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Li H, Gui Y, Zhu K, Wei J, Zhang R, Yang R, Tang L, Zhou H, Liu X. Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1243664. [PMID: 37885666 PMCID: PMC10598656 DOI: 10.3389/fpls.2023.1243664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.
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Affiliation(s)
- Haibi Li
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Yiyun Gui
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kai Zhu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jinju Wei
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ronghua Zhang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Rongzhong Yang
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Liqiu Tang
- Guangxi South Subtropical Agricultural Science Research Institute, Guangxi Academy of Agricultural Sciences, Chongzuo, China
| | - Hui Zhou
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xihui Liu
- Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning, China
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Araujo MAD, Melo AARD, Silva VM, Reis ARD. Selenium enhances ROS scavenging systems and sugar metabolism increasing growth of sugarcane plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107798. [PMID: 37301189 DOI: 10.1016/j.plaphy.2023.107798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
Selenium (Se) beneficial effect on plants is related to an increase in nitrogen (N) assimilation and its role as an abiotic stress mitigator by reactive oxygen species (ROS) scavenging enhanced by antioxidant metabolism. This study aimed to evaluate sugarcane (Saccharum spp.) growth, photosynthetic and antioxidant responses, and sugar accumulation in response to Se supply. The experimental design was a factorial scheme 2 × 4: two sugarcane varieties (RB96 6928 and RB86 7515) and four Se application rates (0; 5; 10 and 20 μmol L-1) applied as sodium selenate in the nutrient solution. Leaf Se concentration increased under Se application in both varieties. The enzymes SOD (EC 1.15.1.1) and APX (EC 1.11.1.11) showed increase activities under Se application on variety RB96 6928. Nitrate reductase activity increased in both varieties resulting in the conversion of nitrate into higher total amino acids concentration indicating an enhanced N assimilation. This led to an increased concentration of chlorophylls and carotenoids, increased CO2 assimilation rate, stomatal conductance, and internal CO2 concentration. Selenium provided higher starch accumulation and sugar profiles in leaves boosting plant growth. This study shows valuable information regarding the role of Se on growth, photosynthetic process, and sugar accumulation in sugarcane leaves, which could be used for further field experiments. The application rate of 10 μmol Se L-1 was the most adequate for both varieties studied considering the sugar concentration and plant growth.
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Affiliation(s)
| | | | - Vinicius Martins Silva
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), 14884-900 Jaboticabal, SP, Brazil
| | - André Rodrigues Dos Reis
- São Paulo State University "Júlio de Mesquita Filho" (UNESP), Rua Domingos da Costa Lopes 780, 17602-496 Tupã, SP, Brazil.
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Dinesh Babu KS, Janakiraman V, Palaniswamy H, Kasirajan L, Gomathi R, Ramkumar TR. A short review on sugarcane: its domestication, molecular manipulations and future perspectives. GENETIC RESOURCES AND CROP EVOLUTION 2022; 69:2623-2643. [PMID: 36159774 PMCID: PMC9483297 DOI: 10.1007/s10722-022-01430-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/11/2022] [Indexed: 06/16/2023]
Abstract
Sugarcane (Saccharum spp.) is a special crop plant that underwent anthropogenic evolution from a wild grass species to an important food, fodder, and energy crop. Unlike any other grass species which were selected for their kernels, sugarcane was selected for its high stem sucrose accumulation. Flowering in sugarcane is not favored since flowering diverts the stored sugar resources for the reproductive and developmental energy needs. Cultivars are vegetatively propagated and sugarcane breeding is still essentially focused on conventional methods, since the knowledge of sugarcane genetics has lagged that of other major crops. Cultivar improvement has been extremely challenging due to its polyploidy and aneuploidy nature derived from a few interspecific hybridizations between Saccharum officinarum and Saccharum spontaneum, revealing the coexistence of two distinct genome organization modes in the modern variety. Alongside implementation of modern agricultural techniques, generation of hybrid clones, transgenics and genome edited events will help to meet the ever-growing bioenergy needs. Additionally, there are two common biotechnological approaches to improve plant stress tolerance, which includes marker-assisted selection (MAS) and genetic transformation. During the past two decades, the use of molecular approaches has contributed greatly to a better understanding of the genetic and biochemical basis of plant stress-tolerance and in some cases, it led to the development of plants with enhanced tolerance to abiotic stress. Hence, this review mainly intends on the events that shaped the sugarcane as what it is now and what challenges ahead and measures taken to further improve its yield, production and maximize utilization to beat the growing demands.
