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Jiang G, Li Y, Cheng G, Jiang K, Zhou J, Xu C, Kong L, Yu H, Liu S, Li Q. Transcriptome Analysis of Reciprocal Hybrids Between Crassostrea gigas and C. angulata Reveals the Potential Mechanisms Underlying Thermo-Resistant Heterosis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:235-246. [PMID: 36653591 DOI: 10.1007/s10126-023-10197-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/11/2023] [Indexed: 05/06/2023]
Abstract
Heterosis, also known as hybrid vigor, is widely used in aquaculture, but the molecular causes for this phenomenon remain obscure. Here, we conducted a transcriptome analysis to unveil the gene expression patterns and molecular bases underlying thermo-resistant heterosis in Crassostrea gigas ♀ × Crassostrea angulata ♂ (GA) and C. angulata ♀ × C. gigas ♂ (AG). About 505 million clean reads were obtained, and 38,210 genes were identified, of which 3779 genes were differentially expressed between the reciprocal hybrids and purebreds. The global gene expression levels were toward the C. gigas genome in the reciprocal hybrids. In GA and AG, 95.69% and 92.00% of the differentially expressed genes (DEGs) exhibited a non-additive expression pattern, respectively. We observed all gene expression modes, including additive, partial dominance, high and low dominance, and under- and over-dominance. Of these, 77.52% and 50.00% of the DEGs exhibited under- or over-dominance in GA and AG, respectively. The over-dominance DEGs common to reciprocal hybrids were significantly enriched in protein folding, protein refolding, and intrinsic apoptotic signaling pathway, while the under-dominance DEGs were significantly enriched in cell cycle. As possible candidate genes for thermo-resistant heterosis, GRP78, major egg antigen, BAG, Hsp70, and Hsp27 were over-dominantly expressed, while MCM6 and ANAPC4 were under-dominantly expressed. This study extends our understanding of the thermo-resistant heterosis in oysters.
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Affiliation(s)
- Gaowei Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yin Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Geng Cheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kunyin Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jianmin Zhou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Racedo S, Portnoy I, Vélez JI, San-Juan-Vergara H, Sanjuan M, Zurek E. A new pipeline for structural characterization and classification of RNA-Seq microbiome data. BioData Min 2021; 14:31. [PMID: 34243809 PMCID: PMC8268467 DOI: 10.1186/s13040-021-00266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput sequencing enables the analysis of the composition of numerous biological systems, such as microbial communities. The identification of dependencies within these systems requires the analysis and assimilation of the underlying interaction patterns between all the variables that make up that system. However, this task poses a challenge when considering the compositional nature of the data coming from DNA-sequencing experiments because traditional interaction metrics (e.g., correlation) produce unreliable results when analyzing relative fractions instead of absolute abundances. The compositionality-associated challenges extend to the classification task, as it usually involves the characterization of the interactions between the principal descriptive variables of the datasets. The classification of new samples/patients into binary categories corresponding to dissimilar biological settings or phenotypes (e.g., control and cases) could help researchers in the development of treatments/drugs. RESULTS Here, we develop and exemplify a new approach, applicable to compositional data, for the classification of new samples into two groups with different biological settings. We propose a new metric to characterize and quantify the overall correlation structure deviation between these groups and a technique for dimensionality reduction to facilitate graphical representation. We conduct simulation experiments with synthetic data to assess the proposed method's classification accuracy. Moreover, we illustrate the performance of the proposed approach using Operational Taxonomic Unit (OTU) count tables obtained through 16S rRNA gene sequencing data from two microbiota experiments. Also, compare our method's performance with that of two state-of-the-art methods. CONCLUSIONS Simulation experiments show that our method achieves a classification accuracy equal to or greater than 98% when using synthetic data. Finally, our method outperforms the other classification methods with real datasets from gene sequencing experiments.
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Affiliation(s)
| | - Ivan Portnoy
- Universidad del Norte, Barranquilla, Colombia.
- Productivity and Innovation Department, Universidad de la Costa, Calle 58 # 55-56, Barranquilla, Colombia.
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Alam B, Lǐ J, Gě Q, Khan MA, Gōng J, Mehmood S, Yuán Y, Gǒng W. Endophytic Fungi: From Symbiosis to Secondary Metabolite Communications or Vice Versa? FRONTIERS IN PLANT SCIENCE 2021; 12:791033. [PMID: 34975976 PMCID: PMC8718612 DOI: 10.3389/fpls.2021.791033] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/29/2021] [Indexed: 05/08/2023]
Abstract
Endophytic fungi (EF) are a group of fascinating host-associated fungal communities that colonize the intercellular or intracellular spaces of host tissues, providing beneficial effects to their hosts while gaining advantages. In recent decades, accumulated research on endophytic fungi has revealed their biodiversity, wide-ranging ecological distribution, and multidimensional interactions with host plants and other microbiomes in the symbiotic continuum. In this review, we highlight the role of secondary metabolites (SMs) as effectors in these multidimensional interactions, and the biosynthesis of SMs in symbiosis via complex gene expression regulation mechanisms in the symbiotic continuum and via the mimicry or alteration of phytochemical production in host plants. Alternative biological applications of SMs in modern medicine, agriculture, and industry and their major classes are also discussed. This review recapitulates an introduction to the research background, progress, and prospects of endophytic biology, and discusses problems and substantive challenges that need further study.
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Affiliation(s)
- Beena Alam
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jùnwén Lǐ
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qún Gě
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Mueen Alam Khan
- Department of Plant Breeding & Genetics, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur (IUB), Bahawalpur, Pakistan
| | - Jǔwǔ Gōng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shahid Mehmood
- Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yǒulù Yuán
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Wànkuí Gǒng,
| | - Wànkuí Gǒng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Yǒulù Yuán,
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Ouyang W, Cao Z, Xiong D, Li G, Li X. Decoding the plant genome: From epigenome to 3D organization. J Genet Genomics 2020; 47:425-435. [PMID: 33023833 DOI: 10.1016/j.jgg.2020.06.007] [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: 12/27/2019] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022]
Abstract
The linear genome of eukaryotes is partitioned into diverse chromatin states and packaged into a three-dimensional (3D) structure, which has functional implications in DNA replication, DNA repair, and transcriptional regulation. Over the past decades, research on plant functional genomics and epigenomics has made great progress, with thousands of genes cloned and molecular mechanisms of diverse biological processes elucidated. Recently, 3D genome research has gradually attracted great attention of many plant researchers. Herein, we briefly review the progress in genomic and epigenomic research in plants, with a focus on Arabidopsis and rice, and summarize the currently used technologies and advances in plant 3D genome organization studies. We also discuss the relationships between one-dimensional linear genome sequences, epigenomic states, and the 3D chromatin architecture. This review provides basis for future research on plant 3D genomics.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Department of Resources and Environment, Henan University of Engineering, Zhengzhou, 451191, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Ravi RSD, Siril EA, Nair BR. The efficiency of Cytochrome P450 gene-based markers in accessing genetic variability of drumstick (Moringa oleifera Lam.) accessions. Mol Biol Rep 2020; 47:2929-2939. [PMID: 32236894 DOI: 10.1007/s11033-020-05391-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/24/2020] [Indexed: 11/24/2022]
Abstract
Drumstick (Moringa oleifera Lam.) is an important vegetable as well as forage crop of arid and semi-arid zones of the tropics. The leaves and pods of the plant are rich sources of minerals and vitamins. In the present work, genetic diversity study of 23 genotypes of M. oleifera collected from Kerala, Tamil Nadu and Karnataka states of India was carried out using seven cytochrome P450 (CytP450) markers. By using seven pairs of CytP450 gene-based markers, 88.25% of polymorphism was recorded among the 23 sampled genotypes. The Polymorphic Information Content (PI), Marker Index (MI) and Resolving Power obtained for seven primers were estimated 0.23, 2.96 and 9.83, respectively. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram based on this marker data indicate that genotypes from different geographical regions are placed in the same clusters. The dendrogram and Principal Coordinates Analysis (PCoA) plots derived from the binary data matrices were highly concordant. The investigation, in brief, proved that CytP450 based marker system is efficient in the elucidation of genetic diversity in M. oleifera accessions.
