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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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2
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Li S, Shao Z, Fu X, Xiao W, Li L, Chen M, Sun M, Li D, Gao D. Identification and characterization of Prunus persica miRNAs in response to UVB radiation in greenhouse through high-throughput sequencing. BMC Genomics 2017; 18:938. [PMID: 29197334 PMCID: PMC5712094 DOI: 10.1186/s12864-017-4347-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression of target mRNAs involved in plant growth, development, and abiotic stress. As one of the most important model plants, peach (Prunus persica) has high agricultural significance and nutritional values. It is well adapted to be cultivated in greenhouse in which some auxiliary conditions like temperature, humidity, and UVB etc. are needed to ensure the fruit quality. However, little is known about the genomic information of P. persica under UVB supplement. Transcriptome and expression profiling data for this species are therefore important resources to better understand the biological mechanism of seed development, formation and plant adaptation to environmental change. Using a high-throughput miRNA sequencing, followed by qRT-PCR tests and physiological properties determination, we identified the responsive-miRNAs under low-dose UVB treatment and described the expression pattern and putative function of related miRNAs and target genes in chlorophyll and carbohydrate metabolism. Results A total of 164 known peach miRNAs belonging to 59 miRNA families and 109 putative novel miRNAs were identified. Some of these miRNAs were highly conserved in at least four other plant species. In total, 1794 and 1983 target genes for known and novel miRNAs were predicted, respectively. The differential expression profiles of miRNAs between the control and UVB-supplement group showed that UVB-responsive miRNAs were mainly involved in carbohydrate metabolism and signal transduction. UVB supplement stimulated peach to synthesize more chlorophyll and sugars, which was verified by qRT-PCR tests of related target genes and metabolites’ content measurement. Conclusion The high-throughput sequencing data provided the most comprehensive miRNAs resource available for peach study. Our results identified a series of differentially expressed miRNAs/target genes that were predicted to be low-dose UVB-responsive. The correlation between transcriptional profiles and metabolites contents in UVB supplement groups gave novel clues for the regulatory mechanism of miRNAs in Prunus. Low-dose UVB supplement could increase the chlorophyll and sugar (sorbitol) contents via miRNA-target genes and therefore improve the fruit quality in protected cultivation of peaches. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4347-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shaoxuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, People's Republic of China
| | - Xiling Fu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Wei Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Ling Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Ming Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Mingyue Sun
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Dongmei Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. .,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Dongsheng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, People's Republic of China. .,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
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da Silva AC, Grativol C, Thiebaut F, Hemerly AS, Ferreira PCG. Computational identification and comparative analysis of miRNA precursors in three palm species. PLANTA 2016; 243:1265-1277. [PMID: 26919984 DOI: 10.1007/s00425-016-2486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of miRNA in palm biology. MicroRNAs are small RNAs of 20-25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.
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Affiliation(s)
- Aline Cunha da Silva
- Universidade Federal Rural da Amazonia, Belém, Brazil
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, 2000, P5-227A, Parque Califórnia, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
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4
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Li D, Liu Z, Gao L, Wang L, Gao M, Jiao Z, Qiao H, Yang J, Chen M, Yao L, Liu R, Kan Y. Genome-Wide Identification and Characterization of microRNAs in Developing Grains of Zea mays L. PLoS One 2016; 11:e0153168. [PMID: 27082634 PMCID: PMC4833412 DOI: 10.1371/journal.pone.0153168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 03/24/2016] [Indexed: 11/23/2022] Open
Abstract
The development and maturation of maize kernel involves meticulous and fine gene regulation at transcriptional and post-transcriptional levels, and miRNAs play important roles during this process. Although a number of miRNAs have been identified in maize seed, the ones involved in the early development of grains and in different lines of maize have not been well studied. Here, we profiled four small RNA libraries, each constructed from groups of immature grains of Zea mays inbred line Chang 7–2 collected 4–6, 7–9, 12–14, and 18–23 days after pollination (DAP). A total of 40 known (containing 111 unique miRNAs) and 162 novel (containing 196 unique miRNA candidates) miRNA families were identified. For conserved and novel miRNAs with over 100 total reads, 44% had higher accumulation before the 9th DAP, especially miR166 family members. 42% of miRNAs had highest accumulation during 12–14 DAP (which is the transition stage from embryogenesis to nutrient storage). Only 14% of miRNAs had higher expression 18–23 DAP. Prediction of potential targets of all miRNAs showed that 165 miRNA families had 377 target genes. For miR164 and miR166, we showed that the transcriptional levels of their target genes were significantly decreased when co-expressed with their cognate miRNA precursors in vivo. Further analysis shows miR159, miR164, miR166, miR171, miR390, miR399, and miR529 families have putative roles in the embryogenesis of maize grain development by participating in transcriptional regulation and morphogenesis, while miR167 and miR528 families participate in metabolism process and stress response during nutrient storage. Our study is the first to present an integrated dynamic expression pattern of miRNAs during maize kernel formation and maturation.