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Affiliation(s)
| | - Vardhana Janakiraman
- Department of Biotechnology, Vels Institute of Science, Technology & Advanced studies (VISTAS), Chennai, TN 600117 India
| | - Harunipriya Palaniswamy
- Tissue Culture Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Lakshmi Kasirajan
- Genomics Laboratory, Division of Crop Improvement, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Raju Gomathi
- Plant Physiology Laboratory, Division of Crop Production, ICAR‐Sugarcane Breeding Institute, Coimbatore, TN 641007 India
| | - Thakku R. Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL 32611 USA
- Department of Biological Sciences, Delaware State University, Dover, DE 19001 USA
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MicroSugar: A database of comprehensive miRNA target prediction framework for sugarcane (Saccharum officinarum L.). Genomics 2022; 114:110420. [PMID: 35760231 DOI: 10.1016/j.ygeno.2022.110420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022]
Abstract
microRNA (miRNA) is a group of small non-coding RNA that plays important role in post-transcription of gene expression. With the studies about miRNA increase in sugarcane, the researchers lack an exhaustive resource to achieve the data. To fill this gap, we developed MicroSugar, a database that supported mRNA and miRNA annotation for sugarcane (http://suc.gene-db.com). MicroSugar is an integrated resource developed for 194,528 genes including 80,746 unigenes from long reads of Pacbio platform and 468 miRNAs from 72 samples. Internode elongation (jointing) is the key biological characteristic for the growth of sugarcane tillers into sugarcane stems. The present study combined the sequencing data from the different stages in internode elongation of stem and tiller. In total, the 14,300 3' untranslated region (UTR) sequences were extracted from the gene sequences and 3019 mRNAs as target of 327 miRNA were identified by miRanda algorithm and Spearman's Rho of expression levels. To determine the gene functions regulated by these miRNAs, the gene ontology enrichment analysis was performed and it confirmed that the over-represented Gene Ontology (GO) terms were associated with organism formation indicating the growth controlling function by miRNAs in sugarcane. Moreover, MicroSugar is a comprehensive and integrated database with a user-friendly responsive template. By browsing, searching and downloading of the nucleotide sequences, expression and miRNA targets, the user can retrieve information promptly. The database provides a valuable resource to facilitate the understanding of miRNA in sugarcane development and growth which will contribute to the study of sugarcane and other plants.
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Kumar D, Malik N, Sengar RS, Yadav B, Singh AK, Yadav CL, Yadav MK. Transcriptional Regulation in Sugarcane under Water Deficit during Formative Growth Stage. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721060062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gelaw TA, Sanan-Mishra N. Non-Coding RNAs in Response to Drought Stress. Int J Mol Sci 2021; 22:12519. [PMID: 34830399 PMCID: PMC8621352 DOI: 10.3390/ijms222212519] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.
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Affiliation(s)
- Temesgen Assefa Gelaw
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
- Department of Biotechnology, College of Natural and Computational Science, Debre Birhan University, Debre Birhan P.O. Box 445, Ethiopia
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India;
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Tayyab M, Yang Z, Zhang C, Islam W, Lin W, Zhang H. Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:48080-48096. [PMID: 33904129 DOI: 10.1007/s11356-021-14033-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.
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Affiliation(s)
- Muhammad Tayyab
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Ziqi Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Caifang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- College of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Wenxiong Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agro-ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
| | - Hua Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Selvi A, Devi K, Manimekalai R, Prathima PT, Valiyaparambth R, Lakshmi K. High-throughput miRNA deep sequencing in response to drought stress in sugarcane. 3 Biotech 2021; 11:312. [PMID: 34109097 DOI: 10.1007/s13205-021-02857-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/22/2021] [Indexed: 12/14/2022] Open
Abstract
Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-02857-x.
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Affiliation(s)
- Athiappan Selvi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kaliannan Devi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Ramaswamy Manimekalai
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | | | - Rabisha Valiyaparambth
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | - Kasirajan Lakshmi
- Biotechnology Section, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
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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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Diniz AL, da Silva DIR, Lembke CG, Costa MDBL, ten-Caten F, Li F, Vilela RD, Menossi M, Ware D, Endres L, Souza GM. Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane. Int J Mol Sci 2020; 21:ijms21239124. [PMID: 33266228 PMCID: PMC7729667 DOI: 10.3390/ijms21239124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023] Open
Abstract
The ability to expand crop plantations without irrigation is a major goal to increase agriculture sustainability. To achieve this end, we need to understand the mechanisms that govern plant growth responses under drought conditions. In this study, we combined physiological, transcriptomic, and genomic data to provide a comprehensive picture of drought and recovery responses in the leaves and roots of sugarcane. Transcriptomic profiling using oligoarrays and RNA-seq identified 2898 (out of 21,902) and 46,062 (out of 373,869) transcripts as differentially expressed, respectively. Co-expression analysis revealed modules enriched in photosynthesis, small molecule metabolism, alpha-amino acid metabolism, trehalose biosynthesis, serine family amino acid metabolism, and carbohydrate transport. Together, our findings reveal that carbohydrate metabolism is coordinated with the degradation of amino acids to provide carbon skeletons to the tricarboxylic acid cycle. This coordination may help to maintain energetic balance during drought stress adaptation, facilitating recovery after the stress is alleviated. Our results shed light on candidate regulatory elements and pave the way to biotechnology strategies towards the development of drought-tolerant sugarcane plants.
