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Szymonik K, Klimek-Chodacka M, Lukasiewicz A, Macko-Podgórni A, Grzebelus D, Baranski R. Comparative analysis of the carrot miRNAome in response to salt stress. Sci Rep 2023; 13:21506. [PMID: 38057586 PMCID: PMC10700493 DOI: 10.1038/s41598-023-48900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Soil salinity adversely affects the yield and quality of crops, including carrot. During salt stress, plant growth and development are impaired by restricted water uptake and ion cytotoxicity, leading to nutrient imbalance and oxidative burst. However, the molecular mechanisms of the carrot plant response to salt stress remain unclear. The occurrence and expression of miRNAs that are potentially involved in the regulation of carrot tolerance to salinity stress were investigated. The results of small RNA sequencing revealed that salt-sensitive (DH1) and salt-tolerant (DLBA) carrot varieties had different miRNA expression profiles. A total of 95 miRNAs were identified, including 71 novel miRNAs, of which 30 and 23 were unique to DH1 and DLBA, respectively. The comparison of NGS and qPCR results allowed identification of two conserved and five novel miRNA involved in carrot response to salt stress, and which differentiated the salt-tolerant and salt-sensitive varieties. Degradome analysis supported by in silico-based predictions and followed by expression analysis of exemplary target genes pointed at genes related to proline, glutathione, and glutamate metabolism pathways as potential miRNA targets involved in salt tolerance, and indicated that the regulation of osmoprotection and antioxidant protection, earlier identified as being more efficient in the tolerant variety, may be controlled by miRNAs. Furthermore, potential miRNA target genes involved in chloroplast protection, signal transduction and the synthesis and modification of cell wall components were indicated in plants growing in saline soil.
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Affiliation(s)
- Kamil Szymonik
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Magdalena Klimek-Chodacka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
| | - Aneta Lukasiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland
| | - Rafal Baranski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, AL. Mickiewicza 21, 31-120, Kraków, Poland.
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2
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Cao K, Sun Y, Zhang X, Zhao Y, Bian J, Zhu H, Wang P, Gao B, Sun X, Hu M, Guo Y, Wang X. The miRNA-mRNA regulatory networks of the response to NaHCO 3 stress in industrial hemp (Cannabis sativa L.). BMC PLANT BIOLOGY 2023; 23:509. [PMID: 37875794 PMCID: PMC10594861 DOI: 10.1186/s12870-023-04463-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Industrial hemp is an important industrial crop and has strong resistance to saline-alkaline stress. However, research on the industrial hemp response to NaHCO3 stress is limited. Therefore, the response mechanisms of industrial hemp under NaHCO3 stress were analysed through miRNA-mRNA regulatory networks. RESULTS Seedlings of two salt-alkali tolerant and sensitive varieties were cultured in a solution containing 100 mM NaHCO3 and randomly sampled at 0, 6, 12, and 24 h. With prolonged NaHCO3 stress, the seedlings gradually withered, and the contents of jasmonic acid, lignin, trehalose, soluble protein, peroxidase, and superoxide dismutase in the roots increased significantly. The abscisic acid content decreased and then gradually increased. Overall, 18,215 mRNAs and 74 miRNAs were identified as differentially expressed under NaHCO3 stress. The network showed that 230 miRNA-mRNA interactions involved 16 miRNAs and 179 mRNAs, including some key hub novel mRNAs of these crucial pathways. Carbon metabolism, starch, sucrose metabolism, plant hormone signal transduction, and the spliceosome (SPL) were crucial pathways in industrial hemp's response to NaHCO3 stress. CONCLUSIONS It is speculated that industrial hemp can regulate SPL pathway by upregulating miRNAs such as novel_miR_179 and novel_miR_75, thus affecting starch and sucrose metabolism, plant hormone signal transduction and carbon metabolism and improving key physiological indices such as jasmonic acid content, trehalose content, and peroxidase and superoxide dismutase activities under NaHCO3 stress.
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Affiliation(s)
- Kun Cao
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
- Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Yufeng Sun
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Xiaoyan Zhang
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Yue Zhao
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Jing Bian
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Hao Zhu
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Pan Wang
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Baochang Gao
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Xiaoli Sun
- Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjiang, China
- National Coarse Cereal Engineering Research Center, Daqing, 163319, Heilongjiang, China
- Heilongjaing Province Cultivating Collaborative Innovation Center for The Beidahuang Modern Agricultural Industry Technology, Daqing, 163319, Heilongjiang, China
| | - Ming Hu
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China
| | - Yongxia Guo
- Heilongjiang BaYi Agricultural University, Daqing, 163319, Heilongjiang, China.
- National Coarse Cereal Engineering Research Center, Daqing, 163319, Heilongjiang, China.
- Heilongjaing Province Cultivating Collaborative Innovation Center for The Beidahuang Modern Agricultural Industry Technology, Daqing, 163319, Heilongjiang, China.
| | - Xiaonan Wang
- Daqing Branch of Heilongjiang Academy of Sciences, Daqing, 163319, Heilongjiang, China.
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3
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Qiao H, Jiao B, Wang J, Yang Y, Yang F, Geng Z, Zhao G, Liu Y, Dong F, Wang Y, Zhou S. Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat. Genes (Basel) 2023; 14:1586. [PMID: 37628637 PMCID: PMC10454085 DOI: 10.3390/genes14081586] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.
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Affiliation(s)
- Hualiang Qiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Bo Jiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Jiao Wang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yang Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fan Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yongwei Liu
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fushuang Dong
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Shuo Zhou
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
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Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023; 24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [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: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
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Affiliation(s)
- David Payne
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Charles A Addo-Quaye
- Department of Computer Science and Cybersecurity, Metropolitan State University, Saint Paul, MN 55106, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023; 21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.
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Affiliation(s)
- Ajeet Singh
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Postdoctoral Associate, Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Vivek AT
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Kanika Gupta
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shruti Sharma
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
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6
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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Maryum Z, Luqman T, Nadeem S, Khan SMUD, Wang B, Ditta A, Khan MKR. An overview of salinity stress, mechanism of salinity tolerance and strategies for its management in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:907937. [PMID: 36275563 PMCID: PMC9583260 DOI: 10.3389/fpls.2022.907937] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/20/2022] [Indexed: 05/14/2023]
Abstract
Salinity stress is one of the primary threats to agricultural crops resulting in impaired crop growth and development. Although cotton is considered as reasonably salt tolerant, it is sensitive to salt stress at some critical stages like germination, flowering, boll formation, resulting in reduced biomass and fiber production. The mechanism of partial ion exclusion (exclusion of Na+ and/or Cl-) in cotton appears to be responsible for the pattern of uptake and accumulation of harmful ions (Na+ and Cl) in tissues of plants exposed to saline conditions. Maintaining high tissue K+/Na+ and Ca2+/Na+ ratios has been proposed as a key selection factor for salt tolerance in cotton. The key adaptation mechanism in cotton under salt stress is excessive sodium exclusion or compartmentation. Among the cultivated species of cotton, Egyptian cotton (Gossypium barbadense L.) exhibit better salt tolerance with good fiber quality traits as compared to most cultivated cotton and it can be used to improve five quality traits and transfer salt tolerance into Upland or American cotton (Gossypium hirsutum L.) by interspecific introgression. Cotton genetic studies on salt tolerance revealed that the majority of growth, yield, and fiber traits are genetically determined, and controlled by quantitative trait loci (QTLs). Molecular markers linked to genes or QTLs affecting key traits have been identified, and they could be utilized as an indirect selection criterion to enhance breeding efficiency through marker-assisted selection (MAS). Transfer of genes for compatible solute, which are an important aspect of ion compartmentation, into salt-sensitive species is, theoretically, a simple strategy to improve tolerance. The expression of particular stress-related genes is involved in plant adaptation to environmental stressors. As a result, enhancing tolerance to salt stress can be achieved by marker assisted selection added with modern gene editing tools can boost the breeding strategies that defend and uphold the structure and function of cellular components. The intent of this review was to recapitulate the advancements in salt screening methods, tolerant germplasm sources and their inheritance, biochemical, morpho-physiological, and molecular characteristics, transgenic approaches, and QTLs for salt tolerance in cotton.
