067, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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7
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Lv X, Tian S, Huang S, Wei J, Han D, Li J, Guo D, Zhou Y. Genome-wide identification of the longan R2R3-MYB gene family and its role in primary and lateral root. BMC PLANT BIOLOGY 2023; 23:448. [PMID: 37741992 PMCID: PMC10517564 DOI: 10.1186/s12870-023-04464-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
R2R3-MYB is an important transcription factor family that regulates plant growth and development. Root development directly affects the absorption of water and nutrients by plants. Therefore, to understand the regulatory role of R2R3-MYB transcription factor family in root development of longan, this study identified the R2R3-MYB gene family members at the genome-wide level, and analyzed their phylogenetic characteristics, physical and chemical properties, gene structure, chromosome location and tissue expression. The analysis identified 124 R2R3-MYB family members in the longan genome. Phylogenetic analysis divided these members into 22 subfamilies, and the members of the unified subfamily had similar motifs and gene structures. The result of qRT-PCR showed that expression levels of DlMYB33, DlMYB34, DlMYB59, and DlMYB77 were significantly higher in main roots than in lateral as opposed to those of DlMYB35, DlMYB69, DlMYB70, and DlMYB83, which were significantly lower. SapBase database prediction and miRNAs sequencing results showed that 34 longan miRNAs could cleave R2R3-MYB, including 17 novel miRNAs unique to longan. The qRT-PCR and subcellular localization experiments of DlMYB92 and DlMYB98 showed that DlMYB92 is a key factor that regulates transcription in the nucleus and participates in the regulation of longan lateral root development. Longan also has a conserved miRNA-MYB-lateral root development regulation mechanism. This study provides a reference for further research on the transcriptional regulation of the miRNA-R2R3-MYB module in the root development of longan.
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Affiliation(s)
- Xinmin Lv
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shichang Tian
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shilian Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Junbin Wei
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dongmei Han
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jianguang Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dongliang Guo
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Yan Zhou
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, 524048, China.
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Teng C, Zhang C, Guo F, Song L, Fang Y. Advances in the Study of the Transcriptional Regulation Mechanism of Plant miRNAs. Life (Basel) 2023; 13:1917. [PMID: 37763320 PMCID: PMC10533097 DOI: 10.3390/life13091917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
MicroRNAs (miRNA) are a class of endogenous, non-coding, small RNAs with about 22 nucleotides (nt), that are widespread in plants and are involved in various biological processes, such as development, flowering phase transition, hormone signal transduction, and stress response. The transcriptional regulation of miRNAs is an important process of miRNA gene regulation, and it is essential for miRNA biosynthesis and function. Like mRNAs, miRNAs are transcribed by RNA polymerase II, and these transcription processes are regulated by various transcription factors and other proteins. Consequently, the upstream genes regulating miRNA transcription, their specific expression, and the regulating mechanism were reviewed to provide more information for further research on the miRNA regulatory mechanism and help to further understand the regulatory networks of plant miRNAs.
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Affiliation(s)
| | | | | | | | - Yanni Fang
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China; (C.T.); (C.Z.); (F.G.)
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9
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Yang L, Ping T, Lu W, Song S, Wang J, Wang Q, Chai G, Bai Y, Chen Y. Genome-wide identification of auxin-responsive microRNAs in the poplar stem. Genes Genomics 2023; 45:1073-1083. [PMID: 37336805 DOI: 10.1007/s13258-023-01385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/01/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. OBJECTIVE This report was designed to identify auxin-responsive miRNAs during wood formation. METHODS Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. RESULTS In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. CONCLUSIONS Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.
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Affiliation(s)
- Lihua Yang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tao Ping
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenjin Lu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sangfa Song
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qiao Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
| | - Yue Bai
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
| | - Yan Chen
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China.
