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Chowdhury MR, Chatterjee C, Ghosh D, Mukherjee J, Shaw S, Basak J. Deciphering miRNA-lncRNA-mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:560-567. [PMID: 38520244 DOI: 10.1111/plb.13639] [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: 06/27/2022] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Abstract
Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non-coding genome information. Non-coding RNAs, like miRNAs and long non-coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post-transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine-protein kinase, polygalacturonase, beta-galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA-mRNA-lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca-miR1535a targeting the mRNA for beta-galactosidase, as well as the lncRNA cca-lnc-020033. Our findings increase knowledge of the non-coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.
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Affiliation(s)
- M R Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - C Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - D Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Mukherjee
- Department of Computer Science and Engineering, Birla Institute of Technology, Mesra, India
| | - S Shaw
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
| | - J Basak
- Department of Biotechnology, Visva-Bharati, Santiniketan, India
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Zhao M, Lei Y, Wu L, Qi H, Song Z, Xu M. The miR159a-PeMYB33 module regulates poplar adventitious rooting through the abscisic acid signal pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:879-891. [PMID: 38271219 DOI: 10.1111/tpj.16643] [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: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
As sessile organisms, plants experience variable environments and encounter diverse stresses during their growth and development. Adventitious rooting, orchestrated by multiple coordinated signaling pathways, represents an adaptive strategy evolved by plants to adapt to cope with changing environmental conditions. This study uncovered the role of the miR159a-PeMYB33 module in the formation of adventitious roots (ARs) synergistically with abscisic acid (ABA) signaling in poplar. Overexpression of miR159a increased the number of ARs and plant height while reducing sensitivity to ABA in transgenic plants. In contrast, inhibition of miR159a (using Short Tandem Target Mimic) or overexpression of PeMYB33 decreased the number of ARs in transgenic plants. Additionally, miR159a targets and cleaves transcripts of PeMYB33 using degradome analysis, which was further confirmed by a transient expression experiment of poplar protoplast. We show the miR159a-PeMYB33 module controls ARs development in poplar through ABA signaling. In particular, we demonstrated that miR159a promotes the expression of genes in the ABA signaling pathway. The findings from this study shed light on the intricate regulatory mechanisms governing the development of ARs in poplar plants. The miR159a-PeMYB33 module, in conjunction with ABA signaling, plays a crucial role in modulating AR formation and subsequent plant growth.
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Affiliation(s)
- Meiqi Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yijing Lei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ling Wu
- Jiangsu Yanjiang Institute of Agricultural Science, Nantong, Jiangsu, 226541, China
| | - Haoran Qi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zihe Song
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Meng Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Kaur S, Seem K, Duhan N, Kumar S, Kaundal R, Mohapatra T. Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress. PLANTA 2024; 259:128. [PMID: 38639776 DOI: 10.1007/s00425-024-04399-x] [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: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
MAIN CONCLUSION Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.
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Affiliation(s)
- Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
- ICAR-Research Complex for North Eastern Hill Region (NEH), Umiam, Meghalaya, 793103, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, USA.
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Saroha M, Arya A, Singh G, Sharma P. Genome-wide expression analysis of novel heat-responsive microRNAs and their targets in contrasting wheat genotypes at reproductive stage under terminal heat stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1328114. [PMID: 38660446 PMCID: PMC11039868 DOI: 10.3389/fpls.2024.1328114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Introduction Heat stress at terminal stage of wheat is critical and leads to huge yield losses worldwide. microRNAs (miRNAs) play significant regulatory roles in gene expression associated with abiotic and biotic stress at the post-transcriptional level. Methods In the present study, we carried out a comparative analysis of miRNAs and their targets in flag leaves as well as developing seeds of heat tolerant (RAJ3765) and heat susceptible (HUW510) wheat genotypes under heat stress and normal conditions using small RNA and degradome sequencing. Results and discussion A total of 84 conserved miRNAs belonging to 35 miRNA families and 93 novel miRNAs were identified in the 8 libraries. Tae-miR9672a-3p, tae-miR9774, tae-miR9669-5p, and tae-miR5048-5p showed the highest expression under heat stress. Tae-miR9775, tae-miR9662b-3p, tae-miR1120a, tae-miR5084, tae-miR1122a, tae-miR5085, tae-miR1118, tae-miR1130a, tae-miR9678-3p, tae-miR7757-5p, tae-miR9668-5p, tae-miR5050, tae-miR9652-5p, and tae-miR9679-5p were expressed only in the tolerant genotype, indicating their role in heat tolerance. Comparison between heat-treated and control groups revealed that 146 known and 57 novel miRNAs were differentially expressed in the various tissues. Eight degradome libraries sequence identified 457 targets of the differentially expressed miRNAs. Functional analysis of the targets indicated their involvement in photosynthesis, spliceosome, biosynthesis of nucleotide sugars and protein processing in the endoplasmic reticulum, arginine and proline metabolism and endocytosis. Conclusion This study increases the number of identified and novel miRNAs along with their roles involved in heat stress response in contrasting genotypes at two developing stages of wheat.
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Affiliation(s)
- Monika Saroha
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana, India
| | - Aditi Arya
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana, India
| | - Gyanendra Singh
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
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Peng C, Xu H, Xie S, Zhong X, Chen L, He Y, Li Z, Zhou Y, Duan L. Unveiling the Regulatory Role of miRNAs in Internode Elongation: Integrated Analysis of MicroRNA and mRNA Expression Profiles across Diverse Dwarfing Treatments in Maize ( Zea mays L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7533-7545. [PMID: 38527761 DOI: 10.1021/acs.jafc.3c09507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
MicroRNAs are crucial regulators of gene expression in maize. However, the mechanisms through which miRNAs control internode elongation remain poorly understood. This study engineered varying levels of internode elongation inhibition, revealing that dwarfing treatments diminished gibberellin levels, curtailed cell longitudinal growth, and slowed the rate of internode elongation. Comprehensive transcriptome and miRNA profiling of the internode elongation zone showed gene expression changes that paralleled the extent of the internode length reduction. We identified 543 genes and 29 miRNAs with significant correlations to internode length, predominantly within families, including miR164 and miR396. By incorporating target gene expression levels, we pinpointed nine miRNA-mRNA pairs that are significantly associated with the regulation of the internode elongation. The inhibitory effects of these miRNAs on their target genes were confirmed through dual-luciferase reporter assays. Overexpression of miR164h in maize resulted in increased internode and cell length, suggesting a novel genetic avenue for manipulating plant stature. These miRNAs may also serve as precise spatiotemporal regulators for in vitro plant development.