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Affiliation(s)
- R S Drisya Ravi
- Department of Biotechnology, University of Kerala, Kariavattom, Trivandrum, 695581, India
| | - E A Siril
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India.
| | - Bindu R Nair
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India
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6
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Vasseur F, Fouqueau L, de Vienne D, Nidelet T, Violle C, Weigel D. Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLoS Biol 2019; 17:e3000214. [PMID: 31017902 PMCID: PMC6481775 DOI: 10.1371/journal.pbio.3000214] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/21/2019] [Indexed: 12/22/2022] Open
Abstract
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain phenotypic variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
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Affiliation(s)
- François Vasseur
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux (LEPSE), INRA, Montpellier SupAgro, UMR759, Montpellier, France
- * E-mail: (FV); (DW)
| | - Louise Fouqueau
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Dominique de Vienne
- GQE–Le Moulon, INRA, Univ Paris-Sud, CNRS, AgroParisTech, Univ Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Univ Paul Valéry Montpellier, EPHE, IRD, Montpellier, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail: (FV); (DW)
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7
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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8
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Zhang C, Wang X, Zhang F, Dong L, Wu J, Cheng Q, Qi D, Yan X, Jiang L, Fan S, Li N, Li D, Xu P, Zhang S. Phenylalanine ammonia-lyase2.1 contributes to the soybean response towards Phytophthora sojae infection. Sci Rep 2017; 7:7242. [PMID: 28775360 PMCID: PMC5543151 DOI: 10.1038/s41598-017-07832-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/16/2017] [Indexed: 01/25/2023] Open
Abstract
Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.] caused by Phytophthora sojae is a destructive disease worldwide. Phenylalanine ammonia-lyase (PAL) is one of the most extensively studied enzymes related to plant responses to biotic and abiotic stresses. However, the molecular mechanism of PAL in soybean in response to P. sojae is largely unclear. Here, we characterize a novel member of the soybean PAL gene family, GmPAL2.1, which is significantly induced by P. sojae. Overexpression and RNA interference analysis demonstrates that GmPAL2.1 enhances resistance to P. sojae in transgenic soybean plants. In addition, the PAL activity in GmPAL2.1-OX transgenic soybean is significantly higher than that of non-transgenic plants after infection with P. sojae, while that in GmPAL2.1-RNAi soybean plants is lower. Further analyses show that the daidzein, genistein and salicylic acid (SA) levels and the relative content of glyceollins are markedly increased in GmPAL2.1-OX transgenic soybean. Taken together, these results suggest the important role of GmPAL2.1 functioning as a positive regulator in the soybean response to P. sojae infection, possibly by enhancing the content of glyceollins, daidzein, genistein and SA.
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Affiliation(s)
- Chuanzhong Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xin Wang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
- Heilongjiang Academy of Land Reclamation Sciences, Harbin, Heilongjiang, China
| | - Feng Zhang
- First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lidong Dong
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture P. R. China, Harbin, Heilongjiang, China
| | - Qun Cheng
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Dongyue Qi
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaofei Yan
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Liangyu Jiang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Sujie Fan
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ninghui Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, Heilongjiang, China
| | - Dongmei Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Pengfei Xu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Shuzhen Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China.
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9
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Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, Becker JD, Vandepoele K, Mutwil M. Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:447-465. [PMID: 28161902 DOI: 10.1111/tpj.13502] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/05/2017] [Accepted: 01/25/2017] [Indexed: 05/08/2023]
Abstract
Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de.
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Affiliation(s)
- Colin Ruprecht
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Sebastian Proost
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
| | | | - Carlos Ortiz-Ramirez
- Instituto Gulbekian De Ciencia, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Daniel Lang
- University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Stefan A Rensing
- University of Marburg, Karl-von-Frisch-Str. 8, D-35043, Marburg, Germany
| | - Jörg D Becker
- Instituto Gulbekian De Ciencia, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Klaas Vandepoele
- Department of Plant Systems Biology VIB, Department of Plant Biotechnology and Bioinformatics Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany
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Rouhian S, Ahmadi DN, Sorkheh K. Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (Hordeum vulgare L.) germplasm. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0510-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The application of biotechnology, in terms of using the full range of scientific biological information available, is in its infancy. Although there are concerns being raised by the public that need to be carefully addressed, farmers are adopting the new technologies at an unprecedented rate, and the pipeline is full of new products of more obvious benefit to the consumer. Biotechnology will unlock some of the genetic variation available in the extensive genetic resource collections. Conventional breeding technologies require the crossing of these exotic collections, thus introducing many unwanted genetic traits. Biotechnology will allow the transfer of less than the whole genome, thus allowing easier utilization of these rich genetic resources. The application of molecular genetic markers is efficient for the backcrossing of single-gene traits and will become increasingly important for more complex traits such as those of quality protein maize, where modifier genes play a prominent role. Genomics—the study of the whole genome—is providing unprecedented information useful for the genetic manipulation of crop species. Understanding the structure and function of every gene in a plant will lead to many innovative applications. DNA chip or microarray technologies will allow every gene to be monitored. Comparative mapping indicates great similarity among broadly related species and indicates that genomics knowledge for rice and other model species will be quite informative. With respect to the improvement of human nutrition, a database on nutritional genomics related to crop plants would allow even greater progress than can be made with conventional techniques.
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Affiliation(s)
- Ronald L. Phillips
- Department of Agronomy and Plant Genetics and the Plant Molecular Genetics Institute at the University of Minnesota in St. Paul, Minnesota, USA
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Cheng Q, Li N, Dong L, Zhang D, Fan S, Jiang L, Wang X, Xu P, Zhang S. Overexpression of Soybean Isoflavone Reductase (GmIFR) Enhances Resistance to Phytophthora sojae in Soybean. FRONTIERS IN PLANT SCIENCE 2015; 6:1024. [PMID: 26635848 PMCID: PMC4655237 DOI: 10.3389/fpls.2015.01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/05/2015] [Indexed: 05/18/2023]
Abstract
Isoflavone reductase (IFR) is an enzyme involved in the biosynthetic pathway of isoflavonoid phytoalexin in plants. IFRs are unique to the plant kingdom and are considered to have crucial roles in plant response to various biotic and abiotic environmental stresses. Here, we report the characterization of a novel member of the soybean isoflavone reductase gene family GmIFR. Overexpression of GmIFR transgenic soybean exhibited enhanced resistance to Phytophthora sojae. Following stress treatments, GmIFR was significantly induced by P. sojae, ethephon (ET), abscisic acid (placeCityABA), salicylic acid (SA). It is located in the cytoplasm when transiently expressed in soybean protoplasts. The daidzein levels reduced greatly for the seeds of transgenic plants, while the relative content of glyceollins in transgenic plants was significantly higher than that of non-transgenic plants. Furthermore, we found that the relative expression levels of reactive oxygen species (ROS) of transgenic soybean plants were significantly lower than those of non-transgenic plants after incubation with P. sojae, suggesting an important role of GmIFR might function as an antioxidant to reduce ROS in soybean. The enzyme activity assay suggested that GmIFR has isoflavone reductase activity.