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Affiliation(s)
- Dandan Li
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zongcai Liu
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lei Gao
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Lifang Wang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Meijuan Gao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Zhujin Jiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Huili Qiao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Jianwei Yang
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Min Chen
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- * E-mail: (RYL); (YCK)
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Libratory of insect biology, Nanyang Normal University, Nanyang, Henan, China
- * E-mail: (RYL); (YCK)
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Gurjar AKS, Panwar AS, Gupta R, Mantri SS. PmiRExAt: plant miRNA expression atlas database and web applications. Database (Oxford) 2016; 2016:baw060. [PMID: 27081157 PMCID: PMC4830907 DOI: 10.1093/database/baw060] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022]
Abstract
High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.
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Affiliation(s)
- Anoop Kishor Singh Gurjar
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Abhijeet Singh Panwar
- HPC-Tech, Center for Development of Advance Computing (C-DAC), Pune, Maharashtra, India
| | - Rajinder Gupta
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Shrikant S Mantri
- Computational Biology Laboratory, National Agri Food Biotechnology Institute (NABI), Mohali, Punjab, India
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6
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Wu X, Ding D, Shi C, Xue Y, Zhang Z, Tang G, Tang J. microRNA-dependent gene regulatory networks in maize leaf senescence. BMC PLANT BIOLOGY 2016; 16:73. [PMID: 27000050 PMCID: PMC4802599 DOI: 10.1186/s12870-016-0755-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/14/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Maize grain yield depends mainly on the photosynthetic efficiency of functional leaves, which is controlled by an array of gene networks and other factors, including environmental conditions. MicroRNAs (miRNAs) are small RNA molecules that play important roles in plant developmental regulation. A few senescence-associated miRNAs (SA-miRNAs) have been identified as important participants in regulating leaf senescence by modulating the expression levels of their target genes. RESULTS To elucidate miRNA roles in leaf senescence and their underlying molecular mechanisms in maize, a stay-green line, Yu87-1, and an early leaf senescence line, Early leaf senescence-1 (ELS-1), were selected as experimental materials for the differential expression of candidate miRNAs. Four small RNA libraries were constructed from ear leaves at 20 and 30 days after pollination and sequenced by Illumina deep sequencing technology. Altogether, 81 miRNAs were detected in both lines. Of these, 16 miRNAs of nine families were differentially expressed between ELS-1 andYu87-1. The phenotypic and chlorophyll content analyses of both lines identified these 16 differentially expressed miRNAs as candidate SA-miRNAs. CONCLUSIONS In this study, 16 candidate SA-miRNAs of ELS-1 were identified through small RNA deep sequencing technology. Degradome sequencing results indicated that these candidate SA-miRNAs may regulate leaf senescence through their target genes, mainly transcription factors, and potentially control chlorophyll degradation pathways. The results highlight the regulatory roles of miRNAs during leaf senescence in maize.
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Affiliation(s)
- Xiangyuan Wu
- />National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 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, 95 Wenhua Road, Zhengzhou, 450002 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, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Yadong Xue
- />National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
| | - Zhanhui Zhang
- />National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 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, 95 Wenhua Road, Zhengzhou, 450002 China
- />Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931 USA
| | - Jihua Tang
- />National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002 China
- />Hubei Collaborative Innovation Center for the Grain Industry, Yangtze University, Jingzhou, 434025 China
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7
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de Sousa Cardoso TC, Portilho LG, de Oliveira CL, McKeown PC, Maluf WR, Gomes LAA, Teixeira TA, do Amaral LR, Spillane C, de Souza Gomes M. Genome-wide identification and in silico characterisation of microRNAs, their targets and processing pathway genes in Phaseolus vulgaris L. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:206-219. [PMID: 26250338 DOI: 10.1111/plb.12377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/03/2015] [Indexed: 06/04/2023]
Abstract
Common bean (Phaseolus vulgaris L., Fabaceae) is a globally important staple crop, which is an important source of calories, protein and essential micronutrients. At the genomic level little is known regarding the small non-coding RNAs within the common bean genome. One of the most important classes of such small non-coding RNAs is microRNAs (miRNAs), which control mRNA and protein expression levels in many eukaryotes. Computational methods have been applied to identify putative miRNAs in the genomes of different organisms. In this study, our objective was to comprehensively identify and characterise miRNAs from the genome and transcriptome of P. vulgaris, including both mature and precursor miRNA forms. We also sought to identify the putative proteins involved in miRNA processing and the likely target genes of common bean miRNAs. We identified 221 mature miRNAs and 136 precursor miRNAs distributed across 52 different miRNA families in the P. vulgaris genome. Amongst these, we distinguished 129 novel mature miRNAs and 123 miRNA precursors belonging to 24 different miRNA families. We also identified 31 proteins predicted to participate in the miRNA-processing pathway in P. vulgaris. Finally, we also identified 483 predicted miRNA targets, including many which corroborate results from other species, suggesting that miRNA regulatory systems are evolutionarily conserved and important for plant development. Our results expand the study of miRNAs and their target genes in common bean, and provide new opportunities to understand their roles in the biology of this important staple crop.