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Affiliation(s)
- Chuanxi Peng
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Haidong Xu
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shipeng Xie
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xingyu Zhong
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Limei Chen
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yan He
- National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yuyi Zhou
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Liusheng Duan
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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Yu B, Geng M, Xue Y, Yu Q, Lu B, Liu M, Shao Y, Li C, Xu J, Li J, Hu W, Tang H, Li P, Liu Q, Jing S. Combined miRNA and mRNA sequencing reveals the defensive strategies of resistant YHY15 rice against differentially virulent brown planthoppers. FRONTIERS IN PLANT SCIENCE 2024; 15:1366515. [PMID: 38562566 PMCID: PMC10982320 DOI: 10.3389/fpls.2024.1366515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024]
Abstract
Introduction The brown planthopper (BPH) poses a significant threat to rice production in Asia. The use of resistant rice varieties has been effective in managing this pest. However, the adaptability of BPH to resistant rice varieties has led to the emergence of virulent populations, such as biotype Y BPH. YHY15 rice, which carries the BPH resistance gene Bph15, exhibits notable resistance to biotype 1 BPH but is susceptible to biotype Y BPH. Limited information exists regarding how resistant rice plants defend against BPH populations with varying levels of virulence. Methods In this study, we integrated miRNA and mRNA expression profiling analyses to study the differential responses of YHY15 rice to both avirulent (biotype 1) and virulent (biotype Y) BPH. Results YHY15 rice demonstrated a rapid response to biotype Y BPH infestation, with significant transcriptional changes occurring within 6 hours. The biotype Y-responsive genes were notably enriched in photosynthetic processes. Accordingly, biotype Y BPH infestation induced more intense transcriptional responses, affecting miRNA expression, defenserelated metabolic pathways, phytohormone signaling, and multiple transcription factors. Additionally, callose deposition was enhanced in biotype Y BPH-infested rice seedlings. Discussion These findings provide comprehensive insights into the defense mechanisms of resistant rice plants against virulent BPH, and may potentially guide the development of insect-resistant rice varieties.
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Affiliation(s)
- Bin Yu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Mengjia Geng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yu Xue
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Qingqing Yu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, China
| | - Miao Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yuhan Shao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Chenxi Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jingang Xu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Jintao Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Wei Hu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hengmin Tang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Peng Li
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Qingsong Liu
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shengli Jing
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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Kumar S, Sharma N, Sopory SK, Sanan-Mishra N. miRNAs and genes as molecular regulators of rice grain morphology and yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108363. [PMID: 38281341 DOI: 10.1016/j.plaphy.2024.108363] [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: 07/03/2023] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
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Affiliation(s)
- Sudhir Kumar
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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Qiao L, Wu Q, Yuan L, Huang X, Yang Y, Li Q, Shahzad N, Li H, Li W. SMALL PLANT AND ORGAN 1 ( SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice. Int J Mol Sci 2023; 24:16974. [PMID: 38069299 PMCID: PMC10707047 DOI: 10.3390/ijms242316974] [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: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation.
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Affiliation(s)
- Lei Qiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Qilong Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Liuzhen Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Xudong Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Yutao Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Qinying Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Nida Shahzad
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
| | - Haifeng Li
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenqiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, China (X.H.); (Y.Y.); (Q.L.); (N.S.)
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Wang Q, Wan J, Dang K, Meng S, Hu D, Lin Y, Qiu X, Guo Z, Fu Z, Ding D, Tang J. zma-miR159 targets ZmMYB74 and ZmMYB138 transcription factors to regulate grain size and weight in maize. PLANT PHYSIOLOGY 2023; 193:2430-2441. [PMID: 37590954 DOI: 10.1093/plphys/kiad455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/15/2023] [Accepted: 07/01/2023] [Indexed: 08/19/2023]
Abstract
Endosperm cell number is critical in determining grain size in maize (Zea mays). Here, zma-miR159 overexpression led to enlarged grains in independent transgenic lines, suggesting that zma-miR159 contributes positively to maize grain size. Targeting of ZmMYB74 and ZmMYB138 transcription factor genes by zma-miR159 was validated using 5' RACE and dual-luciferase assay. Lines in which ZmMYB74 was knocked out using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) presented a similar enlarged grain phenotype as those with zma-miR159 overexpression. Downstream genes regulating cell division were identified through DNA affinity purification sequencing using ZmMYB74 and ZmMYB138. Our results suggest that zma-miR159-ZmMYB modules act as an endosperm development hub, participating in the division and proliferation of endosperm cells.
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Affiliation(s)
- Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Kuntai Dang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
- Maize Research Department, Hebi Academy of Agricultural Sciences, Hebi, Henan 458030, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
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Yadav B, Majhi A, Phagna K, Meena MK, Ram H. Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Funct Integr Genomics 2023; 23:317. [PMID: 37837547 DOI: 10.1007/s10142-023-01244-4] [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: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.
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Affiliation(s)
- Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashis Majhi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Phagna
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Wang H, Ouyang J, Jian W, Li M, Zhong J, Yan X, Gao J, Wang X, Li S. Rice miR5504 regulates plant height by affecting cell proliferation and expansion. PHYSIOLOGIA PLANTARUM 2023; 175:e14023. [PMID: 37882316 DOI: 10.1111/ppl.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 10/27/2023]
Abstract
miRNAs play critical roles in the regulation of plant growth and development by cleaving mRNA or repressing transcription. In our previous study, miR5504 with unknown functions was captured by small RNA sequencing. Here, the function and characters of miR5504 were extensively analyzed using CRISPR/Cas9, overexpression strategy, Northern blot, cytological analysis, and transcriptomics analysis. We found that the dwarf phenotype of mir5504 mutants (mir5504-1 and mir5504-2) appeared on 35-day seedlings and became more apparent at the mature stage. The cytological results showed a substantial decrease in the vascular bundle number, cell number and cell length in the mir5504 mutant compared with NIP. In addition, we found that miR5504 regulated plant height by targeting LOC_Os08g16914. The results of RNA-seq revealed that numerous biological processes were mainly enriched, including DNA-binding transcription factor activity, transferase activity, regulation of transcription, metabolic process, and protein binding. Meanwhile, KEEG analysis showed that numerous proteins were associated with cellular processes and metabolism pathways. Taken together, miR5504 may be involved in the regulation of plant height by affecting cell expansion and division of internode in rice.