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Affiliation(s)
- Zahra Maryum
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sahar Nadeem
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Allah Ditta
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology-Constituent College (NIAB-C), Pakistan Institute of Engineering and Applied Science Nilore, Islamabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
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8
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Hussain A, Asif N, Pirzada AR, Noureen A, Shaukat J, Burhan A, Zaynab M, Ali E, Imran K, Ameen A, Mahmood MA, Nazar A, Mukhtar MS. Genome wide study of cysteine rich receptor like proteins in Gossypium sp. Sci Rep 2022; 12:4885. [PMID: 35318409 PMCID: PMC8941122 DOI: 10.1038/s41598-022-08943-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/11/2022] [Indexed: 02/08/2023] Open
Abstract
Cysteine-rich receptor-like-kinases (CRKs), a transmembrane subfamily of receptor-like kinase, play crucial roles in plant adaptation. As such cotton is the major source of fiber for the textile industry, but environmental stresses are limiting its growth and production. Here, we have performed a deep computational analysis of CRKs in five Gossypium species, including G. arboreum (60 genes), G. raimondii (74 genes), G. herbaceum (65 genes), G. hirsutum (118 genes), and G. barbadense (120 genes). All identified CRKs were classified into 11 major classes and 43 subclasses with the finding of several novel CRK-associated domains including ALMT, FUSC_2, Cript, FYVE, and Pkinase. Of these, DUF26_DUF26_Pkinase_Tyr was common and had elevated expression under different biotic and abiotic stresses. Moreover, the 35 land plants comparison identified several new CRKs domain-architectures. Likewise, several SNPs and InDels were observed in CLCuD resistant G. hirsutum. The miRNA target side prediction and their expression profiling in different tissues predicted miR172 as a major CRK regulating miR. The expression profiling of CRKs identified multiple clusters with co-expression under certain stress conditions. The expression analysis under CLCuD highlighted the role of GhCRK057, GhCRK059, GhCRK058, and GhCRK081 in resistant accession. Overall, these results provided primary data for future potential functional analysis as well as a reference study for other agronomically important crops.
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Affiliation(s)
- Athar Hussain
- Genomics Lab, School of Food and Agricultural Sciences (SFAS), University of Management and Technology (UMT), Lahore, 54000, Pakistan.
| | - Naila Asif
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Abdul Rafay Pirzada
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Azka Noureen
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan.,PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, 46300, Pakistan
| | - Javeria Shaukat
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Akif Burhan
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Madiha Zaynab
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Sciences, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 51807, China
| | - Ejaz Ali
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, 54000, Pakistan
| | - Koukab Imran
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Ayesha Ameen
- Office of Research Innovation and Commercialization, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - Muhammad Arslan Mahmood
- National Institute for Biotechnology and Genetic Engineering (NIBGE), College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, 38000, Pakistan
| | - Aquib Nazar
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 54000, Pakistan
| | - M Shahid Mukhtar
- Department of Biology, the University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL, 35294, USA
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9
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Kabir N, Zhang X, Liu L, Qanmber G, Zhang L, Wang YX, Sun Z, Zhao N, Wang G. RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum. BMC Genomics 2022; 23:40. [PMID: 35012446 PMCID: PMC8744286 DOI: 10.1186/s12864-021-08248-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 12/25/2022] Open
Abstract
Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08248-z.
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Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Le Liu
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Yu Xuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Na Zhao
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Gang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China.
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10
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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11
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Wang Z, Li N, Yu Q, Wang H. Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes. Int J Mol Sci 2021; 22:12238. [PMID: 34830118 PMCID: PMC8625345 DOI: 10.3390/ijms222212238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022] Open
Abstract
Soil salinization is a major environmental stress that causes crop yield reductions worldwide. Therefore, the cultivation of salt-tolerant crops is an effective way to sustain crop yield. Tomatoes are one of the vegetable crops that are moderately sensitive to salt stress. Global market demand for tomatoes is huge and growing. In recent years, the mechanisms of salt tolerance in tomatoes have been extensively investigated; however, the molecular mechanism through which non-coding RNAs (ncRNAs) respond to salt stress is not well understood. In this study, we utilized small RNA sequencing and whole transcriptome sequencing technology to identify salt-responsive microRNAs (miRNAs), messenger RNAs (mRNAs), and circular RNAs (circRNAs) in roots of M82 cultivated tomato and Solanum pennellii (S. pennellii) wild tomato under salt stress. Based on the theory of competitive endogenous RNA (ceRNA), we also established several salt-responsive ceRNA networks. The results showed that circRNAs could act as miRNA sponges in the regulation of target mRNAs of miRNAs, thus participating in the response to salt stress. This study provides insights into the mechanisms of salt tolerance in tomatoes and serves as an effective reference for improving the salt tolerance of salt-sensitive cultivars.
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Affiliation(s)
- Zhongyu Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
- Key Laboratory of Horticulture Crop Genomics and Genetic Improvement in Xinjiang, Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
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12
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Yusuf NHM, Latip MA, Kumar VS. Artificial microRNA derived from the precursors of Ananas comosus, Arabidopsis thaliana, and Oryza sativa effectively silences endogenous genes in MD2 pineapple. PLANT GENE 2021; 26:100289. [DOI: 10.1016/j.plgene.2021.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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13
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Chaudhary S, Grover A, Sharma PC. MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops. Life (Basel) 2021; 11:life11040289. [PMID: 33800690 PMCID: PMC8066829 DOI: 10.3390/life11040289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/24/2022] Open
Abstract
Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.
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Affiliation(s)
- Saurabh Chaudhary
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
- Correspondence: (S.C.); (P.C.S.)
| | - Atul Grover
- Defence Institute of Bio-Energy Research, Defence Research and Development Organisation (DRDO), Haldwani 263139, India;
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India
- Correspondence: (S.C.); (P.C.S.)
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14
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Xu T, Zhang L, Yang Z, Wei Y, Dong T. Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:665439. [PMID: 34220888 PMCID: PMC8247772 DOI: 10.3389/fpls.2021.665439] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 05/07/2023]
Abstract
Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.
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Affiliation(s)
- Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Tao Xu,
| | - Long Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tingting Dong,
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15
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Zhang Y, Gong H, Li D, Zhou R, Zhao F, Zhang X, You J. Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.). BMC Genomics 2020; 21:494. [PMID: 32682396 PMCID: PMC7368703 DOI: 10.1186/s12864-020-06913-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) exhibit important regulatory roles in the response to abiotic stresses by post-transcriptionally regulating the target gene expression in plants. However, their functions in sesame response to salt stress are poorly known. To dissect the complex mechanisms underlying salt stress response in sesame, miRNAs and their targets were identified from two contrasting sesame genotypes by a combined analysis of small RNAs and degradome sequencing. RESULTS A total of 351 previously known and 91 novel miRNAs were identified from 18 sesame libraries. Comparison of miRNA expressions between salt-treated and control groups revealed that 116 miRNAs were involved in salt stress response. Using degradome sequencing, potential target genes for some miRNAs were also identified. The combined analysis of all the differentially expressed miRNAs and their targets identified miRNA-mRNA regulatory networks and 21 miRNA-mRNA interaction pairs that exhibited contrasting expressions in sesame under salt stress. CONCLUSIONS This comprehensive integrated analysis may provide new insights into the genetic regulation mechanism of miRNAs underlying the adaptation of sesame to salt stress.
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Affiliation(s)
- Yujuan Zhang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Huihui Gong
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Fengtao Zhao
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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16
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MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:241-255. [PMID: 32531477 PMCID: PMC7801212 DOI: 10.1016/j.gpb.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 11/24/2022]
Abstract
Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about the role of microRNAs (miRNAs) in this process. We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible (N6) or resistant (BT-1) inbred lines from uninfected plants and upon F. verticillioides infection. We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple miRNAs, including new members of previously annotated miRNA families. A combination of transcriptomic, degradomic, and bioinformatics analyses revealed that F. verticillioides-responsive miRNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes. Functional category analysis uncovered preferential enrichment of the pathogen-responsive miRNAs and their targets in the phenylpropanoid metabolic processes, plant-pathogen interactions, and plant phytohormone signal transduction pathways. Furthermore, transgenic maize plants overexpressing miR408b exhibited reduced resistance to F. verticillioides infection in a susceptible maize line. These findings provide new insights into the regulatory roles of miRNAs in maize immunity against FER and new resources for breeding disease resistance into maize.