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Affiliation(s)
- T C de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil
| | - L G Portilho
- Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil
| | - C L de Oliveira
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - P C McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Áras de Brún, National University of Ireland, Galway, Ireland
| | - W R Maluf
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - L A A Gomes
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - T A Teixeira
- Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil
| | - L R do Amaral
- Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil
| | - C Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, Áras de Brún, National University of Ireland, Galway, Ireland
| | - M de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis - INGEB/FACOM, Federal University of Uberlandia, Patos de Minas, Brazil
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Kong X, Zhang M, Xu X, Li X, Li C, Ding Z. System analysis of microRNAs in the development and aluminium stress responses of the maize root system. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1108-21. [PMID: 24985700 DOI: 10.1111/pbi.12218] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes through mRNA cleavage or translational inhibition. miRNA is known to play an important role in the root development and environmental responses in both the Arabidopsis and rice. However, little information is available to form a complete view of miRNAs in the development of the maize root system and Al stress responses in maize. Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR) and crown roots (CR). Through integrative analysis, we identified 278 miRNAs (246 conserved and 32 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. The potential targets of the identified conserved and novel miRNAs were also predicted. In addition, our data showed that CR is more resistant to Al stress compared with PR and SR, and the differentially expressed miRNAs are likely to play significant roles in different roots in response to environmental stress such as Al stress. Here, we demonstrate that the expression patterns of miRNAs are highly diversified in different maize roots. The differentially expressed miRNAs are correlated with both the development and environmental responses in the maize root. This study not only improves our knowledge about the roles of miRNAs in maize root development but also reveals the potential role of miRNAs in the environmental responses of different maize roots.
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Affiliation(s)
- Xiangpei Kong
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, China
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9
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Thiebaut F, Rojas CA, Grativol C, Motta MR, Vieira T, Regulski M, Martienssen RA, Farinelli L, Hemerly AS, Ferreira PCG. Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize. BMC Genomics 2014; 15:766. [PMID: 25194793 PMCID: PMC4168055 DOI: 10.1186/1471-2164-15-766] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 08/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. Results Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription. Conclusion Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-766) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Cidade Universitária, Avenida Carlos Chagas Filho, 373, CCS, Bl,L-29ss, Rio de Janeiro RJ 21941-599, Brazil.
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10
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Zhang S, Wang Y, Li K, Zou Y, Chen L, Li X. Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean. Int J Mol Sci 2014; 15:13596-614. [PMID: 25100171 PMCID: PMC4159813 DOI: 10.3390/ijms150813596] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 11/18/2022] Open
Abstract
As a warm climate species, soybean is highly sensitive to chilling temperatures. Exposure to chilling temperatures causes a significant reduction in the nitrogen fixation rate in soybean plants and subsequent yield loss. However, the molecular basis for the sensitivity of soybean to chilling is poorly understood. In this study, we identified cold-responsive miRNAs in nitrogen-fixing nodules of soybean. Upon chilling, the expression of gma-miR397a, gma-miR166u and gma-miR171p was greatly upregulated, whereas the expression of gma-miR169c, gma-miR159b, gma-miR319a/b and gma-miR5559 was significantly decreased. The target genes of these miRNAs were predicted and validated using 5' complementary DNA ends (5'-RACE) experiments, and qPCR analysis identified putative genes targeted by the cold-responsive miRNAs in response to chilling temperatures. Taken together, our results reveal that miRNAs may be involved in the protective mechanism against chilling injury in mature nodules of soybean.
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Affiliation(s)
- Senlei Zhang
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
| | - Youning Wang
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
| | - Kexue Li
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
| | - Yanmin Zou
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
| | - Liang Chen
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
| | - Xia Li
- The State Key Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Research Resources, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021, China.
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