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Affiliation(s)
- Augusto Lima Diniz
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Danielle Izilda Rodrigues da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Center for Applied Plant Sciences (CAPS), The Ohio State University, Columbus, OH 43210, USA
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Carolina Gimiliani Lembke
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Maximiller Dal-Bianco Lamas Costa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Felipe ten-Caten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
| | - Forrest Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
| | - Romel Duarte Vilela
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Marcelo Menossi
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil;
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (F.L.); (D.W.)
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Lauricio Endres
- Centro de Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, AL 57100-000, Brazil; (R.D.V.); (L.E.)
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil; (A.L.D.); (D.I.R.d.S.); (C.G.L.); (M.D.-B.L.C.); (F.t.-C.)
- Correspondence:
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Current breeding and genomic approaches to enhance the cane and sugar productivity under abiotic stress conditions. 3 Biotech 2020; 10:440. [PMID: 33014683 PMCID: PMC7501393 DOI: 10.1007/s13205-020-02416-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
Sugarcane (Saccharum spp.) crop is vulnerable to many abiotic stresses such as drought, salinity, waterlogging, cold and high temperature due to climate change. Over the past few decades new breeding and genomic approaches have been used to enhance the genotypic performance under abiotic stress conditions. In sugarcane, introgression of genes from wild species and allied genera for abiotic stress tolerance traits plays a significant role in the development of several stress-tolerant varieties. Moreover, the genomics and transcriptomics approaches have helped to elucidate the key genes/TFs and pathways involved in abiotic stress tolerance in sugarcane. Several novel miRNAs families /proteins or regulatory elements that are responsible for drought, salinity, and cold tolerance have been identified through high-throughput sequencing. The existing sugarcane monoploid genome sequence information opens new gateways and opportunities for researchers to improve the desired traits through efficient genome editing tools, such as the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system. TALEN mediated mutations in a highly conserved region of the caffeic acid O-methyltransferase (COMT) of sugarcane significantly reduces the lignin content in the cell wall which is amenable for biofuel production from lignocellulosic biomass. In this review, we focus on current breeding with genomic approaches and their substantial role in enhancing cane production under the abiotic stress conditions, which is expected to provide new insights to plant breeders and biotechnologists to modify their strategy in developing stress-tolerant sugarcane varieties, which can highlight the future demand of cane, bio-energy, and viability of sugar industries.
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da Silva RG, Rosa-Santos TM, França SDC, Kottapalli P, Kottapalli KR, Zingaretti SM. Microtranscriptome analysis of sugarcane cultivars in response to aluminum stress. PLoS One 2019; 14:e0217806. [PMID: 31697688 PMCID: PMC6837492 DOI: 10.1371/journal.pone.0217806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
Although several metallic elements are required for plant growth, excessive amounts of aluminum ions (Al3+) can result in the inhibition of root growth, thus triggering water and nutrient deficiencies. Plants under stress undergo gene expression changes in specific genes or post-transcriptional gene regulators, such as miRNAs, that can lead to stress tolerance. In this study, we investigated the miRNAs involved in the response of sugarcane to aluminum stress. Four miRNA libraries were generated using sugarcane roots of one tolerant and one sensitive sugarcane cultivar grown under aluminum stress and used to identify the miRNAs involved in the sugarcane aluminum toxicity response. The contrast in field phenotypes of sugarcane cultivars in the field during aluminum stress was reflected in the micro-transcriptome expression profiles. We identified 394 differentially expressed miRNAs in both cultivars, 104 of which were tolerant cultivar-specific, 116 were sensitive cultivar-specific, and 87 of which were common among cultivars. In addition, 52% of differentially expressed miRNAs were upregulated in the tolerant cultivar while the majority of differentially expressed miRNAs in the sensitive cultivar were downregulated. Real-time quantitative polymerase chain reaction was used to validate the expression levels of differentially expressed miRNAs. We also attempted to identify target genes of miRNAs of interest. Our results show that selected differentially expressed miRNAs of aluminum-stressed sugarcane cultivars play roles in signaling, root development, and lateral root formation. These genes thus may be important for aluminum tolerance in sugarcane and could be used in breeding programs to develop tolerant cultivars.
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Affiliation(s)
- Renan Gonçalves da Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Thiago Mateus Rosa-Santos
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | - Pratibha Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Kameswara Rao Kottapalli
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, United States of America
| | - Sonia Marli Zingaretti
- Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- * E-mail:
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13
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Qiu L, Chen R, Fan Y, Huang X, Luo H, Xiong F, Liu J, Zhang R, Lei J, Zhou H, Wu J, Li Y. Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.). BMC Genomics 2019; 20:817. [PMID: 31699032 PMCID: PMC6836457 DOI: 10.1186/s12864-019-6201-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.
