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Dussert S, Serret J, Bastos-Siqueira A, Morcillo F, Déchamp E, Rofidal V, Lashermes P, Etienne H, JOët T. Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1583-1597. [PMID: 29361125 PMCID: PMC5888931 DOI: 10.1093/jxb/erx492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/20/2017] [Indexed: 05/24/2023]
Abstract
The 'intermediate seed' category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage and has implications for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. To gain insight into the mechanisms governing such differences, changes in desiccation tolerance (DT), hormone contents, and the transcriptome were analysed in developing coffee seeds. Acquisition of DT coincided with a dramatic transcriptional switch characterised by the repression of primary metabolism, photosynthesis, and respiration, and the up-regulation of genes coding for late-embryogenesis abundant (LEA) proteins, heat-shock proteins (HSPs), and antioxidant enzymes. Analysis of the heat-stable proteome in mature coffee seeds confirmed the accumulation of LEA proteins identified at the transcript level. Transcriptome analysis also suggested a major role for ABA and for the transcription factors CaHSFA9, CaDREB2G, CaANAC029, CaPLATZ, and CaDOG-like in DT acquisition. The ability of CaHSFA9 and CaDREB2G to trigger HSP gene transcription was validated by Agrobacterium-mediated transformation of coffee somatic embryos.
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Affiliation(s)
| | | | | | | | | | - Valérie Rofidal
- Biochimie et physiologie moléculaire des plantes, CNRS, INRA, Montpellier Supagro, Université Montpellier, France
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2
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Ivamoto ST, Reis O, Domingues DS, dos Santos TB, de Oliveira FF, Pot D, Leroy T, Vieira LGE, Carazzolle MF, Pereira GAG, Pereira LFP. Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis. PLoS One 2017; 12:e0169595. [PMID: 28068432 PMCID: PMC5221826 DOI: 10.1371/journal.pone.0169595] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 12/17/2016] [Indexed: 11/20/2022] Open
Abstract
Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.
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Affiliation(s)
- Suzana Tiemi Ivamoto
- Programa de Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas, Universidade Estadual de Londrina (UEL), Londrina, Brazil
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná (IAPAR), Londrina, Brazil
| | - Osvaldo Reis
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Douglas Silva Domingues
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | | | | | - David Pot
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, (CIRAD), UMR AGAP, Montpellier, France
| | - Thierry Leroy
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, (CIRAD), UMR AGAP, Montpellier, France
| | - Luiz Gonzaga Esteves Vieira
- Programa de Pós Graduação em Agronomia, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Luiz Filipe Protasio Pereira
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná (IAPAR), Londrina, Brazil
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa Café), Brasília, Brazil
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3
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Nguyen Dinh S, Sai TZT, Nawaz G, Lee K, Kang H. Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa). JOURNAL OF PLANT PHYSIOLOGY 2016; 201:85-94. [PMID: 27448724 DOI: 10.1016/j.jplph.2016.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Despite the increasing understanding of the regulation of chloroplast gene expression in plants, the importance of intron splicing and processing of chloroplast RNA transcripts under stress conditions is largely unknown. Here, to understand how abiotic stresses affect the intron splicing and expression patterns of chloroplast genes in dicots and monocots, we carried out a comprehensive analysis of the intron splicing and expression patterns of chloroplast genes in the coffee plant (Coffea arabica) as a dicot and rice (Oryza sativa) as a monocot under abiotic stresses, including drought, cold, or combined drought and heat stresses. The photosynthetic activity of both coffee plants and rice seedlings was significantly reduced under all stress conditions tested. Analysis of the transcript levels of chloroplast genes revealed that the splicing of tRNAs and mRNAs in coffee plants and rice seedlings were significantly affected by abiotic stresses. Notably, abiotic stresses affected differently the splicing of chloroplast tRNAs and mRNAs in coffee plants and rice seedlings. The transcript levels of most chloroplast genes were markedly downregulated in both coffee plants and rice seedlings upon stress treatment. Taken together, these results suggest that coffee and rice plants respond to abiotic stresses via regulating the intron splicing and expression of different sets of chloroplast genes.
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Affiliation(s)
- Sy Nguyen Dinh
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea; Institute of Environment and Biotechnology, Taynguyen University, 567 Le Duan Street, Buon Ma Thuot City, Daklak Province, Viet Nam
| | - Than Zaw Tun Sai
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Ghazala Nawaz
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea.