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10
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Lee KW, Chen JJW, Wu CS, Chang HC, Chen HY, Kuo HH, Lee YS, Chang YL, Chang HC, Shiue SY, Wu YC, Ho YC, Chen PW. Auxin plays a role in the adaptation of rice to anaerobic germination and seedling establishment. PLANT, CELL & ENVIRONMENT 2023; 46:1157-1175. [PMID: 36071575 DOI: 10.1111/pce.14434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Auxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies revealed that excessive levels of indole-3-acetic acid(IAA) frequently cause the inhibition of plant growth and development. In this study, the high-level accumulation of endogenous IAA is observed under dark submergence, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167-ARF-GH3 pathway. The OsGH3-8 encodes an IAA-amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressing OsGH3-8 increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. Our studies reveal that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance.
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Affiliation(s)
- Kuo-Wei Lee
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Shen Wu
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Ho-Chun Chang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Hong-Yue Chen
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Hsin-Hao Kuo
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Ya-Shan Lee
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Yan-Lun Chang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Hung-Chia Chang
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Shiau-Yu Shiue
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Yi-Chen Wu
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Yi-Cheng Ho
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
| | - Peng-Wen Chen
- Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan
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Song X, Xiong Y, Kong X, Huang G. Roles of auxin response factors in rice development and stress responses. PLANT, CELL & ENVIRONMENT 2023; 46:1075-1086. [PMID: 36397176 DOI: 10.1111/pce.14494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Auxin signalling plays a key role in various developmental processes ranging from embryogenesis to senescence in plants. Auxin response factor (ARF), a key component of auxin signalling, functions by binding to auxin response element within promoter of auxin response genes, activating or repressing the target genes. Increasing evidences show that ARFs are crucial for plant response to stresses. This review summarises the recent advance on the functions and their regulatory pathways of rice ARFs in development and responding to stresses. The importance of OsARFs is demonstrated by their roles in triggering various physiological, biochemical and molecular reactions to resist adverse environmental conditions. We also describe the transcriptional and post-transcriptional regulation of OsARFs, and discuss the major challenges in this area.
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Affiliation(s)
- Xiaoyun Song
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Xiong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuzhen Kong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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12
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Khan AH, Min L, Ma Y, Zeeshan M, Jin S, Zhang X. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:680-697. [PMID: 36221230 PMCID: PMC10037161 DOI: 10.1111/pbi.13946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 05/16/2023]
Abstract
Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Muhammad Zeeshan
- Guangxi Key Laboratory for Agro‐Environment and Agro‐Product Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, College of AgricultureGuanxi UniversityNanningChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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13
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Sang Q, Fan L, Liu T, Qiu Y, Du J, Mo B, Chen M, Chen X. MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis. Nat Commun 2023; 14:1449. [PMID: 36949101 PMCID: PMC10033679 DOI: 10.1038/s41467-023-36774-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/14/2023] [Indexed: 03/24/2023] Open
Abstract
MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remain ambiguous. Here we show that HYPONASTIC LEAVES 1 (HYL1)-a key component of miRNA biogenesis-acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in the temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 allele that rescues hyl1-2's defects in miRNA biogenesis and thermoresponsive hypocotyl elongation. Genome-wide miRNA and transcriptome analysis revealed microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-PROTEIN-LIKE 9 (SPL9) to be critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miR156/SPL9 module as a previously uncharacterized genetic circuit that enables plant growth plasticity in response to environmental temperature and light changes.
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Affiliation(s)
- Qing Sang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Lusheng Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Tianxiang Liu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of the Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, 100871, China.