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Cui Y, Su Y, Wang J, Jia B, Wu M, Pei W, Zhang J, Yu J. Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6. Int J Mol Sci 2020; 21:E863. [PMID: 32013234 PMCID: PMC7037685 DOI: 10.3390/ijms21030863] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.
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Affiliation(s)
- Yupeng Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Ying Su
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China;
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Bing Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Man Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA;
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang 455000, China; (Y.C.); (J.W.); (B.J.); (M.W.); (W.P.)
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19
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Ayubov MS, Mirzakhmedov MH, Sripathi VR, Buriev ZT, Ubaydullaeva KA, Usmonov DE, Norboboyeva RB, Emani C, Kumpatla SP, Abdurakhmonov IY. Role of MicroRNAs and small RNAs in regulation of developmental processes and agronomic traits in Gossypium species. Genomics 2019; 111:1018-1025. [PMID: 30026106 DOI: 10.1016/j.ygeno.2018.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/08/2023]
Abstract
Small RNAs (sRNAs) are short, non-coding, 17-24 nucleotides long RNA molecules that play vital roles in regulating gene expression in every known organism investigated to date including cotton (Gossypium ssp.). These tiny RNA molecules target diverse categories of genes from different bioliogical and metabolic processes and have been reported in the three domains of life. Small RNAs, including miRNAs, are involved in ovule and fiber development, biotic and abiotic stresses, fertility, and other biochemical processes in cotton species. Also, sRNAs are the critical components in RNA interference pathway. In this article, we have reviewed the research efforts related to the isolation and characterization of miRNAs using molecular and genomic approaches. The progress made in understanding the functional roles of miRNAs in regulation, alteration, and inactivation of fundamental plant processes and traits of importance in cotton are presented here.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Mukhammad H Mirzakhmedov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan; Faculty of Agricultural Science, University of Hohenheim, Germany
| | - Venkateswara R Sripathi
- Center for Molecular Biology, Department of Biological and Environmental Sciences, Alabama A and M University, AL, USA
| | - Zabardast T Buriev
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | | | - Dilshod E Usmonov
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
| | - Risolat B Norboboyeva
- Center of Genomics and bioinformatics, Academy of Sciences Republic of Uzbekistan, Uzbekistan
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20
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Ravichandran S, Ragupathy R, Edwards T, Domaratzki M, Cloutier S. MicroRNA-guided regulation of heat stress response in wheat. BMC Genomics 2019; 20:488. [PMID: 31195958 PMCID: PMC6567507 DOI: 10.1186/s12864-019-5799-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. Results Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins. Conclusion The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5799-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sridhar Ravichandran
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Raja Ragupathy
- Plant Science Department, University of Manitoba, Winnipeg, Manitoba, Canada.,Present address: Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Tara Edwards
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada.
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Sun M, Shen Y, Li H, Yang J, Cai X, Zheng G, Zhu Y, Jia B, Sun X. The multiple roles of OsmiR535 in modulating plant height, panicle branching and grain shape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:60-69. [PMID: 31128716 DOI: 10.1016/j.plantsci.2019.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/18/2019] [Accepted: 02/03/2019] [Indexed: 05/20/2023]
Abstract
The miR156/miR529-SPL module acts a vital role in regulating plant growth and development. Though miR535 shows very high sequence identity to miR156 and miR529, it is still unknown whether miR535 could control plant growth and development. In this study, we performed the evolutionary analyses of miR535s in land plants and found that miR535s were less conserved than miR156s during evolution. In rice, miR535 expressed at a very low level during the vegetative growth but highly accumulated in young panicles, which is similar with OsmiR529, but opposite to OsmiR156. Expectedly, OsmiR535 overexpression in rice reduced plant height by decreasing the 1st and 2nd internode length. Furthermore, OsmiR535 overexpression imposed great influence in panicle architecture, such as more but shorter panicles, and fewer primary/secondary panicle branches. Moreover, OsmiR535 overexpression increased the grain length, but did not affect grain width. Through quantitative real-time PCR analyses, we further revealed that OsmiR535 overexpression repressed the expression of OsSPL7/12/16, as well as the OsSPLs downstream panicle related genes, including OsPIN1B, OsDEP1, OsLOG and OsSLR1. Taken together, our findings suggest that OsmiR535 multiply modulates plant height, panicle architecture and grain shape possibly by regulating OsSPLs genes in rice.
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Affiliation(s)
- Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin, 150030, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Hongyu Li
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Guiping Zheng
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yanming Zhu
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Plant Bioengineering Laboratory, Northeast Agricultural University, Harbin, 150030, China
| | - Bowei Jia
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Heilongjiang Provincial Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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Pegler JL, Oultram JMJ, Grof CPL, Eamens AL. Profiling the Abiotic Stress Responsive microRNA Landscape of Arabidopsis thaliana. PLANTS 2019; 8:plants8030058. [PMID: 30857364 PMCID: PMC6473545 DOI: 10.3390/plants8030058] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/01/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022]
Abstract
It is well established among interdisciplinary researchers that there is an urgent need to address the negative impacts that accompany climate change. One such negative impact is the increased prevalence of unfavorable environmental conditions that significantly contribute to reduced agricultural yield. Plant microRNAs (miRNAs) are key gene expression regulators that control development, defense against invading pathogens and adaptation to abiotic stress. Arabidopsis thaliana (Arabidopsis) can be readily molecularly manipulated, therefore offering an excellent experimental system to alter the profile of abiotic stress responsive miRNA/target gene expression modules to determine whether such modification enables Arabidopsis to express an altered abiotic stress response phenotype. Towards this goal, high throughput sequencing was used to profile the miRNA landscape of Arabidopsis whole seedlings exposed to heat, drought and salt stress, and identified 121, 123 and 118 miRNAs with a greater than 2-fold altered abundance, respectively. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) was next employed to experimentally validate miRNA abundance fold changes, and to document reciprocal expression trends for the target genes of miRNAs determined abiotic stress responsive. RT-qPCR also demonstrated that each miRNA/target gene expression module determined to be abiotic stress responsive in Arabidopsis whole seedlings was reflective of altered miRNA/target gene abundance in Arabidopsis root and shoot tissues post salt stress exposure. Taken together, the data presented here offers an excellent starting platform to identify the miRNA/target gene expression modules for future molecular manipulation to generate plant lines that display an altered response phenotype to abiotic stress.
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Affiliation(s)
- Joseph L Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Jackson M J Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Christopher P L Grof
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
| | - Andrew L Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, Faculty of Science, University of Newcastle, Callaghan 2308, Australia.
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23
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Wang W, Liu D, Chen D, Cheng Y, Zhang X, Song L, Hu M, Dong J, Shen F. MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress. RNA Biol 2019; 16:362-375. [PMID: 30676211 PMCID: PMC6380294 DOI: 10.1080/15476286.2019.1574163] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022] Open
Abstract
Salinity stress is a major abiotic stress affecting the productivity and fiber quality of cotton. Although reactive oxygen species (ROS) play critical roles in plant stress responses, their complex molecular regulatory mechanism under salinity stress is largely unknown in cotton, especially microRNA (miRNA)-mediated regulation of superoxide dismutase gene expression. Here, we report that a cotton iron superoxide dismutase gene GhFSD1 and the cotton miRNA ghr-miR414c work together in response to salinity stress. The miRNA ghr-miR414c targets the coding sequence region of GhFSD1, inhibiting expression of transcripts of this antioxidase gene, which represents the first line of defense against stress-induced ROS. Expression of GhFSD1 was induced by salinity stress. Under salinity stress, ghr-miR414c showed expression patterns opposite to those of GhFSD1. Ectopic expression of GhFSD1 in Arabidopsis conferred salinity stress tolerance by improving primary root growth and biomass, whereas Arabidopsis constitutively expressing ghr-miR414c showed hypersensitivity to salinity stress. Silencing GhFSD1 in cotton caused an excessive hypersensitive phenotype to salinity stress, whereas overexpressing miR414c decreased the expression of GhFSD1 and increased sensitivity to salinity stress, yielding a phenotype similar to that of GhFSD1-silenced cotton. Taken together, our results demonstrated that ghr-miR414c was involved in regulation of plant response to salinity stress by targeting GhFSD1 transcripts. This study provides a new strategy and method for plant breeding in order to improve plant salinity tolerance.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Dongdong Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Lirong Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Mengjiao Hu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, People’s Republic of China
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Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 146:112-122. [PMID: 30802474 DOI: 10.1016/j.pbiomolbio.2019.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/09/2023]
Abstract
Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs.
