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Pradhan UK, Mahapatra A, Naha S, Gupta A, Parsad R, Gahlaut V, Rath SN, Meher PK. ASPTF: A computational tool to predict abiotic stress-responsive transcription factors in plants by employing machine learning algorithms. Biochim Biophys Acta Gen Subj 2024; 1868:130597. [PMID: 38490467 DOI: 10.1016/j.bbagen.2024.130597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/10/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Abiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic stresses. Therefore, it is crucial to identify TFs associated with abiotic stress response for breeding of abiotic stress tolerant crop cultivars. METHODS Based on a machine learning framework, a computational model was envisaged to predict TFs associated with abiotic stress response in plants. To numerically encode TF sequences, four distinct sequence derived features were generated. The prediction was performed using ten shallow learning and four deep learning algorithms. For prediction using more pertinent and informative features, feature selection techniques were also employed. RESULTS Using the features chosen by the light-gradient boosting machine-variable importance measure (LGBM-VIM), the LGBM achieved the highest cross-validation performance metrics (accuracy: 86.81%, auROC: 92.98%, and auPRC: 94.03%). Further evaluation of the proposed model (LGBM prediction method + LGBM-VIM selected features) was also done using an independent test dataset, where the accuracy, auROC and auPRC were observed 81.98%, 90.65% and 91.30%, respectively. CONCLUSIONS To facilitate the adoption of the proposed strategy by users, the approach was implemented as a prediction server called ASPTF, accessible at https://iasri-sg.icar.gov.in/asptf/. The developed approach and the corresponding web application are anticipated to supplement experimental methods in the identification of transcription factors (TFs) responsive to abiotic stress in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Anuradha Mahapatra
- Department of Bioinformatics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
| | - Vijay Gahlaut
- University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India.
| | - Surya Narayan Rath
- Department of Bioinformatics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, Odisha, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India.
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Pradhan UK, Meher PK, Naha S, Rao AR, Kumar U, Pal S, Gupta A. ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Funct Integr Genomics 2023; 23:92. [PMID: 36939943 DOI: 10.1007/s10142-023-01014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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Brewster C, Hayes F, Fenner N. Ozone Tolerance Found in Aegilops tauschii and Primary Synthetic Hexaploid Wheat. PLANTS (BASEL, SWITZERLAND) 2019; 8:E195. [PMID: 31261799 PMCID: PMC6681361 DOI: 10.3390/plants8070195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022]
Abstract
Modern wheat cultivars are increasingly sensitive to ground level ozone, with 7-10% mean yield reductions in the northern hemisphere. In this study, three of the genome donors of bread wheat, Triticum urartu (AA), T. dicoccoides (AABB), and Aegilops tauschii (DD) along with a modern wheat cultivar (T. aestivum 'Skyfall'), a 1970s cultivar (T. aestivum 'Maris Dove'), and a line of primary Synthetic Hexaploid Wheat were grown in 6 L pots of sandy loam soil in solardomes (Bangor, North Wales) and exposed to low (30 ppb), medium (55 ppb), and high (110 ppb) levels of ozone over 3 months. Measurements were made at harvest of shoot biomass and grain yield. Ae. tauschii appeared ozone tolerant with no significant effects of ozone on shoot biomass, seed head biomass, or 1000 grain + husk weight even under high ozone levels. In comparison, T. urartu had a significant reduction in 1000 grain + husk weight, especially under high ozone (-26%). The older cultivar, 'Maris Dove', had a significant reduction in seed head biomass (-9%) and 1000 grain weight (-11%) but was less sensitive than the more recent cultivar 'Skyfall', which had a highly significant reduction in its seed head biomass (-21%) and 1000 grain weight (-27%) under high ozone. Notably, the line of primary Synthetic Hexaploid Wheat was ozone tolerant, with no effect on total seed head biomass (-1%) and only a 5% reduction in 1000 grain weight under high ozone levels. The potential use of synthetic wheat in breeding ozone tolerant wheat is discussed.
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Affiliation(s)
- Clare Brewster
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor LL57 2UW, UK.