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Affiliation(s)
- Huihui Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiexiu Ouyang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Wenjia Jian
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiancong Zhong
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Xin Yan
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiadong Gao
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Guangzhou, China
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xin Wang
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, China
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shaobo Li
- Key Laboratory of Molecular Biology and Genetic Engineering of Jiangxi Province, School of Life Sciences, Nanchang University, Nanchang, 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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Yang X, Fu T, Yu R, Zhang L, Yang Y, Xiao D, Wang Y, Wang Y, Wang Y. miR159a modulates poplar resistance against different fungi and bacteria. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107899. [PMID: 37494825 DOI: 10.1016/j.plaphy.2023.107899] [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: 04/07/2023] [Revised: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
Abstract
Trees are inevitably attacked by different kinds of pathogens in their life. However, little is known about the regulatory factors in poplar response to different pathogen infections. MicroRNA159 (miR159) is a highly conserved microRNA (miRNA) in plants and regulates plant development and stress responses. Here, transgenic poplar overexpressing pto-miR159a (OX-159) showed antagonistic regulation mode to poplar stem disease caused by fungi Cytospora chrysosperma and bacteria Lonsdalea populi. OX-159 lines exhibited a higher susceptibility after inoculation with bacterium L. populi, whereas enhanced disease resistance to necrotrophic fungi C. chrysosperma compared with wild-type (WT) poplars. Intriguingly, further disease assay found that OX159 line rendered the poplar susceptible to hemi-biotrophic fungi Colletotrichum gloeosporioide, exhibiting larger necrosis and lower ROS accumulation than WT lines. Transcriptome analyses revealed that more down-regulated differentially expressed genes with disease-resistant domains in OX-159 line compared with WT line. Moreover, the central mediator NPR1 of salicylic acid (SA) pathway showed a decrease in expression level, while jasmonic acid/ethylene (JA/ET) signal pathway marker genes ERF, as well as PR3, MPK3, and MPK6 genes showed an increase level in OX159-2 and OX159-5 compared with WT lines. Further spatio-temporal expression analysis revealed JA/ET signaling was involved in the dynamic response process to C. gloeosporioides in WT and OX159 lines. These results demonstrate that overexpression of pto-miR159a resulted in the crosstalk changes of the downstream hub genes, thereby controlling the disease resistance of poplars, which provides clues for understanding pto-miR159a role in coordinating poplar-pathogen interactions.
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Affiliation(s)
- 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
| | - Tiantian Fu
- 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
| | - Ruen Yu
- 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
| | - Lichun Zhang
- 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; Forestry Investigation and Planning Institute of Liaoning Province, Liaoning, 110122, China
| | - Yuzhang 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
| | - Dandan Xiao
- 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
| | - YuanYuan Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, China
| | - Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, 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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Shen Y, Yang G, Miao X, Shi Z. OsmiR159 Modulate BPH Resistance Through Regulating G-Protein γ Subunit GS3 Gene in Rice. RICE (NEW YORK, N.Y.) 2023; 16:30. [PMID: 37402009 DOI: 10.1186/s12284-023-00646-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
Brown planthopper (BPH) is the most destructive insect pest to rice that causes tremendous yield loss each year in rice planting Asia and South-East Asia areas. Compared with traditional chemical-based treatment, utilization of plant endogenous resistance is a more effective and environmental-friendly way for BPH control. Accordingly, quite a few quantitative trait loci (QTLs) for BPH resistance were cloned using forward genetics. However, BPH is apt to change quickly into new biotypes to overcome plant resistance, therefore, new resistance resources and genes are continuously needed. miRNAs are important regulators in both plant development and physiological regulation including immunity, and might be used as effective supplements for BPH resistance QTLs. miR159 is an ancient and conserved miRNA. In this study, we found that each OsMIR159 gene in rice responded to BPH feeding very obviously, and genetic function assay proved them to negatively regulate BPH resistance, with STTM159 showing resistance to BPH, and over expression of OsmiR159d susceptible to BPH. One target genes of OsmiR159, OsGAMYBL2, positively regulated BPH resistance. Further biochemical studies revealed that OsGAMYBL2 could directly bind to the promoter of G-protein γ subunit encoding GS3 gene and repress its expression. And genetically, GS3 responded to BPH feeding promptly and negatively regulated BPH resistance, GS3 over expression plants were susceptible to BPH, while GS3 knock-out plants were resistant to BPH. Thus, we identified new function of OsmiR159-OsGAMYBL2 in mediating BPH response, and revealed a new OsmiR159-G protein pathway that mediates BPH resistance in rice.
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Affiliation(s)
- Yanjie Shen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guiqiang Yang
- Wuzhou Agricultural Product Quality and Safety Integrated Test Center, Wuzhou, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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15
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Zhang J, Zhang X, Liu X, Pai Q, Wang Y, Wu X. Molecular Network for Regulation of Seed Size in Plants. Int J Mol Sci 2023; 24:10666. [PMID: 37445843 DOI: 10.3390/ijms241310666] [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: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The size of seeds is particularly important for agricultural development, as it is a key trait that determines yield. It is controlled by the coordinated development of the integument, endosperm, and embryo. Large seeds are an important way of improving the ultimate "sink strength" of crops, providing more nutrients for early plant growth and showing certain tolerance to abiotic stresses. There are several pathways for regulating plant seed size, including the HAIKU (IKU) pathway, ubiquitin-proteasome pathway, G (Guanosine triphosphate) protein regulatory pathway, mitogen-activated protein kinase (MAPK) pathway, transcriptional regulators pathway, and phytohormone regulatory pathways including the auxin, brassinosteroid (BR), gibberellin (GA), jasmonic acid (JA), cytokinin (CK), Abscisic acid (ABA), and microRNA (miRNA) regulatory pathways. This article summarizes the seed size regulatory network and prospective ways of improving yield. We expect that it will provide a valuable reference to researchers in related fields.
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Affiliation(s)
- Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuan Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xueman Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaofeng Pai
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yahui Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
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Othman SMIS, Mustaffa AF, Che-Othman MH, Samad AFA, Goh HH, Zainal Z, Ismail I. Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology. PLANTS (BASEL, SWITZERLAND) 2023; 12:669. [PMID: 36771753 PMCID: PMC9918958 DOI: 10.3390/plants12030669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - M. Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Abdul Fatah A. Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Zamri Zainal
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
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Kumar K, Mandal SN, Neelam K, de los Reyes BG. MicroRNA-mediated host defense mechanisms against pathogens and herbivores in rice: balancing gains from genetic resistance with trade-offs to productivity potential. BMC PLANT BIOLOGY 2022; 22:351. [PMID: 35850632 PMCID: PMC9290239 DOI: 10.1186/s12870-022-03723-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 06/29/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials. RESULTS Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits. CONCLUSIONS Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.
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Affiliation(s)
- Kishor Kumar
- Faculty Centre for Integrated Rural Development and Management, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur, Kolkata, 700103 India
| | - Swarupa Nanda Mandal
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX-79415 USA
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Extended Campus, Burdwan, West Bengal 713101 India
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab 141004 India
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Shaw BP, Sekhar S, Panda BB, Sahu G, Chandra T, Parida AK. Biochemical and molecular processes contributing to grain filling and yield in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 179:120-133. [PMID: 35338943 DOI: 10.1016/j.plaphy.2022.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 05/02/2023]
Abstract
The increase in much required rice production through breeding programmes is on decline. The primary reason being poor filling of grains in the basal spikelets of the heavy and compact panicle rice developed. These spikelets are genetically competent to develop into well filled grains, but fail to do so because the carbohydrate assimilates available to them remain unutilized, reportedly due to poor activities of the starch biosynthesizing enzymes, high production of ethylene leading to enhanced synthesis of the downstream signaling component RSR1 protein that inhibits GBSS1 activity, poor endosperm cell division and endoreduplication of the endosperm nuclei, altered expression of the transcription factors influencing grain filling, enhanced expression and phosphorylation of 14-3-3 proteins, poor expression of the seed storage proteins, reduced synthesis of the hormones like cytokinins and IAA that promote grain filling, and altered expression of miRNAs preventing their normal role in grain filling. Since the basal spikelets are genetically competent to develop into well filled mature grains, biotechnological interventions in terms of spikelet-specific overexpression of the genes encoding enzymes involved in grain filling and/or knockdown/overexpression of the genes influencing the activities of the starch biosynthesizing enzymes, various cell cycle events and hormone biosynthesis could increase rice production by as much as 30%, much more than the set production target of 800 mmt. Application of these biotechnological interventions in the heavy and compact panicle cultivars producing grains of desired quality would also maintain the quality of the grains having demand in market besides increasing the rice production per se.