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25
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The Catalase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis. Cells 2019; 8:cells8020086. [PMID: 30682777 PMCID: PMC6406514 DOI: 10.3390/cells8020086] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022] Open
Abstract
Catalases (CATs), which were coded by the catalase gene family, were a type notably distinguished ROS-metabolizing proteins implicated to perform various physiological functions in plant growth, development and stress responses. However, no systematical study has been performed in cotton. In the present study, we identified 7 and 7 CAT genes in the genome of Gossypium hirsutum L. Additionally, G. barbadense L., respectively. The results of the phylogenetic and synteny analysis showed that the CAT genes were divided into two groups, and whole-genome duplication (WGD) or polyploidy events contributed to the expansion of the GossypiumCAT gene family. Expression patterns analysis showed that the CAT gene family possessed temporal and spatial specificity and was induced by the Verticillium dahliae infection. In addition, we predicted the putative molecular regulatory mechanisms of the CAT gene family. Based on the analysis and preliminary verification results, we hypothesized that the CAT gene family, which might be regulated by transcription factors (TFs), alternative splicing (AS) events and miRNAs at different levels, played roles in cotton development and stress tolerance through modulating the reactive oxygen species (ROS) metabolism. This is the first report on the genome-scale analysis of the cotton CAT gene family, and these data will help further study the roles of CAT genes during stress responses, leading to crop improvement.
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26
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Sun X, Lin L, Sui N. Regulation mechanism of microRNA in plant response to abiotic stress and breeding. Mol Biol Rep 2018; 46:1447-1457. [PMID: 30465132 DOI: 10.1007/s11033-018-4511-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
microRNAs (miRNAs) in plants are a class of small RNAs consisting of approximately 21-24 nucleotides. The mature miRNA binds to the target mRNA through the formation of a miRNA-induced silencing complex (MIRISC), and cleaves or inhibits translation, thereby achieving negative regulation of the target gene. Based on miRNA plays an important role in regulating plant gene expression, studies on the prediction, identification, function and evolution of plant miRNAs have been carried out. In addition, many researches prove that miRNAs are also involved in many kinds of abiotic and biotic stress, under abiotic stress, plants can express some miRNA, and act on stress-related target genes, which can make plants adapt to stress in physiological response. In this review, the synthetic pathway and mechanism of plant miRNA are briefly described, and we discuss the biological functions and regulatory mechanisms of miRNAs responding to abiotic stresses including low temperature, salt, drought stress and breeding to lay the foundation for further exploring the mechanism of action of miRNAs in stress resistance of plant. And analyze its utilization prospects in plant stress resistance research.
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Affiliation(s)
- Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China
| | - Lin Lin
- Water Research Institute of Shandong Province, Jinan, People's Republic of China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China.
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Guo N, Zhang Y, Sun X, Fan H, Gao J, Chao Y, Liu A, Yu X, Cai Y, Lin Y. Genome-wide identification of differentially expressed miRNAs induced by ethephon treatment in abscission layer cells of cotton (Gossypium hirsutum). Gene 2018; 676:263-268. [PMID: 30125660 DOI: 10.1016/j.gene.2018.08.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
Cotton is one of the most important economic crops and its production is influenced by various adverse factors. Boll shedding at an inappropriate period causes the severe loss of cotton yield. Ethephon can promote the formation of abscission layer cells, resulting in boll shedding. To genome-widely investigate the differentially expressed miRNAs involved in the formation of abscission layer cells, two sRNA libraries were constructed using abscission tissues of cotton pedicels treated with ethephon or water. A total of 55,264,755 and 59,069,866 clean reads were generated in two libraries. 460 mature miRNAs were identified, including 301 known miRNAs and 159 novel miRNAs. Among them, one known gra-MIR530b and seven novel miRNAs (gar-novel-miR88-3p/gra-novel-miR8-3p, gar-novel-miR16-5p, gar-novel-miR100-3p, gar-novel-miR75-3p/gra-novel-miR92-3p,gar-novel-miR32-5p/gra-novel-miR30-5p, gar-novel-miR9-5p and gra-novel-miR61-3p) were expressed differentially in abscission tissues. Seven-two genes were predicted as potential targets of the eight miRNAs. Gene ontology (GO) analyses revealed that most of these target genes are auxin response factors (ARFs), GTPase activators, and the regulators of oxidative phosphorylation and photosynthesis. Hence, we speculate that these miRNAs might regulate cell separation and aging to affect the formation of bscission layer cells. Our findings will provide a new insight into the regulatory mechanism of miRNAs involved in boll shedding.
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Affiliation(s)
- Ning Guo
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Yujiang Zhang
- School of Life Science, Anhui University, 111 Jiu Long Road, Hefei 230601, PR China.
| | - Xu Sun
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Honghong Fan
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Junsan Gao
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Yunpeng Chao
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Anfeng Liu
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Xiantao Yu
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, PR China.
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28
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Peng Z, He S, Gong W, Xu F, Pan Z, Jia Y, Geng X, Du X. Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton. BMC PLANT BIOLOGY 2018; 18:128. [PMID: 29925319 PMCID: PMC6011603 DOI: 10.1186/s12870-018-1350-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/12/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. RESULTS In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure. CONCLUSION We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.
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Affiliation(s)
- Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Feifei Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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29
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Deng F, Zhang X, Wang W, Yuan R, Shen F. Identification of Gossypium hirsutum long non-coding RNAs (lncRNAs) under salt stress. BMC PLANT BIOLOGY 2018; 18:23. [PMID: 29370759 PMCID: PMC5785843 DOI: 10.1186/s12870-018-1238-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/17/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed into shorter microRNAs (miRNAs) and small interfering RNAs. Long noncoding RNAs (lncRNAs) are arbitrarily defined as RNA genes larger than 200 nt in length that have no apparent coding potential. lncRNAs have emerged as playing important roles in various biological regulatory processes and are expressed in a more tissue-specific manner than mRNA. Emerging evidence shows that lncRNAs participate in stress-responsive regulation. RESULTS In this study, in order to develop a comprehensive catalogue of lncRNAs in upland cotton under salt stress, we performed whole-transcriptome strand-specific RNA sequencing for three-leaf stage cotton seedlings treated with salt stress (S_NaCl) and controls (S_CK). In total we identified 1117 unique lncRNAs in this study and 44 differentially expressed RNAs were identified as potential non-coding RNAs. For the differentially expressed lncRNAs that were identified as intergenic lncRNAs (lincRNA), we analysed the gene ontology enrichment of cis targets and found that cis target protein-coding genes were mainly enriched in stress-related categories. Real-time quantitative PCR confirmed that all selected lincRNAs responsive to salt stress. We found lnc_388 was likely as regulator of Gh_A09G1182. And lnc_883 may participate in regulating tolerance to salt stress by modulating the expression of Gh_D03G0339 MS_channel. We then predicted the target mimics for miRNA in Gossypium. six miRNAs were identified, and the result of RT-qPCR with lncRNA and miRNA suggested that lnc_973 and lnc_253 may regulate the expression of ghr-miR399 and ghr-156e as a target mimic under salt stress. CONCLUSIONS We identified 44 lincRNAs that were differentially expressed under salt stress. These lincRNAs may target protein-coding genes via cis-acting regulation. We also discovered that specifically-expressed lincRNAs under salt stress may act as endogenous target mimics for conserved miRNAs. These findings extend the current view on lincRNAs as ubiquitous regulators under stress stress.