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Affiliation(s)
- Qun Cheng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Ninghui Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural SciencesJiamusi, China
| | - Lidong Dong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Dayong Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Sujie Fan
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Liangyu Jiang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Xin Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
- Heilongjiang Academy of Land Reclamation SciencesHarbin, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
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Watching Grass Grow: The Emergence of Brachypodium distachyon as a Model for the Poaceae. ARCHIMEDES 2015. [DOI: 10.1007/978-3-319-12185-7_23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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14
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Patra AK. An Overview of Antimicrobial Properties of Different Classes of Phytochemicals. DIETARY PHYTOCHEMICALS AND MICROBES 2012. [PMCID: PMC7121617 DOI: 10.1007/978-94-007-3926-0_1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Plants produce a great diversity of phytochemicals, the beneficial properties of which have been used by humans for centuries since the advent of human civilization. With the discovery of effective and potent antimicrobial compounds, these synthetic antimicrobial compounds are widely used to prevent and cure microbial diseases. However, the development of antibiotic resistant strains of bacteria, reduced efficacy and safety of antimicrobials and the search of new antimicrobials against emerging incurable diseases by conventional antimicrobial agents have revived to explore phytochemicals as an alternative to synthetic antimicrobial compounds. Although numerous studies have been conducted in vitro and in vivo in the recent years on the efficacy of plant phytochemicals as antimicrobial agents, this chapter provides an overview of the antimicrobial properties of some major group of phytochemicals, namely, different phenolic compounds, alkaloids, saponins, iridoids and secoiridoids, polyacetylenes, glucosinolates, terpenoids, sulfinate, limonoids (tetranortepenoids) and anthranoids against pathogenic bacteria, fungi, viruses and commensal bacteria in the intestinal tracts of humans and animals. This chapter also discusses their antimicrobial mechanisms of action, the efficiency of different groups of phytochemicals against multiple-drug resistant bacteria, the effect of active dietary phytometabolites on the beneficial and pathogenic microbes of the gastrointestinal tracts and the outcomes of combination of phytofactors and drugs interactions.
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Affiliation(s)
- Amlan K. Patra
- of Animal and Fishery Sciences, Department of Animal Nutrition, West Bengal University, Kshudiram Bose Sarani 37, Belgachia, Kolkata, 700 037 India
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15
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Pichersky E. New synthesis--duplicated genes in the ecological interactions of plants with their environment. J Chem Ecol 2012; 37:923. [PMID: 21845433 DOI: 10.1007/s10886-011-0004-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Jaligot E, Adler S, Debladis É, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. ANNALS OF BOTANY 2011; 108:1453-62. [PMID: 21224269 PMCID: PMC3219487 DOI: 10.1093/aob/mcq266] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/19/2010] [Indexed: 05/24/2023]
Abstract
BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.
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Affiliation(s)
- Estelle Jaligot
- UMR DIADE (IRD, UM2), IRD/CIRAD Palm Development Group, 911 avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France.
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17
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Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.). J Genet 2011; 89:121-33. [PMID: 20861563 DOI: 10.1007/s12041-010-0052-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300-450 mg/100 g), medium calcium (200-300 mg/100 g) and low calcium (100-200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops.
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18
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Likić VA, McConville MJ, Lithgow T, Bacic A. Systems biology: the next frontier for bioinformatics. Adv Bioinformatics 2011; 2010:268925. [PMID: 21331364 PMCID: PMC3038413 DOI: 10.1155/2010/268925] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 11/01/2010] [Indexed: 01/01/2023] Open
Abstract
Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from 'omics platform technologies, in particular "downstream" technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a) quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b) development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c) applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems.
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Affiliation(s)
- Vladimir A. Likić
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Malcolm J. McConville
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Antony Bacic
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
- Australian Centre for Plant Functional Genomics, School of Botany, The University of Melbourne, Parkville, VIC, 3010, Australia
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Pichersky E, Lewinsohn E. Convergent evolution in plant specialized metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:549-66. [PMID: 21275647 DOI: 10.1146/annurev-arplant-042110-103814] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants synthesize a multitude of compounds that contribute to adaptation to their ecological niches. Such compounds serve as attractants of other living organisms beneficial to the plants or as defense against other biotic as well as abiotic agents. Selection for increased fitness, a never-ending process, has resulted in each plant lineage synthesizing a distinct set of specialized metabolites appropriate for its environment. The total number of specialized metabolites found in the plant kingdom far exceeds the capacity of any one plant genome to encode the necessary enzymes, and just as a plant lineage acquires the ability to make new specialized compounds during evolution, it also loses the ability to make others. Although the ability of plants to make novel, specialized metabolites continues to evolve, there are also many examples in which different plants have independently evolved the ability to make compounds already present in other plant lineages or to make different compounds that fulfill the same role-both are examples of convergent evolution. Here, we discuss many examples of convergent evolution in specialized metabolism. There are many genetic and biochemical mechanisms that can give rise to convergent evolution, and we conclude that, overall, convergent evolution in plant specialized metabolism is surprisingly common.
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Affiliation(s)
- Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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20
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Lee Y, Voit EO. Mathematical modeling of monolignol biosynthesis in Populus xylem. Math Biosci 2010; 228:78-89. [PMID: 20816867 DOI: 10.1016/j.mbs.2010.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/04/2010] [Accepted: 08/05/2010] [Indexed: 10/19/2022]
Abstract
Recalcitrance of lignocellulosic biomass to sugar release is a central issue in the production of biofuel as an economically viable energy source. Among all contributing factors, variations in lignin content and its syringyl-guaiacyl monomer composition have been directly linked with the yield of fermentable sugars. While recent advances in genomics and metabolite profiling have significantly broadened our understanding of lignin biosynthesis, its regulation at the pathway level is yet poorly understood. During the past decade, computational and mathematical methods of systems biology have become effective tools for deciphering the structure and regulation of complex metabolic networks. As increasing amounts of data from various organizational levels are being published, the application of these methods to studying lignin biosynthesis appears to be very beneficial for the future development of genetically engineered crops with reduced recalcitrance. Here, we use techniques from flux balance analysis and nonlinear dynamic modeling to construct a mathematical model of monolignol biosynthesis in Populus xylem. Various types of experimental data from the literature are used to identify the statistically most significant parameters and to estimate their values through an ensemble approach. The thus generated ensemble of models yields results that are quantitatively consistent with several transgenic experiments, including two experiments not used in the model construction. Additional model results not only reveal probable substrate saturation at steps leading to the synthesis of sinapyl alcohol, but also suggest that the ratio of syringyl to guaiacyl monomers might not be affected by genetic modulations prior to the reactions involving coniferaldehyde. This latter model prediction is directly supported by data from transgenic experiments. Finally, we demonstrate the applicability of the model in metabolic engineering, where the pathway is to be optimized toward a higher yield of xylose through modification of the relative amounts of the two major monolignols. The results generated by our preliminary model of in vivo lignin biosynthesis are encouraging and demonstrate that mathematical modeling is poised to become an effective and predictive complement to traditional biotechnological and transgenic approaches, not just in microorganisms but also in plants.