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Affiliation(s)
- Birendra Prasad Shaw
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Sudhanshu Sekhar
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Binay Bhushan Panda
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Gyanasri Sahu
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Tilak Chandra
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
| | - Ajay Kumar Parida
- Abiotic Stress and Agro-Biotechnology Lab, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, Odisha, India.
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miRNAomic Approach to Plant Nitrogen Starvation. Int J Genomics 2021; 2021:8560323. [PMID: 34796230 PMCID: PMC8595019 DOI: 10.1155/2021/8560323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.
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Lin Y, Zhu Y, Cui Y, Chen R, Chen Z, Li G, Fan M, Chen J, Li Y, Guo X, Zheng X, Chen L, Wang F. Derepression of specific miRNA-target genes in rice using CRISPR/Cas9. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7067-7077. [PMID: 34283216 PMCID: PMC8547147 DOI: 10.1093/jxb/erab336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/20/2021] [Indexed: 05/20/2023]
Abstract
MicroRNAs (miRNAs) target specific mRNA molecules based on sequence complementarity for their degradation or repression of translation, thereby regulating various developmental and physiological processes in eukaryotic organisms. Expressing the target mimicry (MIM) and short tandem target mimicry (STTM) can block endogenous activity of mature miRNAs and eliminate the inhibition of their target genes, resulting in phenotypic changes due to higher expression of the target genes. Here, we report a strategy to achieve derepression of interested miRNA-target genes through CRISPR/Cas9-based generation of in-frame mutants within the miRNA-complementary sequence of the target gene. We show that two rice genes, OsGRF4 (GROWTH REGULATING FACTOR 4) and OsGRF8 carrying in-frame mutants with disruption of the miR396 recognition sites, escape from miR396-mediated post-transcriptional silencing, resulting in enlarged grain size and increase in brown planthopper (BPH) resistance, in their respective transgenic rice lines. These results demonstrate that CRISPR/Cas9-mediated disruption of miRNA target sites can be effectively employed to precisely derepress particular target genes of functional importance for trait improvement in plants.
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Affiliation(s)
- Yarong Lin
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yiwang Zhu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Rui Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Zaijie Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Gang Li
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Meiying Fan
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Jianmin Chen
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xinrui Guo
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
| | - Xijun Zheng
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- Correspondence: or
| | - Feng Wang
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fuzhou, China
- Correspondence: or
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21
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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22
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Chowdhury MR, Bahadur RP, Basak J. Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation. PLANTA 2021; 254:72. [PMID: 34519918 DOI: 10.1007/s00425-021-03689-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
We have predicted miRNAs, their targets and lncRNAs from the genome of Brassica oleracea along with their functional annotation. Selected miRNAs and their targets are experimentally validated. Roles of these non-coding RNAs in post-transcriptional gene regulation are also deciphered. Cauliflower (Brassica oleracea var. Botrytis) is an important vegetable crop for its dietary and medicinal values with rich source of vitamins, dietary fibers, flavonoids and antioxidants. MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs), which regulate gene expression by inhibiting translation or by degrading messenger RNAs (mRNAs). On the other hand, long non-coding RNAs (lncRNAs) are responsible for the up regulation and the down regulation of transcription. Although the genome of cauliflower is reported, yet the roles of these ncRNAs in post-transcriptional gene regulation (PTGR) remain elusive. In this study, we have computationally predicted 355 miRNAs, of which 280 miRNAs are novel compared to miRBase 22.1. All the predicted miRNAs belong to 121 different families. We have also identified 934 targets of 125 miRNAs along with their functional annotation. These targets are further classified into biological processes, molecular functions and cellular components. Moreover, we have predicted 634 lncRNAs, of which 61 are targeted by 30 novel miRNAs. Randomly chosen 10 miRNAs and 10 lncRNAs are experimentally validated. Five miRNA targets including squamosa promoter-binding-like protein 9, homeobox-leucine zipper protein HDG12-like, NAC domain-containing protein 100, CUP-SHAPED COTYLEDON 1 and kinesin-like protein NACK2 of four miRNAs including bol-miR156a, bol-miR162a, bol-miR164d and bol-miR2673 are also experimentally validated. We have built network models of interactions between miRNAs and their target mRNAs, as well as between miRNAs and lncRNAs. Our findings enhance the knowledge of non-coding genome of cauliflower and their roles in PTGR, and might play important roles in improving agronomic traits of this economically important crop.
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Affiliation(s)
- Moumita Roy Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Jolly Basak
- Department of Biotechnology, Visva-Bharati University, Santiniketan, 731235, India.
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23
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Zhou J, Wu JT. Physiological characteristics and miRNA sequencing of two root zones with contrasting ammonium assimilation patterns in Populus. Genes Genomics 2021; 44:39-51. [PMID: 34455578 DOI: 10.1007/s13258-021-01156-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/13/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The net ammonium fluxes differ among the different root zones of Populus, but the physiological and microRNA regulatory mechanisms are unclear. OBJECTIVE To elucidate the physiological and miRNA regulatory mechanisms, we investigated the two root zones displaying significant differences in net NH4+ effluxes of P. × canescens. METHODS Populus plantlets were cultivated with 500 μM NH4Cl for 10 days. Six plants were randomly selected to determine the net NH4+ fluxes using a noninvasive microtest technique. High-throughput sequencing were used to determine the dynamic expression profile of miRNA among the different root zones of Populus. RESULTS Net NH4+ efflux in zone I (from 0 to 40 mm from the root apex) was - 19.64 pmol cm-2 s-1 and in zone II (from 40 to 80 mm) it was - 43.96 pmol cm-2 s-1. The expression of eleven miRNAs was significantly upregulated, whereas fifteen miRNAs were downregulated. Moreover, eighty-eight target genes of the significantly differentially expressed miRNAs were identified in root zone II compared with zone I. Particularly, ptc-miR171a/b/e and their target, SCL6, were found to be important for the difference in net NH4+ effluxes in the two root zones. Moreover, the expression of the target of ptc-miR169d, NFYA3 was upregulated in root zone II compared with root zone I, contributing to increased NH4+ efflux and decreased NH4+ assimilation in root zone II. CONCLUSION These results indicate that miRNAs regulate the expression levels of their target genes and thus play key roles in net NH4+ fluxes and NH4+ assimilation in different poplar root zones.