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Affiliation(s)
- Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Rui Yuan
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018 Shandong People’s Republic of China
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30
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Comparative Analysis of Cotton Small RNAs and Their Target Genes in Response to Salt Stress. Genes (Basel) 2017; 8:genes8120369. [PMID: 29206160 PMCID: PMC5748687 DOI: 10.3390/genes8120369] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 11/21/2022] Open
Abstract
Small RNAs play an important role in regulating plant responses to abiotic stress. Depending on the method of salt application, whether sudden or gradual, plants may experience either salt shock or salt stress, respectively. In this study, small RNA expression in response to salt shock and long-term salt stress in parallel experiments was described. Cotton small RNA libraries were constructed and sequenced under normal conditions, as well as sudden and gradual salt application. A total of 225 cotton microRNAs (miRNAs) were identified and of these 24 were novel miRNAs. There were 88 and 75 miRNAs with differential expression under the salt shock and long-term salt stress, respectively. Thirty one transcripts were found to be targets of 20 miRNA families. Eight targets showed a negative correlation in expression with their corresponding miRNAs. We also identified two TAS3s with two near-identical 21-nt trans-acting small interfering RNA (tasiRNA)-Auxin Response Factors (ARFs) that coaligned with the phases D7(+) and D8(+) in three Gossypium species. The miR390/tasiRNA-ARFs/ARF4 pathway was identified and showed altered expression under salt stress. The identification of these small RNAs as well as elucidating their functional significance broadens our understanding of post-transcriptional gene regulation in response to salt stress.
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31
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Dong Z, Zhang J, Zhu Q, Zhao L, Sui S, Li Z, Zhang Y, Wang H, Tian D, Zhao Y. Identification of microRNAs involved in drought stress responses in early-maturing cotton by high-throughput sequencing. Genes Genomics 2017; 40:305-314. [PMID: 29892798 DOI: 10.1007/s13258-017-0637-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 01/19/2023]
Abstract
Drought stress is one of the most important abiotic stresses. Cotton is classified as drought tolerant crop but the regulatory mechanism is unknown. MicroRNAs (miRNAs) have been implicated important roles in stress responses in many plants. However, the study of miRNAs in cotton responsive to drought stress is limited, especially in early-maturing cotton. In this study, we performed deep sequencing of small RNAs to identify known and novel miRNAs involved in the regulation of drought stress and understand the expression profile of miRNAs in early-maturing cotton. Three cotton small RNA libraries: non-stressed Shizao1 (early-maturing cotton variety) library (NSS), drought-stressed Shizao1 library (DSS) and non-stressed Jimian958 (medium-maturing cotton variety) library (NSJ) were constructed for deep sequencing. As a result, we identified a total of 64 known and 67 novel miRNAs in the 3 libraries and 88 of them were dramatically differentially expressed (greater than twofold) during drought stress. In addition, we found the expression of 41 miRNAs increased or reduced more than twofold in early-maturing cotton variety compared with that in medium-maturing cotton variety. Our results significantly increased the number of miRNAs in cotton and revealed for the first time the expression profile of miRNAs for early-maturing cotton.
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Affiliation(s)
- Zhanghui Dong
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 598 Heping Road, Shijiazhuang, 050051, Hebei, China
| | - Qingzhu Zhu
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Lifen Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Shuxiang Sui
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Zengshu Li
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yanli Zhang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Hu Wang
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Dongliang Tian
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
| | - Yankun Zhao
- Shijiazhuang Academy of Agricultural and Forestry Sciences, 479 Shenglidajie Road, Shijiazhuang, 050041, Hebei, China
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32
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Nawaz MA, Rehman HM, Imtiaz M, Baloch FS, Lee JD, Yang SH, Lee SI, Chung G. Systems Identification and Characterization of Cell Wall Reassembly and Degradation Related Genes in Glycine max (L.) Merill, a Bioenergy Legume. Sci Rep 2017; 7:10862. [PMID: 28883533 PMCID: PMC5589831 DOI: 10.1038/s41598-017-11495-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/24/2017] [Indexed: 12/22/2022] Open
Abstract
Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Soo In Lee
- Metabolic Engineering Division, Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), Jeonju, 54874, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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Bakshi M, Sherameti I, Meichsner D, Thürich J, Varma A, Johri AK, Yeh KW, Oelmüller R. Piriformospora indica Reprograms Gene Expression in Arabidopsis Phosphate Metabolism Mutants But Does Not Compensate for Phosphate Limitation. Front Microbiol 2017; 8:1262. [PMID: 28747898 PMCID: PMC5506084 DOI: 10.3389/fmicb.2017.01262] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/23/2017] [Indexed: 01/12/2023] Open
Abstract
Piriformospora indica is an endophytic fungus of Sebacinaceae which colonizes the roots of many plant species and confers benefits to the hosts. We demonstrate that approximately 75% of the genes, which respond to P. indica in Arabidopsis roots, differ among seedlings grown on normal phosphate (Pi) or Pi limitation conditions, and among wild-type and the wrky6 mutant impaired in the regulation of the Pi metabolism. Mapman analyses suggest that the fungus activates different signaling, transport, metabolic and developmental programs in the roots of wild-type and wrky6 seedlings under normal and low Pi conditions. Under low Pi, P. indica promotes growth and Pi uptake of wild-type seedlings, and the stimulatory effects are identical for mutants impaired in the PHOSPHATE TRANSPORTERS1;1, -1;2 and -1;4. The data suggest that the fungus does not stimulate Pi uptake, but adapts the expression profiles to Pi limitation in Pi metabolism mutants.
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Affiliation(s)
- Madhunita Bakshi
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
| | - Irena Sherameti
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
| | - Doreen Meichsner
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
| | - Johannes Thürich
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity UniversityNoida, India
| | - Atul K Johri
- School of Life Sciences, Jawaharlal Nehru UniversityNew Delhi, India
| | - Kai-Wun Yeh
- Institute of Plant Biology, Taiwan National UniversityTaipei, Taiwan
| | - Ralf Oelmüller
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University JenaJena, Germany
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Wei Y, Xu Y, Lu P, Wang X, Li Z, Cai X, Zhou Z, Wang Y, Zhang Z, Lin Z, Liu F, Wang K. Salt stress responsiveness of a wild cotton species (Gossypium klotzschianum) based on transcriptomic analysis. PLoS One 2017; 12:e0178313. [PMID: 28552980 PMCID: PMC5446155 DOI: 10.1371/journal.pone.0178313] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/11/2017] [Indexed: 11/22/2022] Open
Abstract
Cotton is a pioneer of saline land crop, while salt stress still causes its growth inhibition and fiber production decrease. Phenotype identification showed better salt tolerance of a wild diploid cotton species Gossypium klotzschianum. To elucidate the salt-tolerant mechanisms in G. klotzschianum, we firstly detected the changes in hormones, H2O2 and glutathione (GSSH and GSH), then investigated the gene expression pattern of roots and leaves treated with 300 mM NaCl for 0, 3, 12, 48 h, and each time control by RNA-seq on the Illumina-Solexa platform. Physiological determination proved that the significant increase in hormone ABA at 48 h, while that in H2O2 was at 12 h, likewise, the GSH content decrease at 48 h and the GSSH content increase at 48 h, under salt stress. In total, 37,278 unigenes were identified from the transcriptome data, 8,312 and 6,732 differentially expressed genes (DEGs) were discovered to be involved in salt stress tolerance in roots and leaves, respectively. Gene function annotation and expression analysis elucidated hormone biosynthesis and signal transduction, reactive oxygen species (ROS), and salt overly sensitive (SOS) signal transduction related genes revealed the important roles of them in signal transmission, oxidation balance and ion homeostasis in response to salinity stress. This is a report which focuses on primary response to highly salty stress (upto 300 mM NaCl) in cotton using a wild diploid Gossypium species, broadening our understanding of the salt tolerance mechanism in cotton and laying a solid foundation of salt resistant for the genetic improvement of upland cotton with the resistance to salt stress.