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Affiliation(s)
- Yun Lee
- Integrative Biosystems Institute and The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
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21
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Heath LS, Ramakrishnan N, Sederoff RR, Whetten RW, Chevone BI, Struble CA, Jouenne VY, Chen D, van Zyl L, Grene R. Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system. Comp Funct Genomics 2010; 3:226-43. [PMID: 18628855 PMCID: PMC2447276 DOI: 10.1002/cfg.169] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2001] [Accepted: 04/04/2002] [Indexed: 12/20/2022] Open
Abstract
Conception, design, and implementation of cDNA microarray experiments present a
variety of bioinformatics challenges for biologists and computational scientists. The multiple
stages of data acquisition and analysis have motivated the design of Expresso, a
system for microarray experiment management. Salient aspects of Expresso include
support for clone replication and randomized placement; automatic gridding, extraction of
expression data from each spot, and quality monitoring; flexible methods of combining
data from individual spots into information about clones and functional categories; and the
use of inductive logic programming for higher-level data analysis and mining. The
development of Expresso is occurring in parallel with several generations of microarray
experiments aimed at elucidating genomic responses to drought stress in loblolly pine
seedlings. The current experimental design incorporates 384 pine cDNAs replicated and
randomly placed in two specific microarray layouts. We describe the design of Expresso as
well as results of analysis with Expresso that suggest the importance of molecular
chaperones and membrane transport proteins in mechanisms conferring successful
adaptation to long-term drought stress.
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Affiliation(s)
- Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, USA
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22
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Panwar P, Saini RK, Sharma N, Yadav D, Kumar A. Efficiency of RAPD, SSR and cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions. Mol Biol Rep 2010; 37:4075-82. [PMID: 20333550 DOI: 10.1007/s11033-010-0067-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 03/05/2010] [Indexed: 10/19/2022]
Abstract
Finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. Three DNA marker techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P(450) gene based markers were used for the detection of genetic polymorphism in 83 accessions of finger millet collected from various geographical regions of India and Africa. A total of 18 RAPD, 10 SSR and 10 pairs of cytochrome P(450) gene based markers were generated 56.17, 70.19 and 54.29% polymorphism, respectively. Mean polymorphism information content (PIC) for each of these marker systems (0.280 for RAPD, 0.89 for SSR and 0.327 for cytochrome P(450) gene based markers) suggested that SSR marker were highly effective in determining polymorphism. The phenograms based on the three markers data indicate that genotypes from different geographical regions are clearly distinguishable as separate clusters. Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.90 for all the three marker systems. The dendrograms and PCA plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Based on the results of present study, SSR and cytochrome P(450) gene based markers appear to be particularly useful for the estimation of genetic diversity. This study reveals the potential of RAPD, SSR and gene based markers for characterizing germplasm of Eleusine coracana and narrow down the vast germplasm into distinct core groups.
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Affiliation(s)
- Preety Panwar
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, India
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23
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Yang L, Stöckigt J. Trends for diverse production strategies of plant medicinal alkaloids. Nat Prod Rep 2010; 27:1469-79. [DOI: 10.1039/c005378c] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Sharma AK, Sharma MK. Plants as bioreactors: Recent developments and emerging opportunities. Biotechnol Adv 2009; 27:811-832. [PMID: 19576278 PMCID: PMC7125752 DOI: 10.1016/j.biotechadv.2009.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 12/18/2022]
Abstract
In recent years, the use of plants as bioreactors has emerged as an exciting area of research and significant advances have created new opportunities. The driving forces behind the rapid growth of plant bioreactors include low production cost, product safety and easy scale up. As the yield and concentration of a product is crucial for commercial viability, several strategies have been developed to boost up protein expression in transgenic plants. Augmenting tissue-specific transcription, elevating transcript stability, tissue-specific targeting, translation optimization and sub-cellular accumulation are some of the strategies employed. Various kinds of products that are currently being produced in plants include vaccine antigens, medical diagnostics proteins, industrial and pharmaceutical proteins, nutritional supplements like minerals, vitamins, carbohydrates and biopolymers. A large number of plant-derived recombinant proteins have reached advanced clinical trials. A few of these products have already been introduced in the market.
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Affiliation(s)
- Arun K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Manoj K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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25
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Wada N, Kajiyama S, Akiyama Y, Kawakami S, No D, Uchiyama S, Otani M, Shimada T, Nose N, Suzuki G, Mukai Y, Fukui K. Bioactive beads-mediated transformation of rice with large DNA fragments containing Aegilops tauschii genes. PLANT CELL REPORTS 2009; 28:759-768. [PMID: 19214515 DOI: 10.1007/s00299-009-0678-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/05/2009] [Accepted: 01/25/2009] [Indexed: 05/27/2023]
Abstract
Transformation with large DNA molecules enables multiple genes to be introduced into plants simultaneously to produce transgenic plants with complex phenotypes. In this study, a large DNA fragment (ca. 100 kb) containing a set of Aegilops tauschii hardness genes was introduced into rice plants using a novel transformation method, called bioactive beads-mediated transformation. Nine transgenic rice plants were obtained and the presence of transgenes in the rice genome was confirmed by PCR and FISH analyses. The results suggested that multiple transgenes were successfully integrated in all transgenic plants. The expression of one of the transgenes, puroindoline b, was confirmed at the mRNA and protein levels in the T(2) generation. Our study clearly demonstrates that the bioactive bead method is capable of producing transgenic rice plants carrying large DNA fragments. This method will facilitate the production of useful transgenic plants by introducing multiple genes simultaneously.
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Affiliation(s)
- Naoki Wada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
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27
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Bräutigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber APM. Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J Biotechnol 2008; 136:44-53. [PMID: 18394738 DOI: 10.1016/j.jbiotec.2008.02.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/22/2008] [Accepted: 02/07/2008] [Indexed: 11/17/2022]
Abstract
Proteomics is a valuable tool for establishing and comparing the protein content of defined tissues, cell types, or subcellular structures. Its use in non-model species is currently limited because the identification of peptides critically depends on sequence databases. In this study, we explored the potential of a preliminary cDNA database for the non-model species Pisum sativum created by a small number of massively parallel pyrosequencing (MPSS) runs for its use in proteomics and compared it to comprehensive cDNA databases from Medicago truncatula and Arabidopsis thaliana created by Sanger sequencing. Each database was used to identify proteins from a pea leaf chloroplast envelope preparation. It is shown that the pea database identified more proteins with higher accuracy, although the sequence quality was low and the sequence contigs were short compared to databases from model species. Although the number of identified proteins in non-species-specific databases could potentially be increased by lowering the threshold for successful protein identifications, this strategy markedly increases the number of wrongly identified proteins. The identification rate with non-species-specific databases correlated with spectral abundance but not with the predicted membrane helix content, and strong conservation is necessary but not sufficient for protein identification with a non-species-specific database. It is concluded that massively parallel sequencing of cDNAs substantially increases the power of proteomics in non-model species.
