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Bazakos C, Manioudaki ME, Therios I, Voyiatzis D, Kafetzopoulos D, Awada T, Kalaitzis P. Comparative transcriptome analysis of two olive cultivars in response to NaCl-stress. PLoS One 2012; 7:e42931. [PMID: 22952621 PMCID: PMC3431368 DOI: 10.1371/journal.pone.0042931] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/12/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Olive (Olea europaea L.) cultivation is rapidly expanding and low quality saline water is often used for irrigation. The molecular basis of salt tolerance in olive, though, has not yet been investigated at a system level. In this study a comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the genotype-dependent differences in the transcriptome response of two olive cultivars, a salt-tolerant and a salt-sensitive one. METHODOLOGY/PRINCIPAL FINDINGS A 135-day long salinity experiment was conducted using one-year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period during the summer. A cDNA library made of olive seedling mRNAs was sequenced and an olive microarray was constructed. Total RNA was extracted from root samples after 15, 45 and 90 days of NaCl-treatment as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations. SAM analysis between the NaCl-stress and the post-stress time course resulted in the identification of 209 and 36 differentially expressed transcripts in the salt-tolerant and salt-sensitive cultivar, respectively. Hierarchical clustering revealed two major, distinct clusters for each cultivar. Despite the limited number of probe sets, transcriptional regulatory networks were constructed for both cultivars while several hierarchically-clustered interacting transcription factor regulators such as JERF and bZIP homologues were identified. CONCLUSIONS/SIGNIFICANCE A systems biology approach was used and differentially expressed transcripts as well as regulatory interactions were identified. The comparison of the interactions among transcription factors in olive with those reported for Arabidopsis might indicate similarities in the response of a tree species with Arabidopsis at the transcriptional level under salinity stress.
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Affiliation(s)
- Christos Bazakos
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria E. Manioudaki
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Ioannis Therios
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Demetrios Voyiatzis
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitris Kafetzopoulos
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH), Crete, Greece
| | - Tala Awada
- School of Natural Resources, University of Nebraska–Lincoln, Lincoln, Nebraska, United States of America
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics & Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
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Song Y, Wang Z, Bo W, Ren Y, Zhang Z, Zhang D. Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis. BMC Genomics 2012; 13:286. [PMID: 22747754 PMCID: PMC3443059 DOI: 10.1186/1471-2164-13-286] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 05/15/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis. RESULTS Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique. CONCLUSION The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.
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Affiliation(s)
- Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Zeliang Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Wenhao Bo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Yuanyuan Ren
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Zhiyi Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
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103
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Chai G, Hu R, Zhang D, Qi G, Zuo R, Cao Y, Chen P, Kong Y, Zhou G. Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa). BMC Genomics 2012; 13:253. [PMID: 22708723 PMCID: PMC3427045 DOI: 10.1186/1471-2164-13-253] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/05/2012] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND CCCH zinc finger proteins contain a typical motif of three cysteines and one histidine residues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCH type zinc finger proteins comprise a large gene family represented by 68 members in Arabidopsis and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has not been studied in the model tree species Populus to date. RESULTS In the present study, a comprehensive analysis of the genes encoding CCCH zinc finger family in Populus was performed. Using a thorough annotation approach, a total of 91 full-length CCCH genes were identified in Populus, of which most contained more than one CCCH motif and a type of non-conventional C-X(11)-C-X(6)-C-X(3)-H motif was unique for Populus. All of the Populus CCCH genes were phylogeneticly clustered into 13 distinct subfamilies. In each subfamily, the gene structure and motif composition were relatively conserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of 90, 90 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairs were identified in Populus, of which 22 pairs (64.7 %) might be created by the whole genome segment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91 CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3 typical RNA-binding proteins. The expression profiles of all Populus CCCH genes have been digitally analyzed in six tissues across different developmental stages, and under various drought stress conditions. A variety of expression patterns of CCCH genes were observed during Populus development, of which 34 genes highly express in root and 22 genes show the highest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR (RT-qPCR) was further performed to confirm the tissue-specific expression and responses to drought stress treatment of 12 selected Populus CCCH genes. CONCLUSIONS This study provides the first systematic analysis of the Populus CCCH proteins. Comprehensive genomic analyses suggested that segmental duplications contribute significantly to the expansion of Populus CCCH gene family. Transcriptome profiling provides first insights into the functional divergences among members of Populus CCCH gene family. Particularly, some CCCH genes may be involved in wood development while others in drought tolerance regulation. Our results presented here may provide a starting point for the functional dissection of this family of potential RNA-binding proteins.