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Affiliation(s)
- Jing Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Jiang Ting Wu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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24
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The Sw5a gene confers resistance to ToLCNDV and triggers an HR response after direct AC4 effector recognition. Proc Natl Acad Sci U S A 2021; 118:2101833118. [PMID: 34385303 DOI: 10.1073/pnas.2101833118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several attempts have been made to identify antiviral genes against Tomato leaf curl New Delhi virus (ToLCNDV) and related viruses. This has led to the recognition of Ty genes (Ty1-Ty6), which have been successful in developing virus-resistant crops to some extent. Owing to the regular appearance of resistance-breaking strains of these viruses, it is important to identify genes related to resistance. In the present study, we identified a ToLCNDV resistance (R) gene, SlSw5a, in a ToLCNDV-resistant tomato cultivar, H-88-78-1, which lacks the known Ty genes. The expression of SlSw5a is controlled by the transcription factor SlMyb33, which in turn is regulated by microRNA159 (sly-miR159). Virus-induced gene silencing of either SlSw5a or SlMyb33 severely increases the disease symptoms and viral titer in leaves of resistant cultivar. Moreover, in SlMyb33-silenced plants, the relative messenger RNA level of SlSw5a was reduced, suggesting SlSw5a is downstream of the sly-miR159-SlMyb33 module. We also demonstrate that SlSw5a interacts physically with ToLCNDV-AC4 (viral suppressor of RNA silencing) to trigger a hypersensitive response (HR) and generate reactive oxygen species at infection sites to limit the spread of the virus. The "RTSK" motif in the AC4 C terminus is important for the interaction, and its mutation completely abolishes the interaction with Sw5a and HR elicitation. Overall, our research reports an R gene against ToLCNDV and establishes a connection between the upstream miR159-Myb33 module and its downstream target Sw5a to activate HR in the tomato, resulting in geminivirus resistance.
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25
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Chen K, Łyskowski A, Jaremko Ł, Jaremko M. Genetic and Molecular Factors Determining Grain Weight in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:605799. [PMID: 34322138 PMCID: PMC8313227 DOI: 10.3389/fpls.2021.605799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 06/22/2021] [Indexed: 05/06/2023]
Abstract
Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.
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Affiliation(s)
- Ke Chen
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Andrzej Łyskowski
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Chemistry, Rzeszow University of Technology, Rzeszow, Poland
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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26
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Singroha G, Sharma P, Sunkur R. Current status of microRNA-mediated regulation of drought stress responses in cereals. PHYSIOLOGIA PLANTARUM 2021; 172:1808-1821. [PMID: 33956991 DOI: 10.1111/ppl.13451] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/20/2021] [Accepted: 05/04/2021] [Indexed: 05/03/2023]
Abstract
Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.
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Affiliation(s)
- Garima Singroha
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Ramanjulu Sunkur
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, USA
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27
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Chen J, Teotia S, Lan T, Tang G. MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:744357. [PMID: 34616418 PMCID: PMC8489592 DOI: 10.3389/fpls.2021.744357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/16/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.
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Affiliation(s)
- Jiwei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Sachin Teotia
- Department of Biotechnology, Sharda University, Greater Noida, India
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- *Correspondence: Ting Lan,
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI, United States
- Guiliang Tang,
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28
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Pachamuthu K, Swetha C, Basu D, Das S, Singh I, Sundar VH, Sujith TN, Shivaprasad PV. Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes. PLANT MOLECULAR BIOLOGY 2021; 105:99-114. [PMID: 32964370 DOI: 10.1007/s11103-020-01071-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/08/2020] [Indexed: 05/27/2023]
Abstract
This manuscript describes the functions of an Argonaute protein named AGO17 in rice. AGO17 is required for the development of rice reproductive tissues. Argonaute (AGO) proteins are a well-conserved multigene family of regulators mediating gene silencing across eukaryotes. Monocot plants have additional members of AGO, the functions of which are poorly understood. Among the non-dicot AGO1 clade members in monocots, AGO17 expresses highly in reproductive tissues. Here we show that overexpression of Oryza sativa indica AGO17 in rice resulted in robust growth and increased yield, whereas its silencing resulted in reduced panicle length, less fertility, and poor growth. Small (s)RNA transcriptome analysis revealed misregulation of several miRNAs and other categories of sRNAs in silenced and overexpression lines, in agreement with its likely competition with other AGO1 clade members. Targets of differentially expressed miRNAs included previously unreported target RNAs coding for proteins involved in development, phase transition, and transport. Our results indicate a distinctive role for OsAGO17 in rice reproductive development that could be harnessed to improve yield.
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Affiliation(s)
- Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Debjani Basu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Soumita Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Indira Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - T N Sujith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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29
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Wang L, Yin Y, Jing X, Wang M, Zhao M, Yu J, Qiu Z, Li YF. Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton ( Gossypium hirsutum L.) Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:643213. [PMID: 33719323 PMCID: PMC7943613 DOI: 10.3389/fpls.2021.643213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/01/2021] [Indexed: 05/06/2023]
Abstract
Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.
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Affiliation(s)
- Li Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
- Li Wang,
| | - Ying Yin
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xiuxiu Jing
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Menglei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Miao Zhao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Juanjuan Yu
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
| | - Zongbo Qiu
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
| | - Yong-Fang Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang, China
- *Correspondence: Yong-Fang Li,
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30
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Mallet J, Laufs P, Leduc N, Le Gourrierec J. Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model. FRONTIERS IN PLANT SCIENCE 2021; 12:770363. [PMID: 35173747 PMCID: PMC8841825 DOI: 10.3389/fpls.2021.770363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 05/05/2023]
Abstract
Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.
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Affiliation(s)
- Julie Mallet
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Patrick Laufs
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Nathalie Leduc
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - José Le Gourrierec
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
- *Correspondence: José Le Gourrierec,
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31
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Yu S, Wang JW. The Crosstalk between MicroRNAs and Gibberellin Signaling in Plants. PLANT & CELL PHYSIOLOGY 2020; 61:1880-1890. [PMID: 32845336 DOI: 10.1093/pcp/pcaa079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/05/2020] [Indexed: 05/14/2023]
Abstract
Gibberellin (GA) is an integral phytohormone that plays prominent roles in controlling seed germination, stem elongation, leaf development and floral induction. It has been shown that GA regulates these diverse biological processes mainly through overcoming the suppressive effects of the DELLA proteins, a family of nuclear repressors of GA response. MicroRNAs (miRNAs), which have been identified as master regulators of gene expression in eukaryotes, are also involved in a wide range of plant developmental events through the repression of their target genes. The pathways of GA biosynthesis and signaling, as well as the pathways of miRNA biogenesis and regulation, have been profoundly delineated in the past several decades. Growing evidence has shown that miRNAs and GAs are coordinated in regulating plant development, as several components in GA pathways are targeted by miRNAs, and GAs also regulate the expression of miRNAs or their target genes vice versa. Here, we review the recent advances in our understanding of the molecular connections between miRNAs and GA, with an emphasis on the two miRNAs, miR156 and miR159.