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Affiliation(s)
- Lihang Qiu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Rongfa Chen
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Yegeng Fan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Xing Huang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Hanmin Luo
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Faqian Xiong
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Junxian Liu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Ronghua Zhang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jingchao Lei
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Huiwen Zhou
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China.,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China
| | - Jianming Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
| | - Yangrui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Sciences, East Daxue Road 172, Nanning, 530004, Guangxi, China. .,Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, and Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi, China.
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14
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Screening of EMS-Induced Drought-Tolerant Sugarcane Mutants Employing Physiological, Molecular and Enzymatic Approaches. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8100226] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Drought stress is one of the major agronomic concerns that lead towards a sharp decline in sugarcane yield. An urgent demand to overcome drought is critical to ensure sugarcane production. Mutation breeding is one of the promising tools available to produce stress-resistant plants, with the induction of new alleles due to point mutation within existing sugarcane germplasm. The current study was directed to chemically mutagenize the calli of two sugarcane cultivars (ROC22 and FN39) via 0.1% EMS, with focus on inducing mutations in their genome. The 1644 regenerated plants of ROC22 and 1398 of FN39 were exposed to 28% PEG-6000 stimulated osmotic stress. Eighteen plants of ROC22 and 2 plants of FN39, that survived after in vitro osmotic stress treatment, were then subjected to preliminary greenhouse pot trials to confirm drought tolerance by analyzing them using various physiological parameters, including photosystem II (PSII) photochemical efficiency (Fv/Fm), leaf chlorophyll content, and photosynthetic rate. The genetic diversity among drought-resistant mutant lines was further assessed by 15 pairs of simple sequence repeat (SSR) markers amplification and CEL (Celery) I endonuclease digestion, to investigate the mutated sites. Mutant lines of ROC22 (i.e., MR22-15 and MR22-20) were found to be promising for future drought resistance breeding, due to better physiological adaptation under drought stress.
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15
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da Silva MD, de Oliveira Silva RL, Ferreira Neto JRC, Benko-Iseppon AM, Kido EA. Genotype-dependent regulation of drought-responsive genes in tolerant and sensitive sugarcane cultivars. Gene 2017; 633:17-27. [PMID: 28855118 DOI: 10.1016/j.gene.2017.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/28/2017] [Accepted: 08/23/2017] [Indexed: 12/20/2022]
Abstract
Drought is the most damaging among the major abiotic stresses. Transcriptomic studies allow a global overview of expressed genes, providing the basis for molecular markers development. Here, the HT-SuperSAGE technique allowed the evaluation of four drought-tolerant cultivars and four-sensitive cultivars, after 24h of irrigation suppression. We identified 9831 induced unitags from roots of the tolerant cultivars with different regulations by the -sensitive cultivars after the applied stress. These unitags allowed a proposal of 15 genes, whose expressed profiles were validated by RT-qPCR, evaluating each cultivar independently. These genes covered broad metabolic processes: ethylene stress attenuation (ACCD); root growth (β-EXP8); protein degradation [ubiquitination pathway (E2, 20SPβ4); plant proteases (AP, C13)]; oxidative detoxification (TRX); fatty acid synthesis (ACC); amino acid transport (AAT), and carbohydrate metabolism [glycolysis (PFK, TPI, FBA); TCA cycle (LDP, MDH); pentose phosphate pathway (TKT)]. The expressed profiles showed a genotype-dependent regulation of the target genes. Two drought-tolerant cultivars (SP83-2847; CTC6) presented each one, nine of the induced genes. Among the -sensitive cultivars, CTC13 induced only one, while SP90-1636 induced two genes. These genes should help breeders to identify accessions managing drought stress tolerance responses, showing better ethylene stress attenuation, energy allocation, amino acid transport, and protein homeostasis.
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Affiliation(s)
- Manassés Daniel da Silva
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil
| | | | | | - Ana Maria Benko-Iseppon
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil
| | - Ederson Akio Kido
- Federal University of Pernambuco (UFPE), Bioscience Center, Department of Genetics, 50670-420 Recife, PE, Brazil.
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16
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Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/06/2017] [Indexed: 05/20/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
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Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
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17
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Swapna M, Kumar S. MicroRNAs and Their Regulatory Role in Sugarcane. FRONTIERS IN PLANT SCIENCE 2017; 8:997. [PMID: 28659947 PMCID: PMC5468422 DOI: 10.3389/fpls.2017.00997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 05/26/2017] [Indexed: 05/31/2023]
Abstract
Sugarcane, one of the most photosynthetically efficient crops, is an important source of sugar and feedstock for green energy and co-generation. The high level of polyploidy and genomic peculiarities in this crop point towards a complex mechanism of regulation for the economically important traits like sugar content, cane yield related traits, resistance to biotic and abiotic stresses etc. The regulatory pathways for these traits comprise of a number of genes, transcription factors and different categories of RNAs like small interference RNAs (siRNAs), and Micro RNAs (miRNAs). MicroRNAs (miRNAs) are found to play an important regulatory role in many crops. As in other crops, several miRNAs have been identified in sugarcane too and these are speculated to have a role in regulating the various metabolic processes. Role of miRNAs in relation to drought tolerance has been studied to a great extent in this crop. miRNAs have been predicted to be linked to expression of other traits like disease resistance, salinity tolerance, waterlogging and axillary bud growth in sugarcane. miRNAs can have a significant role in biomass production in sugarcane, as reported in several biofuel crops. Till now, miRNAs linked to sugar accumulation have not been identified in sugarcane, but studies suggest an important role for miRNAs in sugar metabolic pathway in crops like Sorghum and switch grass. It is presumed that in sugarcane too, sugar accumulation as well as the other important metabolic pathways might be regulated to some extent by the miRNAs. The review examines the progress made in understanding the miRNA regulation in sugarcane and the extent to which miRNA mediated regulation can be utilized in sugarcane improvement.