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14
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Chen Y, Yang W, Gao R, Chen Y, Zhou Y, Xie J, Zhang F. Genome-Wide Analysis of microRNAs and Their Target Genes in Dongxiang Wild Rice ( Oryza rufipogon Griff.) Responding to Salt Stress. Int J Mol Sci 2023; 24:ijms24044069. [PMID: 36835475 PMCID: PMC9960954 DOI: 10.3390/ijms24044069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Rice (Oryza sativa) is a staple food for more than half of the world's population, and its production is critical for global food security. Moreover, rice yield decreases when exposed to abiotic stresses, such as salinity, which is one of the most detrimental factors for rice production. According to recent trends, as global temperatures continue to rise due to climate change, more rice fields may become saltier. Dongxiang wild rice (Oryza rufipogon Griff., DXWR) is a progenitor of cultivated rice and has a high tolerance to salt stress, making it useful for studying the regulatory mechanisms of salt stress tolerance. However, the regulatory mechanism of miRNA-mediated salt stress response in DXWR remains unclear. In this study, miRNA sequencing was performed to identify miRNAs and their putative target genes in response to salt stress in order to better understand the roles of miRNAs in DXWR salt stress tolerance. A total of 874 known and 476 novel miRNAs were identified, and the expression levels of 164 miRNAs were found to be significantly altered under salt stress. The stem-loop quantitative real-time PCR (qRT-PCR) expression levels of randomly selected miRNAs were largely consistent with the miRNA sequencing results, suggesting that the sequencing results were reliable. The gene ontology (GO) analysis indicated that the predicted target genes of salt-responsive miRNAs were involved in diverse biological pathways of stress tolerance. This study contributes to our understanding of DXWR salt tolerance mechanisms regulated by miRNAs and may ultimately improve salt tolerance in cultivated rice breeding using genetic methods in the future.
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Affiliation(s)
- Yong Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Rifang Gao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yaling Chen
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.X.); (F.Z.)
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15
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Lu G, Tian Z, Hao Y, Xu M, Lin Y, Wei J, Zhao Y. Overexpression of soybean microRNA156b enhanced tolerance to phosphorus deficiency and seed yield in Arabidopsis. Sci Rep 2023; 13:652. [PMID: 36635356 PMCID: PMC9837069 DOI: 10.1038/s41598-023-27847-2] [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: 11/01/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
microRNAs (miRNAs) are endogenous small RNAs that are key regulatory factors participating in various biological activities such as the signaling of phosphorus deficiency in the plant. Previous studies have shown that miR156 expression was modulated by phosphorus starvation in Arabidopsis and soybean. However, it is not clear whether the over-expression of soybean miR156b (GmmiR156b) can improve a plant's tolerance to phosphorus deficiency and affect yield component traits. In this study, we generated Arabidopsis transgenic lines overexpressing GmmiR156b and investigated the plant's response to phosphorus deficiency. Compared with the wild type, the transgenic Arabidopsis seedlings had longer primary roots and higher phosphorus contents in roots under phosphorus-deficit conditions, but lower fresh weight root/shoot ratios under either phosphorus-deficient or sufficient conditions. Moreover, the GmmiR156b overexpression transgenic lines had higher phosphorus content in shoots of adult plants and grew better than the wide type under phosphorus-deficient conditions, and exhibited increased seed yields as well as strong pleiotropic developmental morphology such as dwarfness, prolonged growth period, bushy shoot/branching, and shorter silique length, suggesting that the transgenic lines were more tolerant to phosphorus deficiency. In addition, the expression level of four SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes (i.e., AtSPL4/5/6/15) were markedly suppressed in transgenic plants, indicating that they were the main targets negatively regulated by GmmiR156b (especially AtSPL15) and that the enhanced tolerance to phosphorus deficiency and seed yield is conferred mainly by the miR156-mediated downregulation of AtSPL15.
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Affiliation(s)
- Guangyuan Lu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Zhitao Tian
- grid.35155.370000 0004 1790 4137College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430062 People’s Republic of China
| | - Yifan Hao
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Meihua Xu
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongxin Lin
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Jinxing Wei
- grid.459577.d0000 0004 1757 6559College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000 People’s Republic of China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, People's Republic of China.
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16
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Jing X, Zhang H, Huai X, An Q, Qiao Y. Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria × ananassa. BMC Genomics 2022; 23:638. [PMID: 36076187 PMCID: PMC9454143 DOI: 10.1186/s12864-022-08864-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored. RESULTS Here, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified. CONCLUSIONS Taken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.