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK.
| | - Felicity Hayes
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor LL57 2UW, UK
| | - Nathalie Fenner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
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Brew-Appiah RAT, Peracchi LM, Sanguinet KA. Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon. PLANTS 2019; 8:plants8060153. [PMID: 31174296 PMCID: PMC6630600 DOI: 10.3390/plants8060153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 11/25/2022]
Abstract
Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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Miroshnichenko D, Ashin D, Pushin A, Dolgov S. Genetic transformation of einkorn (Triticum monococcum L. ssp. monococcum L.), a diploid cultivated wheat species. BMC Biotechnol 2018; 18:68. [PMID: 30352590 PMCID: PMC6199808 DOI: 10.1186/s12896-018-0477-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Domesticated einkorn (Triticum monococcum L.) is one of the oldest cultivated cereal crops in the world. Its small genome size (~ 5.7 GB), low ploidy (2n = 2x = 14, AmAm) and high genetic polymorphism make this species very attractive for use as a diploid model for understanding the genomics and proteomics of Triticeae. Einkorn, however, is still a recalcitrant monocotyledonous species for the application of modern biotechnologies, including transgenesis. This paper reports the factors that may influence transgene delivery, integration, expression and inheritance in einkorn. RESULTS In this study, we report the successful genetic transformation of einkorn using biolistic-mediated DNA delivery. Immature embryo-derived tissues of spring einkorn were bombarded with a plasmid containing the reporter gene GFP (green fluorescent protein) driven by the rice actin promoter (act1) and the selectable bar gene (bialaphos resistance gene) driven by the maize ubiquitin promoter (ubi1). Adjustments to various parameters such as gas pressure, microcarrier size and developmental stage of target tissue were essential for successful transient and stable transformation. Bombarded einkorn tissues are recalcitrant to regenerating plants, but certain modifications of the culture medium have been shown to increase the production of transgenic events. In various experiments, independent transgenic plants were produced at frequencies ranging from 0.0 to 0.6%. Molecular analysis, marker gene expression and herbicide treatment demonstrated that gfp/bar genes were stably integrated into the einkorn genome and successfully inherited over several generations. The transgenes, as dominant loci, segregated in both Mendelian and non-Mendelian fashion due to multiple insertions. Fertile homozygous T1-T2 populations of transgenic einkorn that are resistant to herbicides were selected. CONCLUSION To the best of our knowledge, this is the first report of the production of genetically modified einkorn plants. We believe that the results of our research could be a starting point for the application of the current biotechnological-based technologies, such as transgenesis and genome editing, to accelerate comparative functional genomics in einkorn and other cereals.
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Affiliation(s)
- Dmitry Miroshnichenko
- Institute of Basic Biological Problems RAS, Pushchino, Moscow Region Russian Federation
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino, Moscow Region Russian Federation
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russian Federation
| | - Danila Ashin
- Institute of Basic Biological Problems RAS, Pushchino, Moscow Region Russian Federation
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino, Moscow Region Russian Federation
| | - Alexander Pushin
- Institute of Basic Biological Problems RAS, Pushchino, Moscow Region Russian Federation
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino, Moscow Region Russian Federation
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russian Federation
| | - Sergey Dolgov
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino, Moscow Region Russian Federation
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russian Federation
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Vu LD, Zhu T, Verstraeten I, van de Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4609-4624. [PMID: 29939309 PMCID: PMC6117581 DOI: 10.1093/jxb/ery204] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 05/20/2023]
Abstract
Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.
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Affiliation(s)
- Lam Dai Vu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Tingting Zhu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Inge Verstraeten
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte van de Cotte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Takahagi K, Inoue K, Mochida K. Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1163. [PMID: 30135697 PMCID: PMC6092485 DOI: 10.3389/fpls.2018.01163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/23/2018] [Indexed: 05/20/2023]
Abstract
Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.