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18
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Ghorecha V, Zheng Y, Liu L, Sunkar R, Krishnayya NSR. MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:291-300. [PMID: 28461718 PMCID: PMC5391358 DOI: 10.1007/s12298-017-0426-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/14/2017] [Accepted: 03/03/2017] [Indexed: 05/14/2023]
Abstract
Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a drought-tolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Drought-sensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.
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Affiliation(s)
- Vallabhi Ghorecha
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727, South Jingming Road, Kunming, 650500 Yunnan China
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74074 USA
| | - N. S. R. Krishnayya
- Ecology Laboratory, Botany Department, Faculty of Science, M.S. University of Baroda, Baroda, 390002 India
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19
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Ferreira THS, Tsunada MS, Bassi D, Araújo P, Mattiello L, Guidelli GV, Righetto GL, Gonçalves VR, Lakshmanan P, Menossi M. Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions. FRONTIERS IN PLANT SCIENCE 2017; 8:1077. [PMID: 28690620 PMCID: PMC5481406 DOI: 10.3389/fpls.2017.01077/full 10.3389/fpls.2017.01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments.
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Affiliation(s)
- Thais H. S. Ferreira
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Max S. Tsunada
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Denis Bassi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Pedro Araújo
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Lucia Mattiello
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Giovanna V. Guidelli
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Germanna L. Righetto
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | - Vanessa R. Gonçalves
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
| | | | - Marcelo Menossi
- Functional Genome Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of CampinasCampinas, Brazil
- *Correspondence: Marcelo Menossi
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20
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Liu SC, Xu YX, Ma JQ, Wang WW, Chen W, Huang DJ, Fang J, Li XJ, Chen L. Small RNA and degradome profiling reveals important roles for microRNAs and their targets in tea plant response to drought stress. PHYSIOLOGIA PLANTARUM 2016; 158:435-451. [PMID: 27282332 DOI: 10.1111/ppl.12477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 04/25/2016] [Accepted: 05/22/2016] [Indexed: 06/06/2023]
Abstract
Tea (Camellia sinensis) is a popular beverage worldwide. Drought stress (DS) is a major constraint on the growth, yield and quality of tea plants. MicroRNAs (miRNAs) play important roles in plant responses to DS. We constructed eight small RNA libraries from the drought-tolerant 'Ningzhou 2' (NZ2) and drought-susceptible 'Zhuyeqi' (ZYQ) cultivars during four stages [control (CK), the fourth day of DS, the eighth day of DS and after recovery (RC)]. A total of 268 conserved and 62 novel miRNAs were identified using small RNA sequencing. In total, 139 (52.9%) and 96 (36.0%) conserved miRNAs were differentially expressed during the four stages (P ≤ 0.05) in NZ2 and ZYQ, respectively. A total of 814 predicted target genes were identified as differentially regulated by 199 miRNAs through degradome sequencing. Among them, 201 and 218 genes were specific to the NZ2 and ZYQ cultivars, respectively, and 395 were common to both cultivars. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological roles of these targets and showed that some of the targets responded to DS in a stress- and cultivar-dependent manner. Correlated expression patterns between miRNA and their targets showed that specific miRNAs target the miRNA effector Argonaute 1 (AGO1), drought signaling-related receptors and enzymes, transcription factors, and other structural and functional proteins. The predicted regulatory networks provide insights into a potential miRNA-mediated regulatory mechanism. These results will contribute to the breeding of drought-tolerant tea plants and to elucidating miRNA regulation in response to drought.