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Affiliation(s)
- Guohua Chai
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Ruibo Hu
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Dongyuan Zhang
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Guang Qi
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Ran Zuo
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Yingping Cao
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Peng Chen
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Yingzhen Kong
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Gongke Zhou
- Key Laboratory of Biofuels, Chinese Academy of Sciences, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
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Benešová M, Holá D, Fischer L, Jedelský PL, Hnilička F, Wilhelmová N, Rothová O, Kočová M, Procházková D, Honnerová J, Fridrichová L, Hniličková H. The physiology and proteomics of drought tolerance in maize: early stomatal closure as a cause of lower tolerance to short-term dehydration? PLoS One 2012; 7:e38017. [PMID: 22719860 PMCID: PMC3374823 DOI: 10.1371/journal.pone.0038017] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/02/2012] [Indexed: 01/05/2023] Open
Abstract
Understanding the response of a crop to drought is the first step in the breeding of tolerant genotypes. In our study, two maize (Zea mays L.) genotypes with contrasting sensitivity to dehydration were subjected to moderate drought conditions. The subsequent analysis of their physiological parameters revealed a decreased stomatal conductance accompanied by a slighter decrease in the relative water content in the sensitive genotype. In contrast, the tolerant genotype maintained open stomata and active photosynthesis, even under dehydration conditions. Drought-induced changes in the leaf proteome were analyzed by two independent approaches, 2D gel electrophoresis and iTRAQ analysis, which provided compatible but only partially overlapping results. Drought caused the up-regulation of protective and stress-related proteins (mainly chaperones and dehydrins) in both genotypes. The differences in the levels of various detoxification proteins corresponded well with the observed changes in the activities of antioxidant enzymes. The number and levels of up-regulated protective proteins were generally lower in the sensitive genotype, implying a reduced level of proteosynthesis, which was also indicated by specific changes in the components of the translation machinery. Based on these results, we propose that the hypersensitive early stomatal closure in the sensitive genotype leads to the inhibition of photosynthesis and, subsequently, to a less efficient synthesis of the protective/detoxification proteins that are associated with drought tolerance.
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Affiliation(s)
- Monika Benešová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Dana Holá
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petr L. Jedelský
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Laboratory of Mass Spectrometry, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - František Hnilička
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Naďa Wilhelmová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Olga Rothová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Marie Kočová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Dagmar Procházková
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jana Honnerová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lenka Fridrichová
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Helena Hniličková
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
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105
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Jiang H, Peng S, Zhang S, Li X, Korpelainen H, Li C. Transcriptional profiling analysis in Populus yunnanensis provides insights into molecular mechanisms of sexual differences in salinity tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3709-26. [PMID: 22442418 PMCID: PMC3388841 DOI: 10.1093/jxb/ers064] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/02/2012] [Accepted: 02/08/2012] [Indexed: 05/19/2023]
Abstract
Physiological responses to abiotic stress in plants exhibit sexual differences. Females usually experience greater negative effects than males; however, little is known about the molecular mechanisms of sexual differences in abiotic stress responses. In the present study, transcriptional responses to salinity treatments were compared between male and female individuals of the poplar Populus yunnanensis. It was found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes, which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observations showing that salinity inhibited photosynthetic capacity more in females than in males. Furthermore, genes located in autosomes rather than in the female-specific region of the W chromosome are the major contributors to the sexual differences in the salinity tolerance of poplars. In conclusion, this study provided molecular evidence of sexual differences in the salinity tolerance of poplars. The identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences in salinity stress at the transcription level.