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4
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Tran HT, Lee LS, Furtado A, Smyth H, Henry RJ. Advances in genomics for the improvement of quality in coffee. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3300-3312. [PMID: 26919810 DOI: 10.1002/jsfa.7692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 02/08/2016] [Accepted: 02/23/2016] [Indexed: 06/05/2023]
Abstract
Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Hue Tm Tran
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
- Western Highlands Agriculture & Forestry Science Institute (WASI), Daklak, Vietnam
| | - L Slade Lee
- Southern Cross University, East Lismore, NSW 2480, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Heather Smyth
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
| | - Robert J Henry
- Queensland Alliance for Agri culture and Food Innovation (QAAFI), The University of Queensland, St Lucia, Queensland, Australia
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5
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Nie Z, Kang G, Duan C, Li Y, Dai L, Zeng R. Profiling Ethylene-Responsive Genes Expressed in the Latex of the Mature Virgin Rubber Trees Using cDNA Microarray. PLoS One 2016; 11:e0152039. [PMID: 26985821 PMCID: PMC4795647 DOI: 10.1371/journal.pone.0152039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2,973 unique genes (probes) was first developed and used to analyze the gene expression changes in the latex of the mature virgin rubber trees after ethephon treatment at three different time-points: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated rubber trees compared with control trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes. The 163 ethylene-responsive genes were involved in several biological processes including organic substance metabolism, cellular metabolism, primary metabolism, biosynthetic process, cellular response to stimulus and stress. The presented data suggest that the laticifer water circulation, production and scavenging of reactive oxygen species, sugar metabolism, and assembly and depolymerization of the latex actin cytoskeleton might play important roles in ethylene-induced increase of latex production. The results may provide useful insights into understanding the molecular mechanism underlying the effect of ethylene on latex metabolism of H. brasiliensis.
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Affiliation(s)
- Zhiyi Nie
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Guijuan Kang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Cuifang Duan
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Yu Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Longjun Dai
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Rizhong Zeng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
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6
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Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G. The coffee genome hub: a resource for coffee genomes. Nucleic Acids Res 2014; 43:D1028-35. [PMID: 25392413 PMCID: PMC4383925 DOI: 10.1093/nar/gku1108] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager.
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Affiliation(s)
- Alexis Dereeper
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Stéphanie Bocs
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Sébastien Ravel
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Christine Tranchant-Dubreuil
- UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Valérie Poncet
- UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Olivier Garsmeur
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
| | - Philippe Lashermes
- UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France
| | - Gaëtan Droc
- UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France
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Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, Lashermes P, Dussert S. Regulation of galactomannan biosynthesis in coffee seeds. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:323-337. [PMID: 24203356 DOI: 10.1093/jxb/ert380] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The seed of Coffea arabica accumulates large amounts of cell wall storage polysaccharides (CWSPs) of the mannan family in the cell walls of the endosperm. The variability induced by the growing environment and extensive pairwise correlation analysis with stringent significance thresholds was used to investigate transcript-transcript and transcript-metabolite relationships among 26 sugar-related genes, and the amount of CWSPs and seven soluble low molecular weight carbohydrates in the developing coffee endosperm. A dense module of nine quantitatively co-expressed genes was detected at the mid-developmental stage when CWSPs accumulate. This module included the five genes of the core galactomannan synthetic machinery, namely genes coding for the enzymes needed to assemble the mannan backbone (mannan synthase, ManS), and genes that introduce the galactosyl side chains (galactosyltransferase, GMGT), modulate the post-depositional degree of galactose substitution (α-galactosidase), and produce the nucleotide sugar building blocks GDP-mannose and UDP-galactose (mannose-1P guanyltransferase and UDP-glucose 4'-epimerase, respectively). The amount of CWSPs stored in the endosperm at the onset of their accumulation was primarily and quantitatively modulated at the transcriptional level (i.e. positively correlated with the expression level of these key galactomannan biosynthetic genes). This analysis also suggests a role for sorbitol and raffinose family oligosaccharides as transient auxiliary sources of building blocks for galactomannan synthesis. Finally, a microarray-based analysis of the developing seed transcriptome revealed that all genes of the core galactomannan synthesis machinery grouped in a single cluster of 209 co-expressed genes. Analysis of the gene composition of this cluster revealed remarkable functional coherence and identified transcription factors that putatively control galactomannan biosynthesis in coffee.