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Affiliation(s)
- Kotaro Takahagi
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- *Correspondence: Keiichi Mochida,
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8
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Taran N, Storozhenko V, Svietlova N, Batsmanova L, Shvartau V, Kovalenko M. Effect of Zinc and Copper Nanoparticles on Drought Resistance of Wheat Seedlings. NANOSCALE RESEARCH LETTERS 2017; 12:60. [PMID: 28105609 PMCID: PMC5247391 DOI: 10.1186/s11671-017-1839-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/10/2017] [Indexed: 05/20/2023]
Abstract
The effect of a colloidal solution of Cu,Zn-nanoparticles on pro-oxidative/antioxidative balance and content of photosynthetic pigments and leaf area of winter wheat plants of steppe (Acveduc) and forest-steppe (Stolichna) ecotypes was investigated in drought conditions. It has been shown that Cu,Zn-nanoparticles decreased the negative effect of drought action upon plants of steppe ecotype Acveduc. In particular, increased activity of antioxidative enzymes reduced the level of accumulation of thiobarbituric acid reactive substances (TBARS) and stabilized the content of photosynthetic pigments and increased relative water content in leaves. Colloidal solution of Cu,Zn-nanoparticles had less significant influence on these indexes in seedlings of the Stolichna variety under drought.
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Affiliation(s)
- Nataliya Taran
- Educational and Scientific Centre ‘Institute of Biology and Medicine’, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv, 01601 Ukraine
| | - Volodymyr Storozhenko
- Educational and Scientific Centre ‘Institute of Biology and Medicine’, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv, 01601 Ukraine
| | - Nataliia Svietlova
- Educational and Scientific Centre ‘Institute of Biology and Medicine’, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv, 01601 Ukraine
| | - Ludmila Batsmanova
- Educational and Scientific Centre ‘Institute of Biology and Medicine’, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv, 01601 Ukraine
| | - Viktor Shvartau
- Institute of Plant Physiology and Genetics, National Academy of Sciences of Ukraine, 31/17, Vasylkivska St., Kyiv, 03022 Ukraine
| | - Mariia Kovalenko
- Educational and Scientific Centre ‘Institute of Biology and Medicine’, Taras Shevchenko National University of Kyiv, 64/13, Volodymyrska Street, Kyiv, 01601 Ukraine
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Shah ZH, Rehman HM, Akhtar T, Daur I, Nawaz MA, Ahmad MQ, Rana IA, Atif RM, Yang SH, Chung G. Redox and Ionic Homeostasis Regulations against Oxidative, Salinity and Drought Stress in Wheat (A Systems Biology Approach). Front Genet 2017; 8:141. [PMID: 29089961 PMCID: PMC5651134 DOI: 10.3389/fgene.2017.00141] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/21/2017] [Indexed: 01/21/2023] Open
Abstract
Systems biology and omics has provided a comprehensive understanding about the dynamics of the genome, metabolome, transcriptome, and proteome under stress. In wheat, abiotic stresses trigger specific networks of pathways involved in redox and ionic homeostasis as well as osmotic balance. These networks are considerably more complicated than those in model plants, and therefore, counter models are proposed by unifying the approaches of omics and stress systems biology. Furthermore, crosstalk among these pathways is monitored by the regulation and streaming of transcripts and genes. In this review, we discuss systems biology and omics as a promising tool to study responses to oxidative, salinity, and drought stress in wheat.
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Affiliation(s)
- Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronics and Biomedical Engineering, Chonnam National University, Yeosu, South Korea
| | - Tasneem Akhtar
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ihsanullah Daur
- Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad A. Nawaz
- Department of Electronics and Biomedical Engineering, Chonnam National University, Yeosu, South Korea
| | - Muhammad Q. Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Iqrar A. Rana
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Rana M. Atif
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Seung H. Yang
- Department of Electronics and Biomedical Engineering, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Electronics and Biomedical Engineering, Chonnam National University, Yeosu, South Korea
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Xia C, Zhang L, Zou C, Gu Y, Duan J, Zhao G, Wu J, Liu Y, Fang X, Gao L, Jiao Y, Sun J, Pan Y, Liu X, Jia J, Kong X. A TRIM insertion in the promoter of Ms2 causes male sterility in wheat. Nat Commun 2017; 8:15407. [PMID: 28497807 PMCID: PMC5437302 DOI: 10.1038/ncomms15407] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/25/2017] [Indexed: 11/09/2022] Open
Abstract
The male-sterile ms2 mutant has been known for 40 years and has become extremely important in the commercial production of wheat. However, the gene responsible for this phenotype has remained unknown. Here we report the map-based cloning of the Ms2 gene. The Ms2 locus is remarkable in several ways that have implications in basic biology. Beyond having no functional annotation, barely detectable transcription in fertile wild-type wheat plants, and accumulated destructive mutations in Ms2 orthologs, the Ms2 allele in the ms2 mutant has acquired a terminal-repeat retrotransposon in miniature (TRIM) element in its promoter. This TRIM element is responsible for the anther-specific Ms2 activation that confers male sterility. The identification of Ms2 not only unravels the genetic basis of a historically important breeding trait, but also shows an example of how a TRIM element insertion near a gene can contribute to genetic novelty and phenotypic plasticity.