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Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
- Tea Research Institute, Guizhou Academy of Agricultrural Sciences, Guiyang, 550006, China
| | - Yan-Xia Xu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei-Wei Wang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wei Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Dan-Juan Huang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Jie Fang
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xiao-Jie Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
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21
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Hamza NB, Sharma N, Tripathi A, Sanan-Mishra N. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expr Patterns 2016; 20:88-98. [PMID: 26772909 DOI: 10.1016/j.gep.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
Abstract
The regulatory role of small non-coding RNAs that are 20-24 nucleotides in length has become the foremost area of research for biologists. A major class of small RNAs represented by the microRNAs (miRNAs), has been implicated in various aspects of plant development including leaf pattering, meristem function, root patterning etc. Recent findings support that miRNAs are regulated by drought and other abiotic stresses in various plant species. In this study, were report the expression profiling of 8 known abiotic stress deregulated miRNAs in 11 elite sorghum genotypes, under watered and drought conditions. Significant deregulation was observed with miR396, miR393, miR397-5p, miR166, miR167 and miR168. Among these, the expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes. The expression of sbi-miR396 was maximum in the grain sorghum HSD3226 under well-watered conditions and the profile shifted towards HSD3221 under drought stress. Forage accessions, N98 and Atlas, showed an opposite behavior in expression patterns of miR397-5p in drought physiologies. Such dynamic expression patterns could be indicative of prevailing drought tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRNAs which may have potential use in improving drought tolerance in sorghum and other cereal crops.
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Affiliation(s)
- Nada Babiker Hamza
- Department of Molecular Biology, Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box: 2404, Khartoum, Sudan.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India.
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Hivrale V, Zheng Y, Puli COR, Jagadeeswaran G, Gowdu K, Kakani VG, Barakat A, Sunkar R. Characterization of drought- and heat-responsive microRNAs in switchgrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:214-223. [PMID: 26566839 DOI: 10.1016/j.plantsci.2015.07.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/17/2015] [Accepted: 07/25/2015] [Indexed: 05/21/2023]
Abstract
Recent investigations revealed that microRNAs (miRNAs) play crucial roles in plant acclimation to stress conditions. Switchgrass, one of the important biofuel crop species can withstand hot and dry climates but the molecular basis of stress tolerance is relatively unknown. To identify miRNAs that are important for tolerating drought or heat, small RNAs were profiled in leaves of adult plants exposed to drought or heat. Sequence analysis enabled the identification of 29 conserved and 62 novel miRNA families. Notably, the abundances of several conserved and novel miRNAs were dramatically altered following drought or heat. Using at least one fold (log2) change as cut off, we observed that 13 conserved miRNA families were differentially regulated by both stresses, and, five and four families were specifically regulated by drought and heat, respectively. Similarly, using a more stringent cut off of two fold (log2) regulation, we found 5 and 16 novel miRNA families were upregulated but 6 and 7 families were downregulated under drought and heat, respectively. The stress-altered expression of a subset of miRNAs and their targets was confirmed using quantitative PCR. Overall, the switchgrass plants exposed to drought or heat revealed similarities as well as differences with respect to miRNA regulation, which could be important for enduring different stress conditions.
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Affiliation(s)
- Vandana Hivrale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, Yunnan 650500, China
| | - Chandra Obul Reddy Puli
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kanchana Gowdu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Vijaya Gopal Kakani
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Abdelali Barakat
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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Mattiello L, Riaño-Pachón DM, Martins MCM, da Cruz LP, Bassi D, Marchiori PER, Ribeiro RV, Labate MTV, Labate CA, Menossi M. Physiological and transcriptional analyses of developmental stages along sugarcane leaf. BMC PLANT BIOLOGY 2015; 15:300. [PMID: 26714767 PMCID: PMC4696237 DOI: 10.1186/s12870-015-0694-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. RESULTS Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. CONCLUSION This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.
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Affiliation(s)
- Lucia Mattiello
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Marina Camara Mattos Martins
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Larissa Prado da Cruz
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Denis Bassi
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, 13083-970, Campinas, SP, Brazil.
| | - Paulo Eduardo Ribeiro Marchiori
- Laboratório de Fisiologia de Plantas "Coaracy M. Franco", Centro de Pesquisa e Desenvolvimento em Ecofisiologia e Biofísica, Instituto Agronômico, Caixa Postal 28, Campinas, 13020-902, SP, Brazil.
| | - Rafael Vasconcelos Ribeiro
- Departamento de Biologia de Plantas, Universidade Estadual de Campinas, Caixa Postal 6109, Campinas, 13083-970, SP, Brazil.
| | - Mônica T Veneziano Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Carlos Alberto Labate
- Laboratório Max Feffer de Genética de Plantas, Departamento de Genética, Universidade de São Paulo, Caixa Postal 83, Piracicaba, 13400-970, SP, Brazil.
| | - Marcelo Menossi
- Laboratório de Genoma Funcional, Instituto de Biologia, Universidade Estadual de Campinas Campinas, Caixa Postal 6109, Campinas, 13083-862, SP, Brazil.