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Affiliation(s)
- Thierry Joët
- IRD, UMR DIADE, BP 64501, 34394 Montpellier, France
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8
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de Carvalho K, Bespalhok Filho JC, dos Santos TB, de Souza SGH, Vieira LGE, Pereira LFP, Domingues DS. Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization. Mol Biotechnol 2013; 53:315-25. [PMID: 22421886 DOI: 10.1007/s12033-012-9529-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Abiotic stresses are among the most important factors that affect food production. One important step to face these environmental challenges is the transcriptional modulation. Quantitative real-time PCR is a rapid, sensitive, and reliable method for the detection of mRNAs and it has become a powerful tool to mitigate plant stress tolerance; however, suitable reference genes are required for data normalization. Reference genes for coffee plants during nitrogen starvation, salinity and heat stress have not yet been reported. We evaluated the expression stability of ten candidate reference genes using geNorm PLUS, NormFinder, and BestKeeper softwares, in plants submitted to nitrogen starvation, salt and heat stress. EF1, EF1α, GAPDH, MDH, and UBQ10 were ranked as the most stable genes in all stresses and software analyses, while RPL39 and RPII were classified as the less reliable references. For reference gene validation, the transcriptional pattern of a Coffea non-symbiotic hemoglobin (CaHb1) was analyzed using the two new recommended and the most unstable gene references for normalization. The most unstable gene may lead to incorrect interpretation of CaHb1 transcriptional analysis. Here, we recommend two new reference genes in Coffea for use in data normalization in abiotic stresses: MDH and EF1.
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Affiliation(s)
- Kenia de Carvalho
- Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, PR, Brazil.
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Nic-Can GI, López-Torres A, Barredo-Pool F, Wrobel K, Loyola-Vargas VM, Rojas-Herrera R, De-la-Peña C. New insights into somatic embryogenesis: leafy cotyledon1, baby boom1 and WUSCHEL-related homeobox4 are epigenetically regulated in Coffea canephora. PLoS One 2013; 8:e72160. [PMID: 23977240 PMCID: PMC3748027 DOI: 10.1371/journal.pone.0072160] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/07/2013] [Indexed: 01/09/2023] Open
Abstract
Plant cells have the capacity to generate a new plant without egg fertilization by a process known as somatic embryogenesis (SE), in which differentiated somatic cells can form somatic embryos able to generate a functional plant. Although there have been advances in understanding the genetic basis of SE, the epigenetic mechanism that regulates this process is still unknown. Here, we show that the embryogenic development of Coffea canephora proceeds through a crosstalk between DNA methylation and histone modifications during the earliest embryogenic stages of SE. We found that low levels of DNA methylation, histone H3 lysine 9 dimethylation (H3K9me2) and H3K27me3 change according to embryo development. Moreover, the expression of LEAFY cotyledon1 (LEC1) and BABY BOOM1 (BBM1) are only observed after SE induction, whereas WUSCHEL-related homeobox4 (WOX4) decreases its expression during embryo maturation. Using a pharmacological approach, it was found that 5-Azacytidine strongly inhibits the embryogenic response by decreasing both DNA methylation and gene expression of LEC1 and BBM1. Therefore, in order to know whether these genes were epigenetically regulated, we used Chromatin Immunoprecipitation (ChIP) assays. It was found that WOX4 is regulated by the repressive mark H3K9me2, while LEC1 and BBM1 are epigenetically regulated by H3K27me3. We conclude that epigenetic regulation plays an important role during somatic embryogenic development, and a molecular mechanism for SE is proposed.
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Affiliation(s)
- Geovanny I. Nic-Can
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | | | - Felipe Barredo-Pool
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Kazimierz Wrobel
- Facultad de Química, Universidad de Guanajuato, Guanajuato, México
| | - Víctor M. Loyola-Vargas
- Centro de Investigación Científica de Yucatán, Unidad de Bioquímica y Biología Molecular de Plantas, Mérida, Yucatán, México
| | - Rafael Rojas-Herrera
- Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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10
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Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray. PLoS One 2012; 7:e45899. [PMID: 23110046 PMCID: PMC3482228 DOI: 10.1371/journal.pone.0045899] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 08/23/2012] [Indexed: 11/19/2022] Open
Abstract
Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01) allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.
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Marraccini P, Vinecky F, Alves GS, Ramos HJ, Elbelt S, Vieira NG, Carneiro FA, Sujii PS, Alekcevetch JC, Silva VA, DaMatta FM, Ferrão MA, Leroy T, Pot D, Vieira LG, da Silva FR, Andrade AC. Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:4191-212. [PMID: 22511801 PMCID: PMC3398449 DOI: 10.1093/jxb/ers103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The aim of this study was to investigate the molecular mechanisms underlying drought acclimation in coffee plants by the identification of candidate genes (CGs) using different approaches. The first approach used the data generated during the Brazilian Coffee expressed sequence tag (EST) project to select 13 CGs by an in silico analysis (electronic northern). The second approach was based on screening macroarrays spotted with plasmid DNA (coffee ESTs) with separate hybridizations using leaf cDNA probes from drought-tolerant and susceptible clones of Coffea canephora var. Conilon, grown under different water regimes. This allowed the isolation of seven additional CGs. The third approach used two-dimensional gel electrophoresis to identify proteins displaying differential accumulation in leaves of drought-tolerant and susceptible clones of C. canephora. Six of them were characterized by MALDI-TOF-MS/MS (matrix-assisted laser desorption-time of flight-tandem mass spectrometry) and the corresponding proteins were identified. Finally, additional CGs were selected from the literature, and quantitative real-time polymerase chain reaction (qPCR) was performed to analyse the expression of all identified CGs. Altogether, >40 genes presenting differential gene expression during drought acclimation were identified, some of them showing different expression profiles between drought-tolerant and susceptible clones. Based on the obtained results, it can be concluded that factors involved a complex network of responses probably involving the abscisic signalling pathway and nitric oxide are major molecular determinants that might explain the better efficiency in controlling stomata closure and transpiration displayed by drought-tolerant clones of C. canephora.