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Affiliation(s)
- Yangyang Wei
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Pu Lu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenqing Li
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail: (ZL); (FL); (KW)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
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Fausto AKS, Silva TDF, Romanel E, Vaslin MFS. microRNAs as reference genes for quantitative PCR in cotton. PLoS One 2017; 12:e0174722. [PMID: 28414734 PMCID: PMC5393557 DOI: 10.1371/journal.pone.0174722] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/14/2017] [Indexed: 11/18/2022] Open
Abstract
Cotton (Gossypium hirsutum) is the most important non-food plant in the world. Studies concerning the fiber quality and plant fitness of cotton at molecular level depend on high sensitive and reproducible gene-expression assays. However, only a few reports have described genes suitable for normalizing gene expression data. In this study, we report for the first time that microRNAs (miRNAs) are reliable reference genes (RGs) for cotton gene expression normalization in quantitative real-time reverse transcription (RT)-PCR. The stability of cotton miRNAs was assayed in root, stem, leaf and flower samples from three different cultivars [FiberMax (FM966), Delta Opal (DO) and Cedro] and under conditions of biotic stress caused by infection with Cotton leafroll dwarf virus (CLRDV). The stability of mRNAs already described as reference genes in cotton was also assessed. The geNorm, NormFinder, BestKeeper and ΔCt algorithms were used to select the best reference genes. In 8 of the 12 sets tested, miRNAs (miR172, 168 and 390) were found to be the best RGs. To validate the best selected RGs, miR159, miR164, miR2118, miR2910, miR3476, GhDCL2 and GhDCL4 expression levels were evaluated under biotic stress conditions, and miR164 and a putative myo-inositol oxigenase gene (GhMIOX) were assessed in leaves and flowers. The RGs selected in this work proved to be excellent reference genes in the two cases studied. Our results support the use of miRNAs as reference genes for miRNA and protein-coding genes.
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Affiliation(s)
- Anna Karoline Silva Fausto
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
| | - Tatiane da Franca Silva
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brasil
| | - Elisson Romanel
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
- Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brasil
| | - Maite F. S. Vaslin
- Lab. Virologia Molecular Vegetal, Depto. Virologia, IMPPG, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, RJ, Brasil
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Dassanayake M, Larkin JC. Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands. FRONTIERS IN PLANT SCIENCE 2017; 8:406. [PMID: 28400779 PMCID: PMC5368257 DOI: 10.3389/fpls.2017.00406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/09/2017] [Indexed: 05/25/2023]
Abstract
Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes. Salt secretion via salt glands is found in more than 50 species in 14 angiosperm families distributed in caryophyllales, asterids, rosids, and grasses. The salt glands of these distantly related clades can be grouped into four structural classes. Although salt glands appear to have originated independently at least 12 times, they share convergently evolved features that facilitate salt compartmentalization and excretion. We review the structural diversity and evolution of salt glands, major transporters and proteins associated with salt transport and secretion in halophytes, salt gland relevant gene expression regulation, and the prospect for using new genomic and transcriptomic tools in combination with information from model organisms to better understand how salt glands contribute to salt tolerance. Finally, we consider the prospects for using this knowledge to engineer salt glands to increase salt tolerance in model species, and ultimately in crops.
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Affiliation(s)
- Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton RougeLA, USA
| | - John C. Larkin
- Department of Biological Sciences, Louisiana State University, Baton RougeLA, USA
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Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA. Functional Roles of microRNAs in Agronomically Important Plants-Potential as Targets for Crop Improvement and Protection. FRONTIERS IN PLANT SCIENCE 2017; 8:378. [PMID: 28382044 PMCID: PMC5360763 DOI: 10.3389/fpls.2017.00378] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses toward environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic-or abiotic origin.
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Affiliation(s)
- Arnaud T. Djami-Tchatchou
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and BiotechnologyNew Delhi, India
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa (Florida Campus)Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg (Auckland Park Kingsway Campus)Johannesburg, South Africa
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Zahid KR, Ali F, Shah F, Younas M, Shah T, Shahwar D, Hassan W, Ahmad Z, Qi C, Lu Y, Iqbal A, Wu W. Response and Tolerance Mechanism of Cotton Gossypium hirsutum L. to Elevated Temperature Stress: A Review. FRONTIERS IN PLANT SCIENCE 2016; 7:937. [PMID: 27446165 PMCID: PMC4927942 DOI: 10.3389/fpls.2016.00937] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/13/2016] [Indexed: 05/23/2023]
Abstract
Cotton is an important multipurpose crop which is highly sensitive to both biotic and abiotic stresses. Proper management of this cash crop requires systematic understanding of various environmental conditions that are vital to yield and quality. High temperature stress can severely affect the viability of pollens and anther indehiscence, which leads to significant yield losses. Cotton can respond to withstand adverse environmental condition in several phases among which the accumulation of chemicals is extremely vital. Calcium, kinases, reactive oxygen species, carbohydrate, transcription factors, gene expression regulation, and plant hormones signaling pathways are playing a handy role in activating the major genes responsible to encounter and defend elevated temperature stress. The production of heat shock proteins is up-regulated when crops are unleashed to high temperature stress. Molecular breeding can play a functional role to identify superior genes for all the important attributes as well as provide breeder ready markers for developing ideotypes. The development of high-temperature resistant transgenic cultivars of cotton can grant a stability benefit and can also ameliorate the production capacity in response to elevated temperature.
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Affiliation(s)
- Kashif Rafiq Zahid
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Farhan Ali
- Cereal Crops Research InstitutePirsabak, Nowshera, Pakistan
| | - Farooq Shah
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Muhammad Younas
- Department of Biotechnology, Mohi-ud-Din Islamic UniversityAzad Jammu and Kashmir, Pakistan
| | - Tariq Shah
- Department of Agricultural Economics and Management, Huazhong Agricultural UniversityWuhan, China
| | - Durri Shahwar
- Department of Plant Breeding and Genetics, University of SwabiKhyber Pakhtunkhwa, Pakistan
| | - Waseem Hassan
- Department of Soil and Environmental Sciences, Muhammad Nawaz Shareef University of AgricultureMultan, Pakistan
| | - Zahoor Ahmad
- Key Lab of Crop Disease Monitoring and Safety Control, Huazhong Agricultural UniversityWuhan, China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal UniversityWuhan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural UniversityWenjian Sichuan, China
| | - Amjad Iqbal
- Department of Agriculture, Abdul Wali Khan University MardanKhyber Pakhtunkhwa, Pakistan
| | - Wei Wu
- College of Agronomy, Northwest A&F UniversityYangling, China
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Naoumkina M, Thyssen GN, Fang DD, Hinchliffe DJ, Florane CB, Jenkins JN. Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintles-1 (Li 1 ) and -2 (Li 2 ) revealed a role for miRNAs and their targets in cotton fiber elongation. BMC Genomics 2016; 17:360. [PMID: 27184029 PMCID: PMC4869191 DOI: 10.1186/s12864-016-2715-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/06/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The length of cotton fiber is an important agronomic trait that directly affects the quality of yarn and fabric. Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon-lintless-1 (Li 1 ) and -2 (Li 2 ) are monogenic and dominant mutations that result in an extreme reduction in the length of lint fiber on mature seeds. In a near-isogenic state with wild type cotton these two short fiber mutants provide an effective model system to study the mechanisms of fiber elongation. Plant miRNAs regulate many aspects of growth and development. However, the mechanism underlying the miRNA-mediated regulation of fiber development is largely unknown. RESULTS Small RNA libraries constructed from developing fiber cells of the short fiber mutants Li 1 and Li 2 and their near-isogenic wild type lines were sequenced. We identified 24 conservative and 147 novel miRNA families with targets that were detected through degradome sequencing. The distribution of the target genes into functional categories revealed the largest set of genes were transcription factors. Expression profiles of 20 miRNAs were examined across a fiber developmental time course in wild type and short fiber mutations. We conducted correlation analysis between miRNA transcript abundance and the length of fiber for 11 diverse Upland cotton lines. The expression patterns of 4 miRNAs revealed significant negative correlation with fiber lengths of 11 cotton lines. CONCLUSIONS Our results suggested that the mutations have changed the regulation of miRNAs expression during fiber development. Further investigations of differentially expressed miRNAs in the Li 1 and Li 2 mutants will contribute to better understanding of the regulatory mechanisms of cotton fiber development. Four miRNAs negatively correlated with fiber length are good candidates for further investigations of miRNA regulation of important genotype dependent fiber traits. Thus, our results will contribute to further studies on the role of miRNAs in cotton fiber development and will provide a tool for fiber improvement through molecular breeding.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Doug J Hinchliffe
- Cotton Chemistry and Utilization Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Christopher B Florane
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA
| | - Johnie N Jenkins
- Genetics and Sustainable Agriculture Research Unit, USDA-ARS, 810 Highway 12 East, Mississippi State, MS, 39762, USA
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Abdurakhmonov IY, Ayubov MS, Ubaydullaeva KA, Buriev ZT, Shermatov SE, Ruziboev HS, Shapulatov UM, Saha S, Ulloa M, Yu JZ, Percy RG, Devor EJ, Sharma GC, Sripathi VR, Kumpatla SP, van der Krol A, Kater HD, Khamidov K, Salikhov SI, Jenkins JN, Abdukarimov A, Pepper AE. RNA Interference for Functional Genomics and Improvement of Cotton (Gossypium sp.). FRONTIERS IN PLANT SCIENCE 2016; 7:202. [PMID: 26941765 PMCID: PMC4762190 DOI: 10.3389/fpls.2016.00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/05/2016] [Indexed: 02/05/2023]
Abstract
RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium sp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function and biological roles of many key cotton genes involved in fiber development, fertility and somatic embryogenesis, resistance to important biotic and abiotic stresses, and oil and seed quality improvements as well as the key agronomic traits including yield and maturity. Here, we have comparatively reviewed seminal research efforts in previously used antisense approaches and currently applied breakthrough RNAi studies in cotton, analyzing developed RNAi methodologies, achievements, limitations, and future needs in functional characterizations of cotton genes. We also highlighted needed efforts in the development of RNAi-based cotton cultivars, and their safety and risk assessment, small and large-scale field trials, and commercialization.