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24
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Gentile A, Dias LI, Mattos RS, Ferreira TH, Menossi M. MicroRNAs and drought responses in sugarcane. FRONTIERS IN PLANT SCIENCE 2015; 6:58. [PMID: 25755657 PMCID: PMC4337329 DOI: 10.3389/fpls.2015.00058] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 01/22/2015] [Indexed: 05/03/2023]
Abstract
There is a growing demand for renewable energy, and sugarcane is a promising bioenergy crop. In Brazil, the largest sugarcane producer in the world, sugarcane plantations are expanding into areas where severe droughts are common. Recent evidence has highlighted the role of miRNAs in regulating drought responses in several species, including sugarcane. This review summarizes the data from miRNA expression profiles observed in a wide array of experimental conditions using different sugarcane cultivars that differ in their tolerance to drought. We uncovered a complex regulation of sugarcane miRNAs in response to drought and discussed these data with the miRNA profiles observed in other plant species. The predicted miRNA targets revealed different transcription factors, proteins involved in tolerance to oxidative stress, cell modification, as well as hormone signaling. Some of these proteins might regulate sugarcane responses to drought, such as reduction of internode growth and shoot branching and increased leaf senescence. A better understanding on the regulatory network from miRNAs and their targets under drought stress has a great potential to contribute to sugarcane improvement, either as molecular markers as well as by using biotechnological approaches.
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Affiliation(s)
| | | | | | | | - Marcelo Menossi
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de CampinasCampinas, São Paulo, Brazil
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25
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The choice of reference genes for assessing gene expression in sugarcane under salinity and drought stresses. Sci Rep 2014; 4:7042. [PMID: 25391499 PMCID: PMC4229666 DOI: 10.1038/srep07042] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/27/2014] [Indexed: 01/18/2023] Open
Abstract
Sugarcane (Saccharum spp. hybrids) is a world-wide cash crop for sugar and biofuel in tropical and subtropical regions and suffers serious losses in cane yield and sugar content under salinity and drought stresses. Although real-time quantitative PCR has a numerous advantage in the expression quantification of stress-related genes for the elaboration of the corresponding molecular mechanism in sugarcane, the variation happened across the process of gene expression quantification should be normalized and monitored by introducing one or several reference genes. To validate suitable reference genes or gene sets for sugarcane gene expression normalization, 13 candidate reference genes have been tested across 12 NaCl- and PEG-treated sugarcane samples for four sugarcane genotypes using four commonly used systematic statistical algorithms termed geNorm, BestKeeper, NormFinder and the deltaCt method. The results demonstrated that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and eukaryotic elongation factor 1-alpha (eEF-1a) were identified as suitable reference genes for gene expression normalization under salinity/drought-treatment in sugarcane. Moreover, the expression analyses of SuSK and 6PGDH further validated that a combination of clathrin adaptor complex (CAC) and cullin (CUL) as reference should be better for gene expression normalization. These results can facilitate the future research on gene expression in sugarcane under salinity and drought stresses.
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26
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Bloomfield JA, Rose TJ, King GJ. Sustainable harvest: managing plasticity for resilient crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:517-33. [PMID: 24891039 PMCID: PMC4207195 DOI: 10.1111/pbi.12198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/14/2014] [Indexed: 05/18/2023]
Abstract
Maintaining crop production to feed a growing world population is a major challenge for this period of rapid global climate change. No consistent conceptual or experimental framework for crop plants integrates information at the levels of genome regulation, metabolism, physiology and response to growing environment. An important role for plasticity in plants is assisting in homeostasis in response to variable environmental conditions. Here, we outline how plant plasticity is facilitated by epigenetic processes that modulate chromatin through dynamic changes in DNA methylation, histone variants, small RNAs and transposable elements. We present examples of plant plasticity in the context of epigenetic regulation of developmental phases and transitions and map these onto the key stages of crop establishment, growth, floral initiation, pollination, seed set and maturation of harvestable product. In particular, we consider how feedback loops of environmental signals and plant nutrition affect plant ontogeny. Recent advances in understanding epigenetic processes enable us to take a fresh look at the crosstalk between regulatory systems that confer plasticity in the context of crop development. We propose that these insights into genotype × environment (G × E) interaction should underpin development of new crop management strategies, both in terms of information-led agronomy and in recognizing the role of epigenetic variation in crop breeding.
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Affiliation(s)
- Justin A Bloomfield
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Terry J Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
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27
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Shapiro JA. Epigenetic control of mobile DNA as an interface between experience and genome change. Front Genet 2014; 5:87. [PMID: 24795749 PMCID: PMC4007016 DOI: 10.3389/fgene.2014.00087] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/01/2014] [Indexed: 12/29/2022] Open
Abstract
Mobile DNA in the genome is subject to RNA-targeted epigenetic control. This control regulates the activity of transposons, retrotransposons and genomic proviruses. Many different life history experiences alter the activities of mobile DNA and the expression of genetic loci regulated by nearby insertions. The same experiences induce alterations in epigenetic formatting and lead to trans-generational modifications of genome expression and stability. These observations lead to the hypothesis that epigenetic formatting directed by non-coding RNA provides a molecular interface between life history events and genome alteration.