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Affiliation(s)
- Pierre Marraccini
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Felipe Vinecky
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Gabriel S.C. Alves
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | | | - Sonia Elbelt
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Natalia G. Vieira
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Fernanda A. Carneiro
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Patricia S. Sujii
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Jean C. Alekcevetch
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Vânia A. Silva
- UFV, Departamento de Biologia Vegetal, 36570-000 Viçosa, MG, Brazil
| | - Fábio M. DaMatta
- UFV, Departamento de Biologia Vegetal, 36570-000 Viçosa, MG, Brazil
| | - Maria A.G. Ferrão
- INCAPER/EMBRAPA CAFÉ, Rod. BR 363, km 94, 29375-000 Domingos Martins, ES, Brazil
| | - Thierry Leroy
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Avenue d’Agropolis, F 34398 Montpellier, France
| | - Luiz G.E. Vieira
- INCAPER/EMBRAPA CAFÉ, Rod. BR 363, km 94, 29375-000 Domingos Martins, ES, Brazil
| | - Felipe R. da Silva
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
| | - Alan C. Andrade
- EMBRAPA Recursos Genéticos e Biotecnologia (LGM), Parque EB, CP 02372, 70770-917 Brasilia, DF, Brazil
- To whom correspondence should be addressed. E-mail:
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Marraccini P, Freire LP, Alves GSC, Vieira NG, Vinecky F, Elbelt S, Ramos HJO, Montagnon C, Vieira LGE, Leroy T, Pot D, Silva VA, Rodrigues GC, Andrade AC. RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress. BMC PLANT BIOLOGY 2011; 11:85. [PMID: 21575242 PMCID: PMC3121667 DOI: 10.1186/1471-2229-11-85] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/16/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. RESULTS Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the accumulation of the RBCS1 protein under water stress. Altogether, the results presented here suggest that the content of RBCS was not responsible for the loss of photosynthetic capacity that is commonly observed in water-stressed coffee plants. CONCLUSION We showed that the CaCe homeolog was expressed in C. eugenioides and non-introgressed ("pure") genotypes of C. arabica but that it was undetectable in C. canephora. On the other hand, the CaCc homeolog was expressed in C. canephora but highly repressed in C. arabica. Expression of the CaCc homeolog was enhanced in C. arabica cultivars that experienced recent introgression with C. canephora. For both C. canephora and C. arabica species, total RBCS1 gene expression was highly reduced with WS. Unexpectedly, the accumulation of RBCS1 protein was observed in the leaves of C. canephora under WS, possibly coming from nocturnal RBCS1 expression. These results suggest that the increase in the amount of RBCS1 protein could contribute to the antioxidative function of photorespiration in water-stressed coffee plants.
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Affiliation(s)
- Pierre Marraccini
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
- CIRAD UMR AGAP, 34398 Montpellier Cedex 5, France
| | - Luciana P Freire
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Gabriel SC Alves
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Natalia G Vieira
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Felipe Vinecky
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Sonia Elbelt
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
| | - Humberto JO Ramos
- Instituto Agronômico do Paraná (IAPAR/LBI-AMG), Rodovia Celso Garcia Cid, Km 375, CP 481, 86001-970 Londrina, Paraná, Brazil
- Universidade Federal de Viçosa (UFV), PH Rolfs S/A, 36570-000 Viçosa, Minas Gerais, Brazil
| | | | - Luiz GE Vieira
- Instituto Agronômico do Paraná (IAPAR/LBI-AMG), Rodovia Celso Garcia Cid, Km 375, CP 481, 86001-970 Londrina, Paraná, Brazil
| | | | - David Pot
- CIRAD UMR AGAP, 34398 Montpellier Cedex 5, France
| | - Vânia A Silva
- EPAMIG/URESM, Rodovia Lavras/IJACI, Km 02, CP 176, 37200-000 Lavras, Minas Gerais, Brazil
| | - Gustavo C Rodrigues
- Embrapa Cerrados, BR 020 Km18, CP 08223, 73310-970 Planaltina, Distrito Federal, Brazil
| | - Alan C Andrade
- Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917 Brasilia, Distrito Federal, Brazil
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