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Affiliation(s)
- Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
- *Correspondence: Ibrokhim Y. Abdurakhmonov,
| | - Mirzakamol S. Ayubov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Khurshida A. Ubaydullaeva
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Zabardast T. Buriev
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Shukhrat E. Shermatov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Haydarali S. Ruziboev
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Umid M. Shapulatov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
- Laboratory of Plant Physiology, Wageningen UniversityWageningen, Netherlands
| | - Sukumar Saha
- Crop Science Research Laboratory, United States Department of Agriculture – Agricultural Research Service, StarkvilleMS, USA
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, United States Department of Agriculture – Agricultural Research Service, LubbockTX, USA
| | - John Z. Yu
- Crop Germplasm Research Unit, United States Department of Agriculture – Agricultural Research Service, College StationTX, USA
| | - Richard G. Percy
- Crop Germplasm Research Unit, United States Department of Agriculture – Agricultural Research Service, College StationTX, USA
| | - Eric J. Devor
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa CityIA, USA
| | - Govind C. Sharma
- Department of Biological and Environmental Sciences, Alabama A&M University, NormalAL, USA
| | | | | | | | - Hake D. Kater
- Agricultural and Environmental Research, CaryNC, USA
| | - Khakimdjan Khamidov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Shavkat I. Salikhov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Johnie N. Jenkins
- Crop Science Research Laboratory, United States Department of Agriculture – Agricultural Research Service, StarkvilleMS, USA
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Structural and Functional Genomics, Academy of Sciences the Republic of Uzbekistan, Ministry of Agriculture and Water Resources the Republic of Uzbekistan and “Uzpakhtasanoat” AssociationKibray, Uzbekistan
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, Colleges StationTX, USA
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Tripathi A, Goswami K, Sanan-Mishra N. Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol 2015; 6:286. [PMID: 26578966 PMCID: PMC4620411 DOI: 10.3389/fphys.2015.00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022] Open
Abstract
microRNAs (miRs) are a class of 21-24 nucleotide long non-coding RNAs responsible for regulating the expression of associated genes mainly by cleavage or translational inhibition of the target transcripts. With this characteristic of silencing, miRs act as an important component in regulation of plant responses in various stress conditions. In recent years, with drastic change in environmental and soil conditions different type of stresses have emerged as a major challenge for plants growth and productivity. The identification and profiling of miRs has itself been a challenge for research workers given their small size and large number of many probable sequences in the genome. Application of computational approaches has expedited the process of identification of miRs and their expression profiling in different conditions. The development of High-Throughput Sequencing (HTS) techniques has facilitated to gain access to the global profiles of the miRs for understanding their mode of action in plants. Introduction of various bioinformatics databases and tools have revolutionized the study of miRs and other small RNAs. This review focuses the role of bioinformatics approaches in the identification and study of the regulatory roles of plant miRs in the adaptive response to stresses.
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Affiliation(s)
- Anita Tripathi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Kavita Goswami
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Neeti Sanan-Mishra
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
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Deng P, Wang L, Cui L, Feng K, Liu F, Du X, Tong W, Nie X, Ji W, Weining S. Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress. PLoS One 2015; 10:e0137990. [PMID: 26372557 PMCID: PMC4570814 DOI: 10.1371/journal.pone.0137990] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/24/2015] [Indexed: 02/07/2023] Open
Abstract
Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Le Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Fuyan Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (SW); (XD)
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (SW); (XD)
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Sofo A, Scopa A, Nuzzaci M, Vitti A. Ascorbate Peroxidase and Catalase Activities and Their Genetic Regulation in Plants Subjected to Drought and Salinity Stresses. Int J Mol Sci 2015; 16:13561-78. [PMID: 26075872 PMCID: PMC4490509 DOI: 10.3390/ijms160613561] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 01/06/2023] Open
Abstract
Hydrogen peroxide (H2O2), an important relatively stable non-radical reactive oxygen species (ROS) is produced by normal aerobic metabolism in plants. At low concentrations, H2O2 acts as a signal molecule involved in the regulation of specific biological/physiological processes (photosynthetic functions, cell cycle, growth and development, plant responses to biotic and abiotic stresses). Oxidative stress and eventual cell death in plants can be caused by excess H2O2 accumulation. Since stress factors provoke enhanced production of H2O2 in plants, severe damage to biomolecules can be possible due to elevated and non-metabolized cellular H2O2. Plants are endowed with H2O2-metabolizing enzymes such as catalases (CAT), ascorbate peroxidases (APX), some peroxiredoxins, glutathione/thioredoxin peroxidases, and glutathione sulfo-transferases. However, the most notably distinguished enzymes are CAT and APX since the former mainly occurs in peroxisomes and does not require a reductant for catalyzing a dismutation reaction. In particular, APX has a higher affinity for H2O2 and reduces it to H2O in chloroplasts, cytosol, mitochondria and peroxisomes, as well as in the apoplastic space, utilizing ascorbate as specific electron donor. Based on recent reports, this review highlights the role of H2O2 in plants experiencing water deficit and salinity and synthesizes major outcomes of studies on CAT and APX activity and genetic regulation in drought- and salt-stressed plants.
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Affiliation(s)
- Adriano Sofo
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy.
| | - Antonio Scopa
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy.
| | - Maria Nuzzaci
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy.
| | - Antonella Vitti
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy.
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Wang Q, Zhang B. MicroRNAs in cotton: an open world needs more exploration. PLANTA 2015; 241:1303-12. [PMID: 25841643 DOI: 10.1007/s00425-015-2282-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/13/2015] [Indexed: 05/28/2023]
Abstract
This paper reviews the progress and current problems in the field of cotton microRNAs. Cotton is not only one of the most important crops in terms of fiber usage and economic value, but also a model species for investigating cell wall and cellulose biosynthesis as well plant polyploidization. Compared with model plant species, such as Arabidopsis and rice, the research on cotton microRNAs (miRNAs) is lagging, although great progress has been made in the past decade. Since the first reports on identifying miRNAs in cotton in 2007, hundreds of miRNAs have been identified using an in silico comparative genome-based approach and direct cloning. Next-generation deep sequencing has opened the door for cotton miRNA research. In cotton, miRNAs are associated with many biological and metabolic processes, including fiber initiation and development, floral development, embryogenesis, and response to biotic and abiotic stresses. However, the majority of current research is focused on miRNA identification. Although several targets have been predicted using computational approaches and degradome sequencing, more functional studies should be performed in the next couple of years to elucidate the roles of miRNAs in cotton fiber development and response to different environmental stresses using transgenic technology. This paper reviews the history, identification, and function of cotton miRNAs as well as future directions for this research.