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Affiliation(s)
- Chuan Xia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lichao Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Zou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongqiang Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, California 94710, USA
| | - Jialei Duan
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiajie Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaohua Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lifeng Gao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jiaqiang Sun
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghong Pan
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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11
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Alptekin B, Langridge P, Budak H. Abiotic stress miRNomes in the Triticeae. Funct Integr Genomics 2017; 17:145-170. [PMID: 27665284 PMCID: PMC5383695 DOI: 10.1007/s10142-016-0525-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/02/2016] [Accepted: 09/09/2016] [Indexed: 12/14/2022]
Abstract
The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.
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Affiliation(s)
- Burcu Alptekin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Peter Langridge
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Hikmet Budak
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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12
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Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System. PLoS One 2017; 12:e0169686. [PMID: 28103252 PMCID: PMC5245863 DOI: 10.1371/journal.pone.0169686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 11/23/2022] Open
Abstract
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.
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13
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Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017; 8:2055. [PMID: 29234348 PMCID: PMC5712366 DOI: 10.3389/fpls.2017.02055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/16/2017] [Indexed: 05/08/2023]
Abstract
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis. The expression data are feasible to infer network sparsity based on ARX models. We found that genes involved in biological processes such as transcriptional regulation, protein degradation, and post-transcriptional modification and photosynthesis are significantly enriched in the periodic genes, suggesting that these processes might be regulated by circadian rhythm in B. distachyon. On the basis of the time-series expression patterns of the periodic genes, we constructed a chronological gene co-expression network and identified putative transcription factors encoding genes that might be involved in the time-specific regulatory transcriptional network. Moreover, we inferred a transcriptional network composed of the periodic genes in B. distachyon, aiming to identify genes associated with other genes through variable selection by grouping time points for each gene. Based on the ARX model with the group SCAD regularization using our time-series expression datasets of the periodic genes, we constructed gene networks and found that the networks represent typical scale-free structure. Our findings demonstrate that the diurnal changes in the transcriptome in B. distachyon leaves have a sparse network structure, demonstrating the spatiotemporal gene regulatory network over the cyclic phase transitions in B. distachyon diurnal growth.
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Affiliation(s)
- Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | | | - Kotaro Takahagi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Kochi, Japan
| | - Hiroshi Honda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Shinto Eguchi
- The Institute of Statistical Mathematics, Tokyo, Japan
| | - Ryuei Nishii
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
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14
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Akpinar BA, Lucas S, Budak H. A large-scale chromosome-specific SNP discovery guideline. Funct Integr Genomics 2016; 17:97-105. [PMID: 27900504 DOI: 10.1007/s10142-016-0536-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/06/2016] [Accepted: 11/09/2016] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Stuart Lucas
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey. .,Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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15
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Cieśla A, Mituła F, Misztal L, Fedorowicz-Strońska O, Janicka S, Tajdel-Zielińska M, Marczak M, Janicki M, Ludwików A, Sadowski J. A Role for Barley Calcium-Dependent Protein Kinase CPK2a in the Response to Drought. FRONTIERS IN PLANT SCIENCE 2016; 7:1550. [PMID: 27826303 PMCID: PMC5078816 DOI: 10.3389/fpls.2016.01550] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/03/2016] [Indexed: 05/30/2023]
Abstract
Increasing the drought tolerance of crops is one of the most challenging goals in plant breeding. To improve crop productivity during periods of water deficit, it is essential to understand the complex regulatory pathways that adapt plant metabolism to environmental conditions. Among various plant hormones and second messengers, calcium ions are known to be involved in drought stress perception and signaling. Plants have developed specific calcium-dependent protein kinases that convert calcium signals into phosphorylation events. In this study we attempted to elucidate the role of a calcium-dependent protein kinase in the drought stress response of barley (Hordeum vulgare L.), one of the most economically important crops worldwide. The ongoing barley genome project has provided useful information about genes potentially involved in the drought stress response, but information on the role of calcium-dependent kinases is still limited. We found that the gene encoding the calcium-dependent protein kinase HvCPK2a was significantly upregulated in response to drought. To better understand the role of HvCPK2a in drought stress signaling, we generated transgenic Arabidopsis plants that overexpressed the corresponding coding sequence. Overexpressing lines displayed drought sensitivity, reduced nitrogen balance index (NBI), an increase in total chlorophyll content and decreased relative water content. In addition, in vitro kinase assay experiments combined with mass spectrometry allowed HvCPK2a autophosphorylation sites to be identified. Our results suggest that HvCPK2a is a dual-specificity calcium-dependent protein kinase that functions as a negative regulator of the drought stress response in barley.