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Affiliation(s)
- James A. Shapiro
- Department of Biochemistry and Molecular Biology, University of ChicagoChicago, IL, USA
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28
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Chou TC, Moyle RL. Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. BMC PLANT BIOLOGY 2014; 14:92. [PMID: 24708613 PMCID: PMC4021088 DOI: 10.1186/1471-2229-14-92] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Down-regulation or silencing of transgene expression can be a major hurdle to both molecular studies and biotechnology applications in many plant species. Sugarcane is particularly effective at silencing introduced transgenes, including reporter genes such as the firefly luciferase gene.Synthesizing transgene coding sequences optimized for usage in the host plant is one method of enhancing transgene expression and stability. Using specified design rules we have synthesised new coding sequences for both the firefly luciferase and Renilla luciferase reporter genes. We have tested these optimized versions for enhanced levels of luciferase activity and for increased steady state luciferase mRNA levels in sugarcane. RESULTS The synthetic firefly luciferase (luc*) and Renilla luciferase (Renluc*) coding sequences have elevated G + C contents in line with sugarcane codon usage, but maintain 75% identity to the native firefly or Renilla luciferase nucleotide sequences and 100% identity to the protein coding sequences.Under the control of the maize pUbi promoter, the synthetic luc* and Renluc* genes yielded 60x and 15x higher luciferase activity respectively, over the native firefly and Renilla luciferase genes in transient assays on sugarcane suspension cell cultures.Using a novel transient assay in sugarcane suspension cells combining co-bombardment and qRT-PCR, we showed that synthetic luc* and Renluc* genes generate increased transcript levels compared to the native firefly and Renilla luciferase genes.In stable transgenic lines, the luc* transgene generated significantly higher levels of expression than the native firefly luciferase transgene. The fold difference in expression was highest in the youngest tissues. CONCLUSIONS We developed synthetic versions of both the firefly and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. These transgenes will be particularly useful for evaluating the expression patterns conferred by existing and newly isolated promoters in sugarcane tissues. The strategies used to design the synthetic luciferase transgenes could be applied to other transgenes that are aggressively silenced in sugarcane.
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MESH Headings
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genes, Reporter
- Luciferases, Firefly/genetics
- Luciferases, Renilla/genetics
- Luminescent Measurements
- Open Reading Frames/genetics
- Plant Cells/metabolism
- Plant Stems/metabolism
- Plants, Genetically Modified
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Saccharum/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Suspensions
- Synthetic Biology
- Transformation, Genetic
- Transgenes/genetics
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Affiliation(s)
- Ting-Chun Chou
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
| | - Richard L Moyle
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
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29
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Su C, Yang X, Gao S, Tang Y, Zhao C, Li L. Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.). Genomics 2014; 103:298-307. [PMID: 24667243 DOI: 10.1016/j.ygeno.2014.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/29/2014] [Accepted: 03/10/2014] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNAs) represent a class of endogenous regulator for post-transcriptionally modulating gene expression. Elucidating complete miRNA repertoires for individual species is a long-desired goal in miRNA research. So far only 42 have been annotated for common wheat (Triticum aestivum) due to its large genome. Here, we employed miRDeep-P, a program developed previously for retrieving miRNAs from deep sequencing data in plants, to parse 14 sequenced small RNA libraries of wheat using expression sequence tags (ESTs) as the reference in lieu of a complete genome sequence. This effort identified 145 miRNAs along with the corresponding stem-looped precursors with many differentially expressed in development and associated with powdery mildew infection. Examination of the phylogenetic distribution of these miRNAs and their target genes revealed that many are conserved in monocots. The set of miRNAs identified in this study is thus useful to further miRNA research in wheat and other important cereal crop species.
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Affiliation(s)
- Chun Su
- Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Xiaozeng Yang
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Shiqing Gao
- Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Yimiao Tang
- Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Changping Zhao
- Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China.
| | - Lei Li
- Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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30
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Shanker AK, Maheswari M, Yadav SK, Desai S, Bhanu D, Attal NB, Venkateswarlu B. Drought stress responses in crops. Funct Integr Genomics 2014; 14:11-22. [PMID: 24408129 DOI: 10.1007/s10142-013-0356-x] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/04/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023]
Abstract
Among the effects of impending climate change, drought will have a profound impact on crop productivity in the future. Response to drought stress has been studied widely, and the model plant Arabidopsis has guided the studies on crop plants with genome sequence information viz., rice, wheat, maize and sorghum. Since the value of functions of genes, dynamics of pathways and interaction of networks for drought tolerance in plants can only be judged by evidence from field performance, this mini-review provides a research update focussing on the current developments on the response to drought in crop plants. Studies in Arabidopsis provide the basis for interpreting the available information in a systems biology perspective. In particular, the elucidation of the mechanism of drought stress response in crops is considered from evidence-based outputs emerging from recent omic studies in crops.
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Affiliation(s)
- Arun K Shanker
- Division of Crop Sciences, Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad P.O, Hyderabad, 500-059, India,
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31
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de Siqueira Ferreira S, Nishiyama MY, Paterson AH, Souza GM. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era. Genome Biol 2013; 14:210. [PMID: 23805917 PMCID: PMC3707038 DOI: 10.1186/gb-2013-14-6-210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study.
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Affiliation(s)
- Savio de Siqueira Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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