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Affiliation(s)
- Hao Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041, China
| | - Shuming Peng
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041, China
| | - Sheng Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041, China
| | - Xinguo Li
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Helena Korpelainen
- Department of Agricultural Sciences, PO Box 27, FI-00014 University of Helsinki, Finland
| | - Chunyang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, PO Box 416, Chengdu 610041, China
- To whom correspondence should be addressed. E-mail:
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106
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Dong CH, Li C, Yan XH, Huang SM, Huang JY, Wang LJ, Guo RX, Lu GY, Zhang XK, Fang XP, Wei WH. Gene expression profiling of Sinapis alba leaves under drought stress and rewatering growth conditions with Illumina deep sequencing. Mol Biol Rep 2012. [PMID: 22207172 DOI: 10.1007/s11033-011-1395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Sinapis alba has many desirable agronomic traits including tolerance to drought. In this investigation, we performed the genome-wide transcriptional profiling of S. alba leaves under drought stress and rewatering growth conditions in an attempt to identify candidate genes involved in drought tolerance, using the Illumina deep sequencing technology. The comparative analysis revealed numerous changes in gene expression level attributable to the drought stress, which resulted in the down-regulation of 309 genes and the up-regulation of 248 genes. Gene ontology analysis revealed that the differentially expressed genes were mainly involved in cell division and catalytic and metabolic processes. Our results provide useful information for further analyses of the drought stress tolerance in Sinapis, and will facilitate molecular breeding for Brassica crop plants.
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Affiliation(s)
- Cai-Hua Dong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oil Crop Biology and Genetic Breeding of the Ministry of Agriculture, Wuhan, 430062, China
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107
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Deeba F, Pandey AK, Ranjan S, Mishra A, Singh R, Sharma YK, Shirke PA, Pandey V. Physiological and proteomic responses of cotton (Gossypium herbaceum L.) to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 53:6-18. [PMID: 22285410 DOI: 10.1016/j.plaphy.2012.01.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 01/03/2012] [Indexed: 05/18/2023]
Abstract
Cotton genotype RAHS 187 was analyzed for changes in physiology, biochemistry and proteome due to drought stress. The deleterious effect of drought in cotton plants was mainly targeted towards photosynthesis. The gas-exchange parameters of net photosynthesis (A), stomatal conductance (g(s)) and transpiration (E) showed a decreasing trend as the drought intensity increased. The fluorescence parameters of, effective quantum yield of PSII (Φ(PSII)), and electron transport rates (ETR), also showed a declining trend. As the intensity of drought increased, both H(2)O(2) and MDA levels increased indicating oxidative stress. Anthocyanin levels were increased by more than four folds in the droughted plants. Two-dimensional gel electrophoresis detected more than 550 protein spots. Significantly expressed proteins were analyzed by peptide mass fingerprinting (PMF) using MALDI-TOF-TOF. The number of up-regulated spots was found to be 16 while 6 spots were down-regulated. The reasonable implications in drought response of the identified proteins vis-à-vis physiological changes are discussed. Results provide some additional information that can lead to a better understanding of the molecular basis of drought-sensitivity in cotton plants.
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Affiliation(s)
- Farah Deeba
- Plant Physiology Lab, Council of Scientific and Industrial Research - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226 001, U.P., India
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108
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Ren Y, Chen L, Zhang Y, Kang X, Zhang Z, Wang Y. Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress. Funct Integr Genomics 2012; 12:327-39. [PMID: 22415631 DOI: 10.1007/s10142-012-0271-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 02/14/2012] [Accepted: 02/21/2012] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that play important downregulation roles in plants growth, development, and stress responses. To better identify Populus tomentosa miRNAs and understand the functions of miRNAs in response to water stress (drought and flooding), 152 conserved miRNAs belonging to 36 miRNA families, 8 known but non-conserved miRNAs and 64 candidate novel miRNAs belonging to 54 miRNA families were identified and analyzed from three small RNA (sRNA) libraries (drought treatment, flooding treatment, and control) by high-throughput sequencing combined with qRT-PCR. Significant changes in the expression of 17 conserved miRNA families and nine novel miRNAs were observed in response to drought stress, and in seven conserved miRNA families and five novel miRNAs in response to flooding stress. Both miRNA and miRNA*s were involved in the regulation of plant stress responses. The annotation of the potential targets of miRNAs with differential expression indicate that many types of genes encoding transcription factors, enzymes, and signal transduction components are implicated in the abiotic stress response..