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Affiliation(s)
- Agata Cieśla
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Filip Mituła
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Lucyna Misztal
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | | | - Sabina Janicka
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | | | - Małgorzata Marczak
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Maciej Janicki
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Agnieszka Ludwików
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
| | - Jan Sadowski
- Biotechnology Department, Faculty of Biology, Adam Mickiewicz UniversityPoznań, Poland
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16
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Majka J, Majka M, Kwiatek M, Wiśniewska H. Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH). J Appl Genet 2016; 58:151-161. [PMID: 27743251 PMCID: PMC5391381 DOI: 10.1007/s13353-016-0369-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 01/29/2023]
Abstract
In this paper, we highlight the affinity between the genomes of key representatives of the Pooideae subfamily, revealed at the chromosomal level by genomic in situ hybridization (GISH). The analyses were conducted using labeled probes from each species to hybridize with chromosomes of every species used in this study based on a “round robin” rule. As a result, the whole chromosomes or chromosome regions were distinguished or variable types of signals were visualized to prove the different levels of the relationships between genomes used in this study. We observed the unexpected lack of signals in secondary constrictions of rye (RR) chromosomes probed by triticale (AABBRR) genomic DNA. We have also identified unlabeled chromosome regions, which point to species-specific sequences connected with disparate pathways of chromosome differentiation. Our results revealed a conservative character of coding sequence of 35S rDNA among selected species of the genera Aegilops, Brachypodium, Festuca, Hordeum, Lolium, Secale, and Triticum. In summary, we showed strong relationships in genomic DNA sequences between species which have been previously reported to be phylogenetically distant.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maciej Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Halina Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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17
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Tyler L, Lee SJ, Young ND, DeIulio GA, Benavente E, Reagon M, Sysopha J, Baldini RM, Troìa A, Hazen SP, Caicedo AL. Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas. THE PLANT GENOME 2016; 9. [PMID: 27898828 DOI: 10.3835/plantgenome2015.08.0074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The small, annual grass (L.) Beauv., a close relative of wheat ( L.) and barley ( L.), is a powerful model system for cereals and bioenergy grasses. Genome-wide association studies (GWAS) of natural variation can elucidate the genetic basis of complex traits but have been so far limited in by the lack of large numbers of well-characterized and sufficiently diverse accessions. Here, we report on genotyping-by-sequencing (GBS) of 84 , seven , and three accessions with diverse geographic origins including Albania, Armenia, Georgia, Italy, Spain, and Turkey. Over 90,000 high-quality single-nucleotide polymorphisms (SNPs) distributed across the Bd21 reference genome were identified. Our results confirm the hybrid nature of the genome, which appears as a mosaic of -like and -like sequences. Analysis of more than 50,000 SNPs for the accessions revealed three distinct, genetically defined populations. Surprisingly, these genomic profiles are associated with differences in flowering time rather than with broad geographic origin. High levels of differentiation in loci associated with floral development support the differences in flowering phenology between populations. Genome-wide association studies combining genotypic and phenotypic data also suggest the presence of one or more photoperiodism, circadian clock, and vernalization genes in loci associated with flowering time variation within populations. Our characterization elucidates genes underlying population differences, expands the germplasm resources available for , and illustrates the feasibility and limitations of GWAS in this model grass.