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Affiliation(s)
- Andrea Bräutigam
- Institut für Biochemie der Pflanzen, Heinrich-Heine-Universität, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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Carmona MJ, Cubas P, Calonje M, Martínez-Zapater JM. Flowering transition in grapevine (Vitis viniferaL.)This review is one of a selection of papers presented at the symposium onVitisat the XVII International Botanical Congress held in Vienna, Austria, 2005. ACTA ACUST UNITED AC 2007. [DOI: 10.1139/b07-059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The available information on the regulation of flowering transition in model systems, such as Arabidopsis and rice, provides a framework to undertake the study of this process in plant species with different growth strategies. The grapevine ( Vitis vinifera L.) is the most widely cultivated and economically important fruit crop in the world. Understanding the regulation of flowering transition in this species can be relevant for the improvement of yield and quality of the crop. The grapevine is a representative of the family Vitaceae, whose species mostly grow as vines and have evolved climbing organs, tendrils, which are ontogenetically related to the reproductive organs. Here, we summarize the available information on the flowering transition in the grapevine. With this purpose, we first describe the vegetative and reproductive development of the grapevine as well as the reports on the physiology of flowering induction in this species. As well, we review the recent information on the molecular genetics of flowering signal integrator and flower meristem identity genes in the grapevine and compare the process with what is already known in model systems such as Arabidopsis. Finally, we propose a preliminary model to explain the regulation of flower initiation in the grapevine that is useful to identify its differential features and infer future prospects in the understanding of this process.
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Affiliation(s)
- María José Carmona
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Pilar Cubas
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Myriam Calonje
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José Miguel Martínez-Zapater
- Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria, 28003 Madrid, Spain
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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Vij S, Tyagi AK. Emerging trends in the functional genomics of the abiotic stress response in crop plants. PLANT BIOTECHNOLOGY JOURNAL 2007; 5:361-80. [PMID: 17430544 DOI: 10.1111/j.1467-7652.2007.00239.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants are exposed to different abiotic stresses, such as water deficit, high temperature, salinity, cold, heavy metals and mechanical wounding, under field conditions. It is estimated that such stress conditions can potentially reduce the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms developed during evolution to mitigate against stress by plants. Before the advent of the genomics era, researchers primarily used a gene-by-gene approach to decipher the function of the genes involved in the abiotic stress response. However, abiotic stress tolerance is a complex trait and, although large numbers of genes have been identified to be involved in the abiotic stress response, there remain large gaps in our understanding of the trait. The availability of the genome sequences of certain important plant species has enabled the use of strategies, such as genome-wide expression profiling, to identify the genes associated with the stress response, followed by the verification of gene function by the analysis of mutants and transgenics. Certain components of both abscisic acid-dependent and -independent cascades involved in the stress response have already been identified. Information originating from the genome-wide analysis of abiotic stress tolerance will help to provide an insight into the stress-responsive network(s), and may allow the modification of this network to reduce the loss caused by stress and to increase agricultural productivity.
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Affiliation(s)
- Shubha Vij
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Shao HB, Chu LY, Wu G, Zhang JH, Lu ZH, Hu YC. Changes of some anti-oxidative physiological indices under soil water deficits among 10 wheat (Triticum aestivum L.) genotypes at tillering stage. Colloids Surf B Biointerfaces 2007; 54:143-9. [PMID: 17196377 DOI: 10.1016/j.colsurfb.2006.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2006] [Revised: 08/16/2006] [Accepted: 09/07/2006] [Indexed: 11/24/2022]
Abstract
Drought is one of the major ecological factors limiting crop production and food quality globally, especially in the arid and semi-arid areas of the world. Wheat is the staple food for more than 35% of world population and wheat cultivation is mainly restricted to such zones with scarcity of water, so wheat anti-drought physiology study is of importance to wheat production, food safety and quality and biotechnological breeding for the sake of coping with abiotic and biotic conditions. The current study is to investigate changes of anti-oxidative physiological indices of 10 wheat genotypes at tillering stage. The main results and conclusion of tillering stage in terms of activities of POD, SOD, CAT and MDA content as followed: (1) 10 wheat genotypes can be generally grouped into three kinds (A-C, respectively) according to their changing trend of the measured indices; (2) A group performed better drought resistance under the condition of treatment level 1 (appropriate level), whose activities of anti-oxidative enzymes (POD, SOD, CAT) were higher and MDA lower; (3) B group exhibited stronger anti-drought under treatment level 2 (light-stress level), whose activities of anti-oxidative enzymes were higher and MDA lower; (4) C group expressed anti-drought to some extent under treatment level 3 (serious-stress), whose activities of anti-oxidative enzymes were stronger, MDA lower; (5) these results demonstrated that different wheat genotypes have different physiological mechanisms to adapt themselves to changing drought stress, whose molecular basis is discrete gene expression profiling (transcriptom). The study in this respect is the key to wheat anti-drought and biological-saving water in worldwide arid and semi-arid areas; (6) POD, SOD, and CAT activities and MDA content of different wheat genotypes had quite different changing trend at different stages and under different soil water stress conditions, which was linked with their origin of cultivation and individual soil water threshold, which will provide better reference to selecting proper plant species for eco-environmental construction and crops for sustainable agriculture in arid and semi-arid areas.
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31
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Roessner U, Pettolino F. The importance of anatomy and physiology in plant metabolomics. TOPICS IN CURRENT GENETICS 2007. [DOI: 10.1007/4735_2007_0218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hammer G, Cooper M, Tardieu F, Welch S, Walsh B, van Eeuwijk F, Chapman S, Podlich D. Models for navigating biological complexity in breeding improved crop plants. TRENDS IN PLANT SCIENCE 2006; 11:587-93. [PMID: 17092764 DOI: 10.1016/j.tplants.2006.10.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 08/15/2006] [Accepted: 10/24/2006] [Indexed: 05/05/2023]
Abstract
Progress in breeding higher-yielding crop plants would be greatly accelerated if the phenotypic consequences of making changes to the genetic makeup of an organism could be reliably predicted. Developing a predictive capacity that scales from genotype to phenotype is impeded by biological complexities associated with genetic controls, environmental effects and interactions among plant growth and development processes. Plant modelling can help navigate a path through this complexity. Here we profile modelling approaches for complex traits at gene network, organ and whole plant levels. Each provides a means to link phenotypic consequence to changes in genomic regions via stable associations with model coefficients. A unifying feature of the models is the relatively coarse level of granularity they use to capture system dynamics. Much of the fine detail is not directly required. Robust coarse-grained models might be the tool needed to integrate phenotypic and molecular approaches to plant breeding.