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Affiliation(s)
- Yuanyuan Ren
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, 100083 Beijing, People's Republic of China.
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109
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Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G. Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2141-57. [PMID: 22213813 DOI: 10.1093/jxb/err435] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Despite the major physiological dissimilarities between mature root regions and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. japonica) mature root tissue and root tips was monitored using mRNA-Seq at two time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, expression patterns for different tissues and time points were investigated, and at least 1106 novel transcriptionally active regions (nTARs) expressed in rice root tissue were detected. More than 30 000 genes were found to be expressed in rice roots, among which were 1761 root-enriched and 306 tip-enriched transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of, for instance, auxin-responsive and abscisic acid-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-enriched transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. During root maturation, genes involved in cell wall biosynthesis and modification, response to oxidative stress, and secondary metabolism were activated. For some nTARs, a potential role in root development can be put forward based on homology to genes involved in CLAVATA signalling, cell cycle regulators, and hormone signalling. A subset of differentially expressed genes and novel transcripts was confirmed using (quantitative) reverse transcription-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.
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Affiliation(s)
- Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, Ghent, Belgium
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110
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Genome-wide identification, evolutionary expansion, and expression profile of homeodomain-leucine zipper gene family in poplar (Populus trichocarpa). PLoS One 2012; 7:e31149. [PMID: 22359569 PMCID: PMC3281058 DOI: 10.1371/journal.pone.0031149] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 01/03/2012] [Indexed: 12/29/2022] Open
Abstract
Background Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. Principal Findings In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I–IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. Conclusions Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles.
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111
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Padmalatha KV, Dhandapani G, Kanakachari M, Kumar S, Dass A, Patil DP, Rajamani V, Kumar K, Pathak R, Rawat B, Leelavathi S, Reddy PS, Jain N, Powar KN, Hiremath V, Katageri IS, Reddy MK, Solanke AU, Reddy VS, Kumar PA. Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes. PLANT MOLECULAR BIOLOGY 2012; 78:223-46. [PMID: 22143977 DOI: 10.1007/s11103-011-9857-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 11/08/2011] [Indexed: 05/06/2023]
Abstract
Cotton is an important source of natural fibre used in the textile industry and the productivity of the crop is adversely affected by drought stress. High throughput transcriptomic analyses were used to identify genes involved in fibre development. However, not much information is available on cotton genome response in developing fibres under drought stress. In the present study a genome wide transcriptome analysis was carried out to identify differentially expressed genes at various stages of fibre growth under drought stress. Our study identified a number of genes differentially expressed during fibre elongation as compared to other stages. High level up-regulation of genes encoding for enzymes involved in pectin modification and cytoskeleton proteins was observed at fibre initiation stage. While a large number of genes encoding transcription factors (AP2-EREBP, WRKY, NAC and C2H2), osmoprotectants, ion transporters and heat shock proteins and pathways involved in hormone (ABA, ethylene and JA) biosynthesis and signal transduction were up-regulated and genes involved in phenylpropanoid and flavonoid biosynthesis, pentose and glucuronate interconversions and starch and sucrose metabolism pathways were down-regulated during fibre elongation. This study showed that drought has relatively less impact on fibre initiation but has profound effect on fibre elongation by down-regulating important genes involved in cell wall loosening and expansion process. The comprehensive transcriptome analysis under drought stress has provided valuable information on differentially expressed genes and pathways during fibre development that will be useful in developing drought tolerant cotton cultivars without compromising fibre quality.