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18
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Onda Y, Hashimoto K, Yoshida T, Sakurai T, Sawada Y, Hirai MY, Toyooka K, Mochida K, Shinozaki K. Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proc Biol Sci 2016; 282:rspb.2015.0964. [PMID: 26156770 PMCID: PMC4528556 DOI: 10.1098/rspb.2015.0964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Brachypodium distachyon is an emerging model plant for studying biological phenomena in temperate grasses. Study of the growth scale is essential to analyse spatio-temporal changes in molecular factors throughout the life cycle. For sensitive and robust staging based on morphology in B. distachyon, we demonstrated the utility of the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemical industry) scale, which is comparable to the Zadoks scale conventionally used for Triticeae crops. We compared the chronological progression of B. distachyon accessions Bd21 and Bd3-1, in addition to the progression of Chinese Spring wheat. The comparison of growth stages illustrates the morphological similarities and differences in the timing of life cycle events. Furthermore, we compared metabolite accumulation patterns across different growth stages and across different stress conditions using a widely targeted metabolome analysis. Metabolic profiling determined commonalities and specificities in chemical properties that were dependent on organisms, growth stages and/or stress conditions. Most metabolites accumulated equivalently in B. distachyon and wheat. This qualitative similarity indicated the superiority of B. distachyon as a model for Triticeae crops. The growth scale of B. distachyon should provide a conceptual framework for comparative analysis and for knowledge integration between this model grass and crops in the Pooideae subfamily.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kei Hashimoto
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Yuji Sawada
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Masami Yokota Hirai
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Kiminori Toyooka
- Technology Platform Division, Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Biomass Research Platform Team, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
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19
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Alptekin B, Budak H. Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Funct Integr Genomics 2016; 17:171-187. [PMID: 27032785 DOI: 10.1007/s10142-016-0487-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 12/24/2022]
Abstract
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.
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Affiliation(s)
- Burcu Alptekin
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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20
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Kaur S, Dhugga KS, Gill K, Singh J. Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.). PLoS One 2016; 11:e0147046. [PMID: 26771740 PMCID: PMC4714848 DOI: 10.1371/journal.pone.0147046] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production.
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Affiliation(s)
- Simerjeet Kaur
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Kanwarpal S. Dhugga
- Genetic Discovery, DuPont Pioneer, 7300 NW 62nd Avenue, Johnston, IA, United States of America
| | - Kulvinder Gill
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States of America
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
- * E-mail:
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21
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Spannagl M, Nussbaumer T, Bader KC, Martis MM, Seidel M, Kugler KG, Gundlach H, Mayer KFX. PGSB PlantsDB: updates to the database framework for comparative plant genome research. Nucleic Acids Res 2015; 44:D1141-7. [PMID: 26527721 PMCID: PMC4702821 DOI: 10.1093/nar/gkv1130] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/15/2015] [Indexed: 01/29/2023] Open
Abstract
PGSB (Plant Genome and Systems Biology: formerly MIPS) PlantsDB (http://pgsb.helmholtz-muenchen.de/plant/index.jsp) is a database framework for the comparative analysis and visualization of plant genome data. The resource has been updated with new data sets and types as well as specialized tools and interfaces to address user demands for intuitive access to complex plant genome data. In its latest incarnation, we have re-worked both the layout and navigation structure and implemented new keyword search options and a new BLAST sequence search functionality. Actively involved in corresponding sequencing consortia, PlantsDB has dedicated special efforts to the integration and visualization of complex triticeae genome data, especially for barley, wheat and rye. We enhanced CrowsNest, a tool to visualize syntenic relationships between genomes, with data from the wheat sub-genome progenitor Aegilops tauschii and added functionality to the PGSB RNASeqExpressionBrowser. GenomeZipper results were integrated for the genomes of barley, rye, wheat and perennial ryegrass and interactive access is granted through PlantsDB interfaces. Data exchange and cross-linking between PlantsDB and other plant genome databases is stimulated by the transPLANT project (http://transplantdb.eu/).