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Affiliation(s)
- Graeme Hammer
- APSRU, School of Land and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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Phan BH, Jin W, Topp CN, Zhong CX, Jiang J, Dawe RK, Parrott WA. Transformation of rice with long DNA-segments consisting of random genomic DNA or centromere-specific DNA. Transgenic Res 2006; 16:341-51. [PMID: 17103243 DOI: 10.1007/s11248-006-9041-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 09/06/2006] [Indexed: 10/23/2022]
Abstract
Rice was transformed with either long DNA-segments of random genomic DNA from rice, or centromere-specific DNA sequences from either maize or rice. Despite the repetitive nature of the transgenic DNA sequences, the centromere-specific sequences were inserted largely intact and behave as simple Mendelian units. Between 4 and 5% of bombarded callus clusters were transformed when bombarded with just pCAMBIA 1305.2. Frequency of recovery dropped to 2-3% when BACs with random genomic inserts were co-bombarded with pCAMBIA, and fell to less than 1% when BACs with centromeric DNA inserts and pCAMBIA were co-bombarded. A similar effect was noted on regeneration frequency. Differences in transformation ability, regeneration and behavior of plants transgenic for BACs with random genomic DNA inserts, as compared to those with centromeric DNA inserts, suggests functional differences between these two types of DNA.
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Affiliation(s)
- Bao H Phan
- Department of Crop and Soil Sciences, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
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Yang P, Liang Y, Shen S, Kuang T. Proteome analysis of rice uppermost internodes at the milky stage. Proteomics 2006; 6:3330-8. [PMID: 16637012 DOI: 10.1002/pmic.200500260] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Uppermost internodes, which connect the part between the ear and lower stem, form an important pathway transporting mineral nutrition from roots and photosynthates from leaves (especially the flag leaf) to the ear. The milky stage is the first stage of seed ripening. The uppermost internodes of rice at the milky stage are critical for seed quality and yield. Total soluble proteins of the uppermost internodes of rice (Oryza sativa L. ssp. indica) at the milky stage were analyzed using proteomic methods. Using 2-DE, 762 reproducible protein spots were detected. Among them, 132 abundant proteins were analyzed using MALDI-TOF-MS. Searching in the National Center for Biotechnology Information database, we could identify 98 proteins, which represent 80 gene products. These proteins belong to 11 functional groups with energy production-associated proteins in the first place. The large accumulation of proteins involved in metabolism, signaling, and stress resistance indicated that the uppermost internodes of rice have a high physiological and stress-resistant activity. In addition, our results will also enrich the database of the rice proteome.
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Affiliation(s)
- Pingfang Yang
- Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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35
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Ji W, Li Y, Li J, Dai CH, Wang X, Bai X, Cai H, Yang L, Zhu YM. Generation and analysis of expressed sequence tags from NaCl-treated Glycine soja. BMC PLANT BIOLOGY 2006; 6:4. [PMID: 16504061 PMCID: PMC1388217 DOI: 10.1186/1471-2229-6-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 02/22/2006] [Indexed: 05/06/2023]
Abstract
BACKGROUND Salinization causes negative effects on plant productivity and poses an increasingly serious threat to the sustainability of agriculture. Wild soybean (Glycine soja) can survive in highly saline conditions, therefore provides an ideal candidate plant system for salt tolerance gene mining. RESULTS As a first step towards the characterization of genes that contribute to combating salinity stress, we constructed a full-length cDNA library of Glycine soja (50109) leaf treated with 150 mM NaCl, using the SMART technology. Random expressed sequence tag (EST) sequencing of 2,219 clones produced 2,003 cleaned ESTs for gene expression analysis. The average read length of cleaned ESTs was 454 bp, with an average GC content of 40%. These ESTs were assembled using the PHRAP program to generate 375 contigs and 696 singlets. The resulting unigenes were categorized according to the Gene Ontology (GO) hierarchy. The potential roles of gene products associated with stress related ESTs were discussed. We compared the EST sequences of Glycine soja to that of Glycine max by using the blastn algorithm. Most expressed sequences from wild soybean exhibited similarity with soybean. All our EST data are available on the Internet (GenBank_Accn: DT082443-DT084445). CONCLUSION The Glycine soja ESTs will be used to mine salt tolerance gene, whose full-length cDNAs will be obtained easily from the full-length cDNA library. Comparison of Glycine soja ESTs with those of Glycine max revealed the potential to investigate the wild soybean's expression profile using the soybean's gene chip. This will provide opportunities to understand the genetic mechanisms underlying stress response of plants.
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Affiliation(s)
- Wei Ji
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Yong Li
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Jie Li
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Cui-hong Dai
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Xi Wang
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Xi Bai
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Hua Cai
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Liang Yang
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
| | - Yan-ming Zhu
- Plant Bioengineering Laboratory, Northeast Agricultural University, 150030 Harbin, China
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HongBo S, ZongSuo L, MingAn S. Changes of anti-oxidative enzymes and MDA content under soil water deficits among 10 wheat (Triticum aestivum L.) genotypes at maturation stage. Colloids Surf B Biointerfaces 2005; 45:7-13. [PMID: 16102947 DOI: 10.1016/j.colsurfb.2005.06.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Accepted: 06/21/2005] [Indexed: 11/18/2022]
Abstract
Drought is a world-spread problem seriously influencing grain production and quality, the loss of which is the total for other natural disasters, with increasing global climate change making the situation more serious. Wheat is the staple food for more than 35% of world population, so wheat anti-drought physiology study is of importance to wheat production and biological breeding for the sake of coping with abiotic and biotic conditions. Much research is involved in this hot topic, but the pace of progress is not so large because of drought resistance being a multiple-gene-control quantitative character and wheat genome being larger (16,000Mb). On the other hand, stress adaptive mechanisms are quite different, with stress degree, time course, materials, soil quality status and experimental plots, thus increasing the complexity of the issue in question. Additionally, a little study is related to the whole life circle of wheat, which cannot provide a comprehensive understanding of its anti-drought machinery. We selected 10 kinds of wheat genotypes as materials, which have potential to be applied in practice, and measured change of relative physiological indices through wheat whole growing-developmental circle (i.e. seedling, tillering and maturing). Here, we reported the anti-oxidative results of maturation stage (the results of seedling and tillering stage have been published) in terms of activities of POD, SOD, CAT and MDA content as follows: (1) 10 wheat genotypes can be grouped into three kinds (A-C, respectively) according to their changing trend of the measured indices; (2) A group performed better resistance drought under the condition of treatment level 1 (appropriate level), whose activities of anti-oxidative enzymes (POD, SOD, CAT) were higher and MDA lower; (3) B group exhibited stronger anti-drought under treatment level 2 (light-stress level), whose activities of anti-oxidative enzymes were higher and MDA lower; (4) C group expressed anti-drought to some extent under treatment level 3 (serious-stress level), whose activities of anti-oxidative enzymes were stronger, MDA lower; (5) these results demonstrated that different wheat genotypes have different physiological mechanisms to adapt themselves to changing drought stress, whose molecular basis is discrete gene expression profiling (transcriptom); (6) our results also showed that the concept and method accepted and adopted by most researchers [T.C. Hsiao, Plant response to water stress, Ann. Rev. Plant Physiol. 24 (1973) 519-570], that 75% FC is a proper supply for higher plants, was doubted, because this level could not reflect the true suitable level of different wheat genotypes. The study in this respect is the key to wheat anti-drought and biological-saving water agriculture; (7) our research can provide insights into physiological mechanisms of crop anti-drought and direct practical materials for wheat anti-drought breeding; (8) the physiological study of wheat is more urgent up-to-date and molecular aspects are needed, but cannot substitute this important part. The combination of both is an important strategy and a key and (9) POD, SOD and CAT activities and MDA content of different wheat genotypes had quite different changing trend at different stages and under different soil water stress conditions, which was linked with their origin of cultivation and individual soil water threshold.