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Affiliation(s)
- Sha Yu
- Center for RNA research, Institute for Basic Science, Seoul 00826, South Korea
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Kaur R, Bhunia RK, Rajam MV. MicroRNAs as potential targets for improving rice yield via plant architecture modulation: Recent studies and future perspectives. J Biosci 2020. [DOI: 10.1007/s12038-020-00084-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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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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Gao X, Zhang Q, Zhao Y, Yang J, He H, Jia G. The lre-miR159a-LrGAMYB pathway mediates resistance to grey mould infection in Lilium regale. MOLECULAR PLANT PATHOLOGY 2020; 21:749-760. [PMID: 32319186 PMCID: PMC7214475 DOI: 10.1111/mpp.12923] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
Grey mould is one of the most determinative factors of lily growth and plays a major role in limiting lily productivity. MicroRNA159 (miR159) is a highly conserved microRNA in plants, and participates in the regulation of plant development and stress responses. Our previous studies revealed that lre-miR159a participates in the response of Lilium regale to Botrytis elliptica according to deep sequencing analyses; however, the response mechanism remains unknown. Here, lre-miR159a and its target LrGAMYB gene were isolated from L. regale. Transgenic Arabidopsis overexpressing lre-MIR159a exhibited larger leaves and smaller necrotic spots on inoculation with Botrytis than those of wild-type and overexpressing LrGAMYB plants. The lre-MIR159a overexpression also led to repressed expression of two targets of miR159, AtMYB33 and AtMYB65, and enhanced accumulation of hormone-related genes, including AtPR1, AtPR2, AtNPR1, AtPDF1.2, and AtLOX for both the jasmonic acid and salicylic acid pathways. Moreover, lower levels of H2 O2 and O2- were observed in lre-MIR159a transgenic Arabidopsis, which reduced the damage from reactive oxygen species accumulation. Taken together, these results indicate that lre-miR159a positively regulates resistance to grey mould by repressing the expression of its target LrGAMYB gene and activating a defence response.
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Affiliation(s)
- Xue Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Qian Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Yu‐Qian Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Jie Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Heng‐Bin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
| | - Gui‐Xia Jia
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological EnvironmentBeijing Forestry UniversityBeijingPR China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of EducationBeijing Forestry UniversityBeijingPR China
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Zheng Z, Wang N, Jalajakumari M, Blackman L, Shen E, Verma S, Wang MB, Millar AA. miR159 Represses a Constitutive Pathogen Defense Response in Tobacco. PLANT PHYSIOLOGY 2020; 182:2182-2198. [PMID: 32041907 PMCID: PMC7140937 DOI: 10.1104/pp.19.00786] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/24/2020] [Indexed: 05/11/2023]
Abstract
MicroR159 (miR159) regulation of GAMYB expression is highly conserved in terrestrial plants; however, its functional role remains poorly understood. In Arabidopsis (Arabidopsis thaliana), although GAMYB-like genes are constitutively transcribed during vegetative growth, their effects are suppressed by strong and constitutive silencing by miR159. GAMYB expression occurs only if miR159 function is inhibited, which results in detrimental pleiotropic defects, questioning the purpose of the miR159-GAMYB pathway. Here, miR159 function was inhibited in tobacco (Nicotiana tabacum) and rice (Oryza sativa) using miRNA MIM159 technology. Similar to observations in Arabidopsis, inhibition of miR159 in tobacco and rice resulted in pleiotropic defects including stunted growth, implying functional conservation of the miR159-GAMYB pathway among angiosperms. In MIM159 tobacco, transcriptome profiling revealed that genes associated with defense and programmed cell death were strongly activated, including a suite of 22 PATHOGENESIS-RELATED PROTEIN (PR) genes that were 100- to 1,000-fold upregulated. Constitutive expression of a miR159-resistant GAMYB transgene in tobacco resulted in phenotypes similar to that of MIM159 tobacco and activated PR gene expression, verifying the dependence of the above-mentioned changes on GAMYB expression. Consistent with the broad defense response, MIM159 tobacco appeared immune to Phytophthora infection. These findings suggest that the tobacco miR159-GAMYB pathway functions in the biotic defense response, which becomes activated upon miR159 inhibition. However, PR gene expression was not upregulated in Arabidopsis or rice when miR159 was inhibited, suggesting that miR159-GAMYB pathway functional differences exist between species, or factors in addition to miR159 inhibition are required in Arabidopsis and rice to activate this broad defense response.
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Affiliation(s)
- Zihui Zheng
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Naiqi Wang
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Meachery Jalajakumari
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Leila Blackman
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Enhui Shen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Saurabh Verma
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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37
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Technologies to Address Plant microRNA Functions. CONCEPTS AND STRATEGIES IN PLANT SCIENCES 2020. [DOI: 10.1007/978-3-030-35772-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Cheng Z, Hou D, Ge W, Li X, Xie L, Zheng H, Cai M, Liu J, Gao J. Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo. PLANT & CELL PHYSIOLOGY 2020; 61:76-87. [PMID: 31550004 DOI: 10.1093/pcp/pcz179] [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: 04/01/2019] [Accepted: 09/06/2019] [Indexed: 05/11/2023]
Abstract
A flower is an essential organ for sexual reproduction in flowering plants, which has been extensively studied in model plants. In this study, we used transcriptomic, small RNA and degradome analyses to characterize key microRNAs (miRNAs) and their targets in floral organs of moso bamboo. In total, we identified 13,051 differentially expressed genes and 109 known miRNAs from 26 miRNA families. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as novel miRNAs. Sixteen conserved miRNAs were specifically and highly expressed in stamens, including miRNA159 and miRNA166. In situ hybridization shows that miRNA159 plays a key role in the regulation of stamen development, and the expression levels of its targets PheMYB98 and PheMYB42 were low. Furthermore, Phe-MIRNA159 partially recovers phenotypes of mir159ab double mutant. Overexpression of Phe-MIR159 could cause failure in anther dehisce, and the mature pollens could not be dispersed and further reduce fertility in Arabidopsis. Semi-thin section result shows that anther endothelial layer of Phe-MIRNA159 overexpressing lines is lack of secondary thickening, resulting in limited force for anther opening. Phe-miR159 may regulate the expression of genes related to secondary thickening through negative regulation of AtMYB33, affecting the anther dehiscence. Taken together, this study provides insights regarding molecular networks underlying floral organs development of moso bamboo.