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Affiliation(s)
- Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thomas Nussbaumer
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Kai C Bader
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Mihaela M Martis
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany BILS (Bioinformatics Infrastructure for Life Sciences), Division of Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, SE-558185 Linköping, Sweden
| | - Michael Seidel
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Karl G Kugler
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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22
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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23
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Delaplace P, Delory BM, Baudson C, Mendaluk-Saunier de Cazenave M, Spaepen S, Varin S, Brostaux Y, du Jardin P. Influence of rhizobacterial volatiles on the root system architecture and the production and allocation of biomass in the model grass Brachypodium distachyon (L.) P. Beauv. BMC PLANT BIOLOGY 2015; 15:195. [PMID: 26264238 PMCID: PMC4531529 DOI: 10.1186/s12870-015-0585-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plant growth-promoting rhizobacteria are increasingly being seen as a way of complementing conventional inputs in agricultural systems. The effects on their host plants are diverse and include volatile-mediated growth enhancement. This study sought to assess the effects of bacterial volatiles on the biomass production and root system architecture of the model grass Brachypodium distachyon (L.) Beauv. RESULTS An in vitro experiment allowing plant-bacteria interaction throughout the gaseous phase without any physical contact was used to screen 19 bacterial strains for their growth-promotion ability over a 10-day co-cultivation period. Five groups of bacteria were defined and characterised based on their combined influence on biomass production and root system architecture. The observed effects ranged from unchanged to greatly increased biomass production coupled with increased root length and branching. Primary root length was increased only by the volatile compounds emitted by Enterobacter cloacae JM22 and Bacillus pumilus T4. Overall, the most significant results were obtained with Bacillus subtilis GB03, which induced an 81 % increase in total biomass, as well as enhancing total root length, total secondary root length and total adventitious root length by 88.5, 201.5 and 474.5 %, respectively. CONCLUSIONS This study is the first report on bacterial volatile-mediated growth promotion of a grass plant. Contrasting modulations of biomass production coupled with changes in root system architecture were observed. Most of the strains that increased total plant biomass also modulated adventitious root growth. Under our screening conditions, total biomass production was strongly correlated with the length and branching of the root system components, except for primary root length. An analysis of the emission kinetics of the bacterial volatile compounds is being undertaken and should lead to the identification of the compounds responsible for the observed growth-promotion effects. Within the context of the inherent characteristics of our in vitro system, this paper identifies the next critical experimental steps and discusses them from both a fundamental and an applied perspective.
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Affiliation(s)
- Pierre Delaplace
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Benjamin M Delory
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Caroline Baudson
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | | | - Stijn Spaepen
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
| | - Sébastien Varin
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Yves Brostaux
- University of Liège, Gembloux Agro-Bio Tech, Applied Statistics, Computer Science and Modeling, Passage des Déportés 2, 5030, Gembloux, Belgium.
| | - Patrick du Jardin
- University of Liège, Gembloux Agro-Bio Tech, Plant Biology, Passage des Déportés 2, 5030, Gembloux, Belgium.
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24
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González-Calle V, Barrero-Sicilia C, Carbonero P, Iglesias-Fernández R. Mannans and endo-β-mannanases (MAN) in Brachypodium distachyon: expression profiling and possible role of the BdMAN genes during coleorhiza-limited seed germination. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3753-64. [PMID: 25922488 PMCID: PMC4473977 DOI: 10.1093/jxb/erv168] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Immunolocalization of mannans in the seeds of Brachypodium distachyon reveals the presence of these polysaccharides in the root embryo and in the coleorhiza in the early stages of germination (12h), decreasing thereafter to the point of being hardly detected at 27h. Concurrently, the activity of endo-β-mannanases (MANs; EC 3.2.1.78) that catalyse the hydrolysis of β-1,4 bonds in mannan polymers, increases as germination progresses. The MAN gene family is represented by six members in the Brachypodium genome, and their expression has been explored in different organs and especially in germinating seeds. Transcripts of BdMAN2, BdMAN4 and BdMAN6 accumulate in embryos, with a maximum at 24-30h, and are detected in the coleorhiza and in the root by in situ hybridization analyses, before root protrusion (germination sensu stricto). BdMAN4 is not only present in the embryo root and coleorhiza, but is abundant in the de-embryonated (endosperm) imbibed seeds, while BdMAN2 and BdMAN6 are faintly expressed in endosperm during post-germination (36-42h). BdMAN4 and BdMAN6 transcripts are detected in the aleurone layer. These data indicate that BdMAN2, BdMAN4 and BdMAN6 are important for germination sensu stricto and that BdMAN4 and BdMAN6 may also influence reserve mobilization. Whether the coleorhiza in monocots and the micropylar endosperm in eudicots have similar functions, is discussed.