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Affiliation(s)
- Xiaotong Jing
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hong Zhang
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xinjia Huai
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Qi An
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yushan Qiao
- Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China.
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17
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Xue H, Liu J, Oo S, Patterson C, Liu W, Li Q, Wang G, Li L, Zhang Z, Pan X, Zhang B. Differential Responses of Wheat ( Triticum aestivum L.) and Cotton ( Gossypium hirsutum L.) to Nitrogen Deficiency in the Root Morpho-Physiological Characteristics and Potential MicroRNA-Mediated Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:928229. [PMID: 35845660 PMCID: PMC9281546 DOI: 10.3389/fpls.2022.928229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivum L.) and cotton (Gossypium hirsutum L.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton.
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Affiliation(s)
- Huiyun Xue
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Jia Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Sando Oo
- Department of Biology, East Carolina University, Greenville, NC, United States
- Department of Biology, Elizabeth City State University, Elizabeth City, NC, United States
| | - Caitlin Patterson
- Department of Biology, East Carolina University, Greenville, NC, United States
- Department of Biology, Elizabeth City State University, Elizabeth City, NC, United States
| | - Wanying Liu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qian Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Guo Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Lijie Li
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
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18
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Dong Q, Hu B, Zhang C. microRNAs and Their Roles in Plant Development. FRONTIERS IN PLANT SCIENCE 2022; 13:824240. [PMID: 35251094 PMCID: PMC8895298 DOI: 10.3389/fpls.2022.824240] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 05/26/2023]
Abstract
Small RNAs are short non-coding RNAs with a length ranging between 20 and 24 nucleotides. Of these, microRNAs (miRNAs) play a distinct role in plant development. miRNAs control target gene expression at the post-transcriptional level, either through direct cleavage or inhibition of translation. miRNAs participate in nearly all the developmental processes in plants, such as juvenile-to-adult transition, shoot apical meristem development, leaf morphogenesis, floral organ formation, and flowering time determination. This review summarizes the research progress in miRNA-mediated gene regulation and its role in plant development, to provide the basis for further in-depth exploration regarding the function of miRNAs and the elucidation of the molecular mechanism underlying the interaction of miRNAs and other pathways.
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Affiliation(s)
- Qingkun Dong
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Binbin Hu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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19
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Luo P, Di D, Wu L, Yang J, Lu Y, Shi W. MicroRNAs Are Involved in Regulating Plant Development and Stress Response through Fine-Tuning of TIR1/AFB-Dependent Auxin Signaling. Int J Mol Sci 2022; 23:ijms23010510. [PMID: 35008937 PMCID: PMC8745101 DOI: 10.3390/ijms23010510] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/27/2021] [Accepted: 01/01/2022] [Indexed: 11/30/2022] Open
Abstract
Auxin, primarily indole-3-acetic acid (IAA), is a versatile signal molecule that regulates many aspects of plant growth, development, and stress response. Recently, microRNAs (miRNAs), a type of short non-coding RNA, have emerged as master regulators of the auxin response pathways by affecting auxin homeostasis and perception in plants. The combination of these miRNAs and the autoregulation of the auxin signaling pathways, as well as the interaction with other hormones, creates a regulatory network that controls the level of auxin perception and signal transduction to maintain signaling homeostasis. In this review, we will detail the miRNAs involved in auxin signaling to illustrate its in planta complex regulation.
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Affiliation(s)
- Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
- Correspondence: (P.L.); (D.D.)
| | - Dongwei Di
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
- Correspondence: (P.L.); (D.D.)
| | - Lei Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Jiangwei Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.L.); (W.S.)
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20
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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21
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Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley. Genomics 2021; 113:3735-3749. [PMID: 34517091 DOI: 10.1016/j.ygeno.2021.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023]
Abstract
Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.
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