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Affiliation(s)
- Zhanchao Cheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Dan Hou
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Wei Ge
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
| | - Xiangyu Li
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Lihua Xie
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Huifang Zheng
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Miaomiao Cai
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jun Liu
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jian Gao
- International Center for Bamboo and Rattan, Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry and Grassland Administration, Beijing 100102, China
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Watt C, Zhou G, Li C. Harnessing Transcription Factors as Potential Tools to Enhance Grain Size Under Stressful Abiotic Conditions in Cereal Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:1273. [PMID: 33013947 PMCID: PMC7461896 DOI: 10.3389/fpls.2020.01273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/05/2020] [Indexed: 05/07/2023]
Abstract
Predicted climate change is widely cited to significantly reduce yields of the major cereal crop species in a period where demand is rapidly rising due to a growing global population. This requires exhaustive research to develop genetic resources in order to address the expected production deficiencies which will largely be driven by abiotic stress. Modification of multiple genes is an approach that can address the predicted challenges; however, it is time-consuming and costly to modify multiple genes simultaneously. Transcription factors represent a group of proteins regulating multiple genes simultaneously and are therefore promising targets to concurrently improve multiple traits concurrently, such as abiotic stress tolerance and grain size (a contributor to yield). Many studies have identified the complex role that transcription factors of multiple families have contributed toward abiotic stress tolerance or grain size, although research addressing both simultaneously is in its infancy despite its potential significance for cereal crop improvement. Here we discuss the potential role that transcription factors may contribute toward improving cereal crop productivity under adverse environmental conditions and offer research objectives that need to be addressed before the modification of transcription factors becomes routinely used to positively manipulate multiple target traits.
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40
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da Silva RG, Rosa-Santos TM, França SDC, Kottapalli P, Kottapalli KR, Zingaretti SM. Microtranscriptome analysis of sugarcane cultivars in response to aluminum stress. PLoS One 2019; 14:e0217806. [PMID: 31697688 PMCID: PMC6837492 DOI: 10.1371/journal.pone.0217806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Although several metallic elements are required for plant growth, excessive amounts of aluminum ions (Al3+) can result in the inhibition of root growth, thus triggering water and nutrient deficiencies. Plants under stress undergo gene expression changes in specific genes or post-transcriptional gene regulators, such as miRNAs, that can lead to stress tolerance. In this study, we investigated the miRNAs involved in the response of sugarcane to aluminum stress. Four miRNA libraries were generated using sugarcane roots of one tolerant and one sensitive sugarcane cultivar grown under aluminum stress and used to identify the miRNAs involved in the sugarcane aluminum toxicity response. The contrast in field phenotypes of sugarcane cultivars in the field during aluminum stress was reflected in the micro-transcriptome expression profiles. We identified 394 differentially expressed miRNAs in both cultivars, 104 of which were tolerant cultivar-specific, 116 were sensitive cultivar-specific, and 87 of which were common among cultivars. In addition, 52% of differentially expressed miRNAs were upregulated in the tolerant cultivar while the majority of differentially expressed miRNAs in the sensitive cultivar were downregulated. Real-time quantitative polymerase chain reaction was used to validate the expression levels of differentially expressed miRNAs. We also attempted to identify target genes of miRNAs of interest. Our results show that selected differentially expressed miRNAs of aluminum-stressed sugarcane cultivars play roles in signaling, root development, and lateral root formation. These genes thus may be important for aluminum tolerance in sugarcane and could be used in breeding programs to develop tolerant cultivars.
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Affiliation(s)
- Renan Gonçalves da Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Thiago Mateus Rosa-Santos
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Pratibha Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Kameswara Rao Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Sonia Marli Zingaretti
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- * E-mail:
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System Analysis of MIRNAs in Maize Internode Elongation. Biomolecules 2019; 9:biom9090417. [PMID: 31461907 PMCID: PMC6769733 DOI: 10.3390/biom9090417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.
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42
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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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Nadarajah K, Kumar IS. Drought Response in Rice: The miRNA Story. Int J Mol Sci 2019; 20:ijms20153766. [PMID: 31374851 PMCID: PMC6696311 DOI: 10.3390/ijms20153766] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 01/07/2023] Open
Abstract
As a semi-aquatic plant, rice requires water for proper growth, development, and orientation of physiological processes. Stress is induced at the cellular and molecular level when rice is exposed to drought or periods of low water availability. Plants have existing defense mechanisms in planta that respond to stress. In this review we examine the role played by miRNAs in the regulation and control of drought stress in rice through a summary of molecular studies conducted on miRNAs with emphasis on their contribution to drought regulatory networks in comparison to other plant systems. The interaction between miRNAs, target genes, transcription factors and their respective roles in drought-induced stresses is elaborated. The cross talk involved in controlling drought stress responses through the up and down regulation of targets encoding regulatory and functional proteins is highlighted. The information contained herein can further be explored to identify targets for crop improvement in the future.
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Affiliation(s)
- Kalaivani Nadarajah
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
| | - Ilakiya Sharanee Kumar
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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Millar AA, Lohe A, Wong G. Biology and Function of miR159 in Plants. PLANTS 2019; 8:plants8080255. [PMID: 31366066 PMCID: PMC6724108 DOI: 10.3390/plants8080255] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/18/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
MicroR159 (miR159) is ancient, being present in the majority of land plants where it targets a class of regulatory genes called GAMYB or GAMYB-like via highly conserved miR159-binding sites. These GAMYB genes encode R2R3 MYB domain transcription factors that transduce the gibberellin (GA) signal in the seed aleurone and the anther tapetum. Here, GAMYB plays a conserved role in promoting the programmed cell death of these tissues, where miR159 function appears weak. By contrast, GAMYB is not involved in GA-signaling in vegetative tissues, but rather its expression is deleterious, leading to the inhibition of growth and development. Here, the major function of miR159 is to mediate strong silencing of GAMYB to enable normal growth. Highlighting this requirement of strong silencing are conserved RNA secondary structures associated with the miR159-binding site in GAMYB mRNA that promotes miR159-mediated repression. Although the miR159-GAMYB pathway in vegetative tissues has been implicated in a number of different functions, presently no conserved role for this pathway has emerged. We will review the current knowledge of the different proposed functions of miR159, and how this ancient pathway has been used as a model to help form our understanding of miRNA biology in plants.