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Affiliation(s)
- Virginia González-Calle
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Cristina Barrero-Sicilia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and ETSI Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
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25
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Noda S, Shirai T, Mochida K, Matsuda F, Oyama S, Okamoto M, Kondo A. Evaluation of Brachypodium distachyon L-Tyrosine Decarboxylase Using L-Tyrosine Over-Producing Saccharomyces cerevisiae. PLoS One 2015; 10:e0125488. [PMID: 25996877 PMCID: PMC4440718 DOI: 10.1371/journal.pone.0125488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/14/2015] [Indexed: 11/18/2022] Open
Abstract
To demonstrate that herbaceous biomass is a versatile gene resource, we focused on the model plant Brachypodium distachyon, and screened the B. distachyon for homologs of tyrosine decarboxylase (TDC), which is involved in the modification of aromatic compounds. A total of 5 candidate genes were identified in cDNA libraries of B. distachyon and were introduced into Saccharomyces cerevisiae to evaluate TDC expression and tyramine production. It is suggested that two TDCs encoded in the transcripts Bradi2g51120.1 and Bradi2g51170.1 have L-tyrosine decarboxylation activity. Bradi2g51170.1 was introduced into the L-tyrosine over-producing strain of S. cerevisiae that was constructed by the introduction of mutant genes that promote deregulated feedback inhibition. The amount of tyramine produced by the resulting transformant was 6.6-fold higher (approximately 200 mg/L) than the control strain, indicating that B. distachyon TDC effectively converts L-tyrosine to tyramine. Our results suggest that B. distachyon possesses enzymes that are capable of modifying aromatic residues, and that S. cerevisiae is a suitable host for the production of L-tyrosine derivatives.
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Affiliation(s)
- Shuhei Noda
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Tomokazu Shirai
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Keiichi Mochida
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Fumio Matsuda
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan; Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Sachiko Oyama
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Mami Okamoto
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan
| | - Akihiko Kondo
- Biomass Engineering Program, RIKEN, Yokohama, Kanagawa, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
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26
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Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015; 7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
Abstract
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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Affiliation(s)
- Jeffery M Saarela
- Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4
| | - William P Wysocki
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Craig F Barrett
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jerrold I Davis
- Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dustin R Mayfield
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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27
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Mochida K, Saisho D, Hirayama T. Crop improvement using life cycle datasets acquired under field conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:740. [PMID: 26442053 PMCID: PMC4585263 DOI: 10.3389/fpls.2015.00740] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/31/2015] [Indexed: 05/17/2023]
Abstract
Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer "designed crops" to prevent yield shortfalls because of environmental fluctuations due to future climate change.
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Affiliation(s)
- Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- *Correspondence: Keiichi Mochida, Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan,
| | - Daisuke Saisho
- Group of Genome Diversity, Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Takashi Hirayama
- Group of Environmental Response Systems, Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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28
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Dolferus R. To grow or not to grow: a stressful decision for plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:247-261. [PMID: 25443851 DOI: 10.1016/j.plantsci.2014.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Progress in improving abiotic stress tolerance of crop plants using classic breeding and selection approaches has been slow. This has generally been blamed on the lack of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress tolerance is most often measured in terms of yield-capacity under adverse weather conditions. "Yield" is a complex trait and is determined by growth and developmental processes which are controlled by environmental signals throughout the life cycle of the plant. The use of model systems has allowed us to gradually unravel how plants grow and develop, but our understanding of the flexibility and opportunistic nature of plant development and its capacity to adapt growth to environmental cues is still evolving. There is genetic variability for the capacity to maintain yield and productivity under abiotic stress conditions in crop plants such as cereals. Technological progress in various domains has made it increasingly possible to mine that genetic variability and develop a better understanding about the basic mechanism of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for human nutrition, the cereals.
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Affiliation(s)
- Rudy Dolferus
- CSIRO, Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia.
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29
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Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Méry S, Daniel-Vedele F. Brachypodium: a promising hub between model species and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5683-96. [PMID: 25262566 DOI: 10.1093/jxb/eru376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.
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Affiliation(s)
- Thomas Girin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Laure C David
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Camille Chardin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Sylvie Ferrario-Méry
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Françoise Daniel-Vedele
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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