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Affiliation(s)
- Shao HongBo
- Molecular Biology Laboratory, Bioinformatics College, Chongqing University of Posts and Telecommunications, Chongqing 400065, PR China.
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37
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Lei Z, Elmer AM, Watson BS, Dixon RA, Mendes PJ, Sumner LW. A Two-dimensional Electrophoresis Proteomic Reference Map and Systematic Identification of 1367 Proteins from a Cell Suspension Culture of the Model Legume Medicago truncatula. Mol Cell Proteomics 2005; 4:1812-25. [PMID: 16048909 DOI: 10.1074/mcp.d500005-mcp200] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proteome of a Medicago truncatula cell suspension culture was analyzed using two-dimensional electrophoresis and nanoscale HPLC coupled to a tandem Q-TOF mass spectrometer (QSTAR Pulsar i) to yield an extensive protein reference map. Coomassie Brilliant Blue R-250 was used to visualize more than 1661 proteins, which were excised, subjected to in-gel trypsin digestion, and analyzed using nanoscale HPLC/MS/MS. The resulting spectral data were queried against a custom legume protein database using the MASCOT search engine. A total of 1367 of the 1661 proteins were identified with high rigor, yielding an identification success rate of 83% and 907 unique protein accession numbers. Functional annotation of the M. truncatula suspension cell proteins revealed a complete tricarboxylic acid cycle, a nearly complete glycolytic pathway, a significant portion of the ubiquitin pathway with the associated proteolytic and regulatory complexes, and many enzymes involved in secondary metabolism such as flavonoid/isoflavonoid, chalcone, and lignin biosynthesis. Proteins were also identified from most other functional classes including primary metabolism, energy production, disease/defense, protein destination/storage, protein synthesis, transcription, cell growth/division, and signal transduction. This work represents the most extensive proteomic description of M. truncatula suspension cells to date and provides a reference map for future comparative proteomic and functional genomic studies of the response of these cells to biotic and abiotic stress.
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Affiliation(s)
- Zhentian Lei
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73402, USA
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38
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Shao HB, Liang ZS, Shao MA, Sun Q. Dynamic changes of anti-oxidative enzymes of 10 wheat genotypes at soil water deficits. Colloids Surf B Biointerfaces 2005; 42:187-95. [PMID: 15876527 DOI: 10.1016/j.colsurfb.2005.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Accepted: 02/25/2005] [Indexed: 10/25/2022]
Abstract
Drought is a world-spread problem seriously influencing crop production and quality, the loss of which is the total for other natural disasters, with increasing global climate change making the situation more serious. Wheat is the staple food for more than 35% of world population, so wheat anti-drought physiology study is of importance to wheat production and biological breeding for the sake of coping with abiotic and biotic conditions. Much research is involved in this hot topic, but the pace of progress is not so large because of drought resistance being a multiple-gene-control quantitative character and wheat genome being larger (16,000 Mb). On the other hand, stress adaptive mechanisms are quite different, with stress degree, different growth and developmental stages, time course, materials and experimental plots, thus increasing the complexity of the issue in question. Additionally, a little study is related to the whole life circle of wheat, which cannot provide a comprehensive understanding of its anti-drought machinery. We selected 10 kinds of wheat genotypes as materials, which have potential to be applied in practice, and measured change of relative physiological indices through wheat whole growing developmental circle (i.e. seedling, tillage and maturing). Here, we reported the dynamic anti-oxidative results of whole stage (i.e. seedling, tillage and maturing) in terms of activities of POD, SOD, CAT of 10 wheat genotypes as follows: (1) 10 wheat genotypes can be grouped into three kinds (A, B and C, respectively) according to their changing trend of the measured indices; (2) A group performed better resistance drought under the condition of treatment level 1, whose activities of anti-oxidative enzymes (POD, SOD, CAT) were higher; (3) B group exhibited stronger anti-drought under treatment level 2, whose activities of anti-oxidative enzymes were higher; (4) C group expressed anti-drought to some extent under treatment level 3, whose activities of anti-oxidative enzymes were stronger, MDA lower; (5) these results demonstrated that different wheat genotypes have different physiological mechanisms to adapt themselves to changing drought stress, whose molecular basis is discrete gene expression profiling (transcriptom); (6) our results also showed that the concept and method accepted and adopted by most researchers--that 75% FC is a proper supply for higher plants--was doubted because this level could not reflect the true suitable level of different wheat genotypes; (7) our research can provide insights into physiological mechanisms of crop anti-drought and direct practical materials for wheat anti-drought breeding; (8) POD, SOD and CAT activities of different wheat genotypes had quite different changing trend at different stages and under different soil water stress conditions, which was linked with their origin of cultivation and individual soil water stress threshold; (9) our primary results also firstly displayed that the changing trend for wheat adapting to environmental stress during life circle was an S-shaped curve, which is, by chance, consistent with Plant Growth Grand Periodicity Curve.
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Affiliation(s)
- Hong Bo Shao
- State Key Laboratory of Soil Erosion and Dryland Farming, The Center of Soil and Water Conservation and Ecoenvironmental Research, Chinese Academy of Sciences, Yangling 712100, People's Republic of China.
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39
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Adams RP, Morris JA, Pandey RN, Schwarzbach AE. Cryptic speciation between Juniperus deltoides and Juniperus oxycedrus (Cupressaceae) in the Mediterranean. BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2005.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Yang G, Komatsu S. Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice. GENOMICS PROTEOMICS & BIOINFORMATICS 2005; 2:77-83. [PMID: 15629047 PMCID: PMC5172446 DOI: 10.1016/s1672-0229(04)02013-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.
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41
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Hammer GL, Chapman S, van Oosterom E, Podlich DW. Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/ar05157] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits—phenology, osmotic adjustment, transpiration efficiency, stay-green—and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location–season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.
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42
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Sumner LW, Urbanczyk-Wochniak E, Broeckling CD. Metabolomics data analysis, visualization, and integration. Methods Mol Biol 2005; 406:409-36. [PMID: 18287705 DOI: 10.1007/978-1-59745-535-0_20] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Metabolomics is the large-scale analysis of metabolites and as such requires bioinformatics tools for data analysis, visualization, and integration. This chapter describes the basic composition of chromatographically coupled mass spectrometry (MS) data sets used in metabolomics and describes in detail the steps necessary for extracting large-scale qualitative and quantitative information. This process involves noise filtering, peak picking and deconvolution, peak identification, peak alignment, and the creation of a final data matrix for statistical processing. Multivariate tools for comparative analysis are presented and illustrated using data for Medicago truncatula. Additional tools for visualizing and integrating metabolomics data within a biological context are discussed. Two tables are provided listing current metabolomics data processing and visualization software. Because metabolomics is rapidly maturing, a final section is presented concerning the need for data standardization and current efforts.