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Affiliation(s)
- Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia.
| | - Allan Lohe
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Gigi Wong
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
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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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46
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Zhao Y, Peng T, Sun H, Teotia S, Wen H, Du Y, Zhang J, Li J, Tang G, Xue H, Zhao Q. miR1432-OsACOT (Acyl-CoA thioesterase) module determines grain yield via enhancing grain filling rate in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:712-723. [PMID: 30183128 PMCID: PMC6419572 DOI: 10.1111/pbi.13009] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 05/18/2023]
Abstract
Rice grain filling rate contributes largely to grain productivity and accumulation of nutrients. MicroRNAs (miRNAs) are key regulators of development and physiology in plants and become a novel key target for engineering grain size and crop yield. However, there is little studies, so far, showing the miRNA regulation of grain filling and rice yield, in consequence. Here, we show that suppressed expression of rice miR1432 (STTM1432) significantly improves grain weight by enhancing grain filling rate and leads to an increase in overall grain yield up to 17.14% in a field trial. Molecular analysis identified rice Acyl-CoA thioesterase (OsACOT), which is conserved with ACOT13 in other species, as a major target of miR1432 by cleavage. Moreover, overexpression of miR1432-resistant form of OsACOT (OXmACOT) resembled the STTM1432 plants, that is, a large margin of an increase in grain weight up to 46.69% through improving the grain filling rate. Further study indicated that OsACOT was involved in biosynthesis of medium-chain fatty acids. In addition, RNA-seq based transcriptomic analyses of transgenic plants with altered expression of miR1432 demonstrated that downstream genes of miR1432-regulated network are involved in fatty acid metabolism and phytohormones biosynthesis and also overlap with the enrichment analysis of co-expressed genes of OsACOT, which is consistent with the increased levels of auxin and abscisic acid in STTM1432 and OXmACOT plants. Overall, miR1432-OsACOT module plays an important role in grain filling in rice, illustrating its capacity for engineering yield improvement in crops.
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Affiliation(s)
- Ya‐Fan Zhao
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Ting Peng
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Hong‐Zheng Sun
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Department of Biological Sciences and Biotechnology Research Center (BRC)Michigan Technological UniversityHoughtonMIUSA
| | - Hui‐Li Wen
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Yan‐Xiu Du
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Jing Zhang
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Jun‐Zhou Li
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
| | - Gui‐Liang Tang
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Department of Biological Sciences and Biotechnology Research Center (BRC)Michigan Technological UniversityHoughtonMIUSA
| | - Hong‐Wei Xue
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of Sciences (CAS)ShanghaiChina
| | - Quan‐Zhi Zhao
- Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouChina
- Key Laboratory of Rice Biology in Henan ProvinceHenan Agricultural UniversityZhengzhouChina
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47
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Chongloi GL, Prakash S, Vijayraghavan U. Regulation of meristem maintenance and organ identity during rice reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1719-1736. [PMID: 30753578 DOI: 10.1093/jxb/erz046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.
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Affiliation(s)
- Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sandhan Prakash
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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48
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Yang T, Wang Y, Teotia S, Wang Z, Shi C, Sun H, Gu Y, Zhang Z, Tang G. The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis. Sci Rep 2019; 9:2832. [PMID: 30808969 PMCID: PMC6391385 DOI: 10.1038/s41598-019-39397-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/14/2019] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement.
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Affiliation(s)
- Tianxiao Yang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China.,Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Yongyan Wang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China.,Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Sachin Teotia
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China.,Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA.,Department of Biotechnology, Sharda University, Greater Noida, 201306, India
| | - Zhaohui Wang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Chaonan Shi
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Huwei Sun
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Yiyou Gu
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China.
| | - Guiliang Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, P. R. China. .,Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, 49931, USA.
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49
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Peng T, Qiao M, Liu H, Teotia S, Zhang Z, Zhao Y, Wang B, Zhao D, Shi L, Zhang C, Le B, Rogers K, Gunasekara C, Duan H, Gu Y, Tian L, Nie J, Qi J, Meng F, Huang L, Chen Q, Wang Z, Tang J, Tang X, Lan T, Chen X, Wei H, Zhao Q, Tang G. A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants. MOLECULAR PLANT 2018; 11:1400-1417. [PMID: 30243763 DOI: 10.1016/j.molp.2018.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 08/01/2018] [Accepted: 09/06/2018] [Indexed: 05/04/2023]
Abstract
microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.
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Affiliation(s)
- Ting Peng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Mengmeng Qiao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haiping Liu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Sachin Teotia
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhanhui Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Yafan Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Bobo Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China
| | - Dongjie Zhao
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lina Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Cui Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Chathura Gunasekara
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Haitang Duan
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Yiyou Gu
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lei Tian
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinfu Nie
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China; Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jian Qi
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Fanrong Meng
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Lan Huang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Qinghui Chen
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Department of Kinesiology and Integrative Physiology, Life Science and Technology Instituted, Michigan Technological University, Houghton, MI 49931, USA
| | - Zhenlin Wang
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Jinshan Tang
- School of Technology, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China.
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, P.R. China.
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Rice Biology in Henan Province, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guiliang Tang
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China; Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI 49931, USA; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, P.R. China; Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475004, China.
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50
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Xu P, Ali A, Han B, Wu X. Current Advances in Molecular Basis and Mechanisms Regulating Leaf Morphology in Rice. FRONTIERS IN PLANT SCIENCE 2018; 9:1528. [PMID: 30405666 PMCID: PMC6206276 DOI: 10.3389/fpls.2018.01528] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/28/2018] [Indexed: 05/03/2023]
Abstract
Yield is majorly affected by photosynthetic efficiency. Leaves are essential structure for photosynthesis and their morphology especially size and shape in a plant canopy can affect the rate of transpiration, carbon fixation and photosynthesis. Leaf rolling and size are considered key agronomic traits in plant architecture that can subsidize yield parameters. In last era, a number of genes controlling leaf morphology have been molecularly characterized. Despite of several findings, our understanding toward molecular mechanism of leaf rolling and size are under-developed. Here, we proposed a model to apprehend the physiological basis of different genes organized in a complex fashion and govern the final phenotype of leaf morphology. According to this leaf rolling is mainly controlled by regulation of bulliform cells by SRL1, ROC5, OsRRK1, SLL2, CLD1, OsZHD1/2, and NRL1, structure and processes of sclerenchyma cells by SLL1 and SRL2, leaf polarity by ADL1, RFS and cuticle formation by CFL1, and CLD1. Many of above mentioned and several other genes interact in a complex manner in order to sustain cellular integrity and homeostasis for optimum leaf rolling. While, leaf size is synchronized by multifarious interaction of PLA1, PLA2, OsGASR1, and OsEXPA8 in cell division, NAL1, NAL9, NRL1, NRL2 in regulation of number of veins, OsCOW1, OsPIN1, OsARF19, OsOFP2, D1 and GID in regulation of phytohormones and HDT702 in epigenetic aspects. In this review, we curtailed recent advances engrossing regulation and functions of those genes that directly or indirectly can distress leaf rolling or size by encoding different types of proteins and genic expression. Moreover, this effort could be used further to develop comprehensive learning and directing our molecular breeding of rice.
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Affiliation(s)
- Peizhou Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Ministry of Education, Chengdu, China
| | - Asif Ali
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Ministry of Education, Chengdu, China
| | - Baolin Han
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Ministry of Education, Chengdu, China
| | - Xianjun Wu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwest Crop Genetic Resources and Genetic Improvement, Ministry of Education, Chengdu, China
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