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Affiliation(s)
- Qinglian Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, Henan, 453003, People's Republic of China
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Shi G, Guo X, Guo J, Liu L, Hua J. Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). PLANT CELL REPORTS 2015; 34:1005-23. [PMID: 25700980 DOI: 10.1007/s00299-015-1761-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/08/2015] [Indexed: 05/22/2023]
Abstract
By comparing series full-length cDNA libraries stressed and control, the dynamic process of salt stress response in Upland cotton was studied, and reactive oxygen species and gibberellins signaling pathways were proposed. The Upland cotton is the most important fiber plant with highly salt tolerance. However, the molecular mechanism underlying salt tolerance in domesticated cotton was unclear. Here, seven full-length cDNA libraries were constructed for seedling roots of Upland cotton 'Zhong G 5' at 0, 3, 12 and 48 h after the treatment of control or 150 mM NaCl stress. About 3300 colonies in each library were selected robotically for 5'-end pyrosequencing, resulting in 20,358 expressed sequence tags (ESTs) totally. And 8516 uniESTs were then assembled, including 2914 contigs and 5602 singletons, and explored for Gene Ontology (GO) function. GO comparison between serial stress libraries and control reflected the growth regulation, stimulus response, signal transduction and biology regulation processes were conducted dynamically in response to salt stress. MYB, MYB-related, WRKY, bHLH, GRAS and ERF families of transcription factors were significantly enriched in the early response. 65 differentially expressed genes (DEGs), mainly associated with reactive oxygen species (ROS) scavenging, gibberellins (GAs) metabolism, signal transduction, transcription regulation, stress response and transmembrane transport, were identified and confirmed by quantitative real-time PCR. Overexpression of selected DEGs increased tolerance against salt stress in transgenic yeast. Results in this study supported that a ROS-GAs interacting signaling pathway of salt stress response was activated in Upland cotton. Our results provided valuable gene resources for further investigation of the molecular mechanism of salinity tolerance.
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Affiliation(s)
- Gongyao Shi
- Key Lab of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China,
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High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response. PLoS One 2015; 10:e0127412. [PMID: 26010449 PMCID: PMC4444200 DOI: 10.1371/journal.pone.0127412] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/15/2015] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNAs, recognize their mRNA targets based on perfect sequence complementarity. MiRNAs lead to broader changes in gene expression after plants are exposed to stress. High-throughput sequencing is an effective method to identify and profile small RNA populations in non-model plants under salt stresses, significantly improving our knowledge regarding miRNA functions in salt tolerance. Cucurbits are sensitive to soil salinity, and the Cucurbita genus is used as the rootstock of other cucurbits to enhance salt tolerance. Several cucurbit crops have been used for miRNA sequencing but salt stress-related miRNAs in cucurbit species have not been reported. In this study, we subjected two Cucurbita germplasm, namely, N12 (Cucurbita. maxima Duch.) and N15 (Cucurbita. moschata Duch.), with different sodium accumulation patterns, to Illumina sequencing to determine small RNA populations in root tissues after 4 h of salt treatment and control. A total of 21,548,326 and 19,394,108 reads were generated from the control and salt-treated N12 root tissues, respectively. By contrast, 19,108,240 and 20,546,052 reads were obtained from the control and salt-treated N15 root tissues, respectively. Fifty-eight conserved miRNA families and 33 novel miRNAs were identified in the two Cucurbita germplasm. Seven miRNAs (six conserved miRNAs and one novel miRNAs) were up-regulated in salt-treated N12 and N15 samples. Most target genes of differentially expressed novel miRNAs were transcription factors and salt stress-responsive proteins, including dehydration-induced protein, cation/H+ antiporter 18, and CBL-interacting serine/threonine-protein kinase. The differential expression of miRNAs between the two Cucurbita germplasm under salt stress conditions and their target genes demonstrated that novel miRNAs play an important role in the response of the two Cucurbita germplasm to salt stress. The present study initially explored small RNAs in the response of pumpkin to salt stress, and provided valuable information on novel miRNAs and their target genes in Cucurbita.
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Zhang B. MicroRNA: a new target for improving plant tolerance to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1749-61. [PMID: 25697792 PMCID: PMC4669559 DOI: 10.1093/jxb/erv013] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 12/14/2014] [Accepted: 12/17/2014] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are an extensive class of endogenous, small RNA molecules that sit at the heart of regulating gene expression in multiple developmental and signalling pathways. Recent studies have shown that abiotic stresses induce aberrant expression of many miRNAs, thus suggesting that miRNAs may be a new target for genetically improving plant tolerance to certain stresses. These studies have also shown that miRNAs respond to environmental stresses in a miRNA-, stress-, tissue-, and genotype-dependent manner. During abiotic stress, miRNAs function by regulating target genes within the miRNA-target gene network and by controlling signalling pathways and root development. Generally speaking, stress-induced miRNAs lead to down-regulation of negative regulators of stress tolerance whereas stress-inhibited miRNAs allow the accumulation and function of positive regulators. Currently, the majority of miRNA-based studies have focused on the identification of miRNAs that are responsive to different stress conditions and analysing their expression profile changes during these treatments. This has predominately been accomplished using deep sequencing technologies and other expression analyses, such as quantitative real-time PCR. In the future, more function and expression studies will be necessary in order to elucidate the common miRNA-mediated regulatory mechanisms that underlie tolerance to different abiotic stresses. The use of artificial miRNAs, as well as overexpression and knockout/down of both miRNAs and their targets, will be the best techniques for determining the specific roles of individual miRNAs in response to environmental stresses.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms. FRONTIERS IN PLANT SCIENCE 2015; 6:57. [PMID: 25717333 PMCID: PMC4324062 DOI: 10.3389/fpls.2015.00057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/22/2015] [Indexed: 05/14/2023]
Abstract
Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
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Affiliation(s)
- Davide Guerra
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Cristina Crosatti
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Hamid H. Khoshro
- Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran
| | - Anna M. Mastrangelo
- Cereal Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Foggia, Italy
| | - Erica Mica
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Mazzucotelli
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
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49
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Xie F, Wang Q, Sun R, Zhang B. Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:789-804. [PMID: 25371507 PMCID: PMC4321542 DOI: 10.1093/jxb/eru437] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Drought and salinity are two major environmental factors adversely affecting plant growth and productivity. However, the regulatory mechanism is unknown. In this study, the potential roles of small regulatory microRNAs (miRNAs) in cotton response to those stresses were investigated. Using next-generation deep sequencing, a total of 337 miRNAs with precursors were identified, comprising 289 known miRNAs and 48 novel miRNAs. Of these miRNAs, 155 miRNAs were expressed differentially. Target prediction, Gene Ontology (GO)-based functional classification, and Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional enrichment show that these miRNAs might play roles in response to salinity and drought stresses through targeting a series of stress-related genes. Degradome sequencing analysis showed that at least 55 predicted target genes were further validated to be regulated by 60 miRNAs. CitationRank-based literature mining was employed to determinhe the importance of genes related to drought and salinity stress. The NAC, MYB, and MAPK families were ranked top under the context of drought and salinity, indicating their important roles for the plant to combat drought and salinity stress. According to target prediction, a series of cotton miRNAs are associated with these top-ranked genes, including miR164, miR172, miR396, miR1520, miR6158, ghr-n24, ghr-n56, and ghr-n59. Interestingly, 163 cotton miRNAs were also identified to target 210 genes that are important in fibre development. These results will contribute to cotton stress-resistant breeding as well as understanding fibre development.
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Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, PR China
| | - Runrun Sun
- Department of Biology, East Carolina University, Greenville, NC 27858, USA Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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50
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Zhang B, Wang Q. MicroRNA-based biotechnology for plant improvement. J Cell Physiol 2015; 230:1-15. [PMID: 24909308 DOI: 10.1002/jcp.24685] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/21/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are an extensive class of newly discovered endogenous small RNAs, which negatively regulate gene expression at the post-transcription levels. As the application of next-generation deep sequencing and advanced bioinformatics, the miRNA-related study has been expended to non-model plant species and the number of identified miRNAs has dramatically increased in the past years. miRNAs play a critical role in almost all biological and metabolic processes, and provide a unique strategy for plant improvement. Here, we first briefly review the discovery, history, and biogenesis of miRNAs, then focus more on the application of miRNAs on plant breeding and the future directions. Increased plant biomass through controlling plant development and phase change has been one achievement for miRNA-based biotechnology; plant tolerance to abiotic and biotic stress was also significantly enhanced by regulating the expression of an individual miRNA. Both endogenous and artificial miRNAs may serve as important tools for plant improvement.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina; Henan Institute of Sciences and Technology, Xinxiang, Henan, China
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