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Affiliation(s)
- Lloyd W Sumner
- The Samuel Roberts Nobel Foundation, Plant Biology Division, Ardmore, OK, USA
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43
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Abstract
I present an algorithm that determines the longest path between every gene pair in an arbitrarily large genetic network from large scale gene perturbation data. The algorithm's computational complexity is O(nk(2)), where n is the number of genes in the network and k is the average number of genes affected by a genetic perturbation. The algorithm is able to distinguish a large fraction of direct regulatory interactions from indirect interactions, even if the accuracy of its input data is substantially compromised.
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Affiliation(s)
- Andreas Wagner
- University of New Mexico, Department of Biology, Albuquerque, NM 817131-1091, USA.
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44
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Cellini F, Chesson A, Colquhoun I, Constable A, Davies HV, Engel KH, Gatehouse AMR, Kärenlampi S, Kok EJ, Leguay JJ, Lehesranta S, Noteborn HPJM, Pedersen J, Smith M. Unintended effects and their detection in genetically modified crops. Food Chem Toxicol 2004; 42:1089-125. [PMID: 15123383 DOI: 10.1016/j.fct.2004.02.003] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2003] [Accepted: 02/04/2004] [Indexed: 11/28/2022]
Abstract
The commercialisation of GM crops in Europe is practically non-existent at the present time. The European Commission has instigated changes to the regulatory process to address the concerns of consumers and member states and to pave the way for removing the current moratorium. With regard to the safety of GM crops and products, the current risk assessment process pays particular attention to potential adverse effects on human and animal health and the environment. This document deals with the concept of unintended effects in GM crops and products, i.e. effects that go beyond that of the original modification and that might impact primarily on health. The document first deals with the potential for unintended effects caused by the processes of transgene insertion (DNA rearrangements) and makes comparisons with genetic recombination events and DNA rearrangements in traditional breeding. The document then focuses on the potential value of evolving "profiling" or "omics" technologies as non-targeted, unbiased approaches, to detect unintended effects. These technologies include metabolomics (parallel analysis of a range of primary and secondary metabolites), proteomics (analysis of polypeptide complement) and transcriptomics (parallel analysis of gene expression). The technologies are described, together with their current limitations. Importantly, the significance of unintended effects on consumer health are discussed and conclusions and recommendations presented on the various approaches outlined.
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Affiliation(s)
- F Cellini
- Metapontum Agrobios, SS Jonica Km 448.2, I-75010 Metaponto Matera, Italy
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Britto DT, Kronzucker HJ. Bioengineering nitrogen acquisition in rice: can novel initiatives in rice genomics and physiology contribute to global food security? Bioessays 2004; 26:683-92. [PMID: 15170866 DOI: 10.1002/bies.20040] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rice is the most important crop species on earth, providing staple food for 70% of the world's human population. Over the past four decades, successes in classical breeding, fertilization, pest control, irrigation and expansion of arable land have massively increased global rice production, enabling crop scientists and farmers to stave off anticipated famines. If current projections for human population growth are correct, however, present rice yields will be insufficient within a few years. Rice yields will have to increase by an estimated 60% in the next 30 years, or global food security will be in danger. The classical methods of previous green revolutions alone will probably not be able to meet this challenge, without being coupled to recombinant DNA technology. Here, we focus on the promise of these modern technologies in the area of nitrogen acquisition in rice, recognizing that nitrogen deficiency compromises the realization of rice yield potential in the field more than any other single factor. We summarize rice-specific advances in four key areas of research: (1). nitrogen fixation, (2). primary nitrogen acquisition, (3). manipulations of internal nitrogen metabolism, and (4). interactions between nitrogen and photosynthesis. We develop a model for future plant breeding possibilities, pointing out the importance of coming to terms with the complex interactions among the physiological components under manipulation, in the context of ensuring proper targeting of intellectual and financial resources in this crucial area of research.
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Affiliation(s)
- Dev T Britto
- Department of Life Sciences, University of Toronto, Canada
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46
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Brinker M, van Zyl L, Liu W, Craig D, Sederoff RR, Clapham DH, von Arnold S. Microarray analyses of gene expression during adventitious root development in Pinus contorta. PLANT PHYSIOLOGY 2004; 135:1526-39. [PMID: 15247392 PMCID: PMC519068 DOI: 10.1104/pp.103.032235] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2003] [Revised: 04/15/2004] [Accepted: 04/15/2004] [Indexed: 05/18/2023]
Abstract
In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta.
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Affiliation(s)
- Monika Brinker
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.
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Facchini PJ, Bird DA, St-Pierre B. Can Arabidopsis make complex alkaloids? TRENDS IN PLANT SCIENCE 2004; 9:116-22. [PMID: 15003234 DOI: 10.1016/j.tplants.2004.01.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
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Vincentz M, Cara FAA, Okura VK, da Silva FR, Pedrosa GL, Hemerly AS, Capella AN, Marins M, Ferreira PC, França SC, Grivet L, Vettore AL, Kemper EL, Burnquist WL, Targon MLP, Siqueira WJ, Kuramae EE, Marino CL, Camargo LEA, Carrer H, Coutinho LL, Furlan LR, Lemos MVF, Nunes LR, Gomes SL, Santelli RV, Goldman MH, Bacci M, Giglioti EA, Thiemann OH, Silva FH, Van Sluys MA, Nobrega FG, Arruda P, Menck CFM. Evaluation of monocot and eudicot divergence using the sugarcane transcriptome. PLANT PHYSIOLOGY 2004; 134:951-9. [PMID: 15020759 PMCID: PMC389918 DOI: 10.1104/pp.103.033878] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
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Affiliation(s)
- Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Universidade de Campinas, Caixa Postal 6010, 13083-970, Campinas SP, Brazil
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Yamanaka S, Suzuki E, Tanaka M, Takeda Y, Watanabe JA, Watanabe KN. Assessment of cytochrome P450 sequences offers a useful tool for determining genetic diversity in higher plant species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 108:1-9. [PMID: 13679989 DOI: 10.1007/s00122-003-1403-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2003] [Accepted: 07/14/2003] [Indexed: 05/24/2023]
Abstract
To investigate and develop new genetic tools for assessing genome-wide diversity in higher plant-species, polymorphisms of gene analogues of mammalian cytochrome P450 mono-oxygenases were studied. Data mining on Arabidopsis thaliana indicated that a small number of primer-sets derived from P450 genes could provide universal tools for the assessment of genome-wide genetic diversity in diverse plant species that do not have relevant genetic markers, or for which, there is no prior inheritance knowledge of inheritance traits. Results from PCR amplification of 51 plant species from 28 taxonomic families using P450 gene-primer sets suggested that there were at least several mammalian P450 gene mammalian-analogues in plants. Intra- and inter- specific variations were demonstrated following PCR amplifications of P450 analogue fragments, and this suggested that these would be effective genetic markers for the assessment of genetic diversity in plants. In addition, BLAST search analysis revealed that these amplified fragments possessed homologies to other genes and proteins in different plant varieties. We conclude that the sequence diversity of P450 gene-analogues in different plant species reflects the diversity of functional regions in the plant genome and is therefore an effective tool in functional genomic studies of plants.
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Affiliation(s)
- S Yamanaka
- Gene Research Center, Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8572, Tsukuba, Japan
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