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Harfouche A, Meilan R, Kirst M, Morgante M, Boerjan W, Sabatti M, Scarascia Mugnozza G. Accelerating the domestication of forest trees in a changing world. TRENDS IN PLANT SCIENCE 2012; 17:64-72. [PMID: 22209522 DOI: 10.1016/j.tplants.2011.11.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 11/15/2011] [Accepted: 11/29/2011] [Indexed: 05/18/2023]
Abstract
In light of impending water and arable land shortages, population growth and climate change, it is more important than ever to examine how forest tree domestication can be accelerated to sustainably meet future demands for wood, biomass, paper, fuel and biomaterials. Because of long breeding cycles, tree domestication cannot be rapidly achieved through traditional genetic improvement methods alone. Integrating modern genetic and genomic techniques with conventional breeding will expedite tree domestication. Breeders will only embrace these technologies if they are cost-effective and readily accessible, and forest landowners will only adopt end-products that meet with regulatory approval and public acceptance. All parties involved must work together to achieve these objectives for the benefit of society.
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Affiliation(s)
- Antoine Harfouche
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis, Viterbo 01100, Italy.
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113
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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114
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Gene expression profiling of Sinapis alba leaves under drought stress and rewatering growth conditions with Illumina deep sequencing. Mol Biol Rep 2011; 39:5851-7. [PMID: 22207172 DOI: 10.1007/s11033-011-1395-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 12/17/2011] [Indexed: 10/14/2022]
Abstract
Sinapis alba has many desirable agronomic traits including tolerance to drought. In this investigation, we performed the genome-wide transcriptional profiling of S. alba leaves under drought stress and rewatering growth conditions in an attempt to identify candidate genes involved in drought tolerance, using the Illumina deep sequencing technology. The comparative analysis revealed numerous changes in gene expression level attributable to the drought stress, which resulted in the down-regulation of 309 genes and the up-regulation of 248 genes. Gene ontology analysis revealed that the differentially expressed genes were mainly involved in cell division and catalytic and metabolic processes. Our results provide useful information for further analyses of the drought stress tolerance in Sinapis, and will facilitate molecular breeding for Brassica crop plants.
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115
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Villar E, Klopp C, Noirot C, Novaes E, Kirst M, Plomion C, Gion JM. RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus. BMC Genomics 2011; 12:538. [PMID: 22047139 PMCID: PMC3248028 DOI: 10.1186/1471-2164-12-538] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/02/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit. RESULTS Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed. CONCLUSIONS For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.
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Affiliation(s)
- Emilie Villar
- CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France
- CRDPI, BP1291, Pointe Noire, République du Congo
| | - Christophe Klopp
- Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France
| | - Céline Noirot
- Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France
| | - Evandro Novaes
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
- Universidade Federal de Goiás, Caixa Postal 131, CEP 74690-900, Goiânia, Brazil
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France
- Université de Bordeaux, UMR1202 BIOGECO, F-33610 Cestas, France
| | - Jean-Marc Gion
- CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France
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116
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Li B, Qin Y, Duan H, Yin W, Xia X. Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3765-79. [PMID: 21511902 PMCID: PMC3134338 DOI: 10.1093/jxb/err051] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 01/26/2011] [Accepted: 01/31/2011] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. Populus euphratica is a typical abiotic stress-resistant woody species. This study presents an efficient method for genome-wide discovery of new drought stress responsive miRNAs in P. euphratica. High-throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 58 new miRNAs belonging to 38 families were identified, an increase in the number of P. euphratica miRNAs. Twenty-six new and 21 conserved miRNA targets were verified by degradome sequencing, and target annotation showed that these targets were involved in multiple biological processes, including transcriptional regulation and response to stimulus. Furthermore, comparison of high-throughput sequencing with miRNA microarray profiling data indicated that 104 miRNA sequences were up-regulated, whereas 27 were down-regulated under drought stress. This preliminary characterization provides a framework for future analysis of miRNA genes and their roles in key poplar traits such as stress resistance, and could be useful for plant breeding and environmental protection.
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Affiliation(s)
| | | | | | - Weilun Yin
- To whom correspondence should be addressed. E-mail: ;
| | - Xinli Xia
- To whom correspondence should be addressed. E-mail: ;
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Lu FH, Cho MC, Park YJ. Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol Biol Rep 2011; 39:3327-35. [PMID: 21706160 DOI: 10.1007/s11033-011-1102-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 06/15/2011] [Indexed: 12/01/2022]
Abstract
Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.
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Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-802, Republic of Korea
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