in silico Plants最新文献

{"title":"Dynamic modelling of the iron deficiency modulated transcriptome response in Arabidopsis thaliana roots","authors":"Alexandr Koryachko, Anna Matthiadis, Samiul Haque, D. Muhammad, J. Ducoste, James M. Tuck, Terri A. Long, Cranos M. Williams","doi":"10.1093/INSILICOPLANTS/DIZ005","DOIUrl":"https://doi.org/10.1093/INSILICOPLANTS/DIZ005","url":null,"abstract":"The iron deficiency response in plants is a complex biological process with a host of influencing factors. The ability to precisely modulate this process at the transcriptome level would enable genetic manipulations allowing plants to survive in nutritionally poor soils and accumulate increased iron content in edible tissues. Despite the collected experimental data describing different aspects of the iron deficiency response in plants, no attempts have been made towards aggregating this information into a descriptive and predictive model of gene expression changes over time. We formulated and trained a dynamic model of the iron deficiency induced transcriptional response in Arabidopsis thaliana. Gene activity dynamics were modelled with a set of ordinary differential equations that contain biologically tractable parameters. The trained model was able to capture and account for a significant difference in mRNA decay rates under iron sufficient and iron deficient conditions, approximate the expression behaviour of currently unknown gene regulators, unveil potential synergistic effects between the modulating transcription factors and predict the effect of double regulator mutants. The presented modelling approach illustrates a framework for experimental design, data analysis and information aggregation in an effort to gain a deeper understanding of various aspects of a biological process of interest.","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/INSILICOPLANTS/DIZ005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61382473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A theoretical analysis of how plant growth is limited by carbon allocation strategies and respiration","authors":"B. Holland, N. Monk, R. Clayton, C. Osborne","doi":"10.1093/INSILICOPLANTS/DIZ004","DOIUrl":"https://doi.org/10.1093/INSILICOPLANTS/DIZ004","url":null,"abstract":"Improving crop yield is essential to meet increasing global food demands. Boosting crop yield requires the coordination of carbon acquisition by leaves and carbon utilization by roots and seeds. Simple modelling approaches may be used to explain how this coordination is achieved within plant growth. Here, the limits to allocation strategies and the influence of maintenance costs are explored by analysing the sensitivity of a simple root–shoot carbon allocation model for vegetative and reproductive growth. The model is formulated based on fundamental constraints on plant growth and therefore can be applied to all plants. This general but quantitative approach shows that the relative costs of root and leaf respiration alter the relationship between carbon allocation and final plant size, enabling a range of allocation strategies to produce a similar total amount of plant material during vegetative growth. This plasticity is enhanced by increasing assimilation rate within the model. Results show that high leaf allocation during vegetative growth promotes early reproduction with respect to yield. Having higher respiration in leaves than roots delays the optimal age to reproduce for plants with high leaf allocation during vegetative growth and increases the restrictions on flowering time for plants with high root allocation during vegetative growth. It is shown that, when leaf respiration is higher than root respiration, reallocating carbon towards the roots can increase the total amount of plant material. This analysis indicates that crop improvement strategies should consider the effects of maintenance costs on growth, a previously under-appreciated mechanism for yield enhancement.","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/INSILICOPLANTS/DIZ004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46699584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A generic approach to modelling, allocation and redistribution of biomass to and from plant organs","authors":"H. Brown, N. Huth, D. Holzworth, E. Teixeira, E. Wang, R. Zyskowski, B. Zheng","doi":"10.1093/INSILICOPLANTS/DIY004","DOIUrl":"https://doi.org/10.1093/INSILICOPLANTS/DIY004","url":null,"abstract":"","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/INSILICOPLANTS/DIY004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61382456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biological reality and parsimony in crop models—why we need both in crop improvement!","authors":"G. Hammer, C. Messina, A. Wu, M. Cooper","doi":"10.1093/insilicoplants/diz010","DOIUrl":"https://doi.org/10.1093/insilicoplants/diz010","url":null,"abstract":"The potential to add significant value to the rapid advances in plant breeding technologies associated with statistical whole-genome prediction methods is a new frontier for crop physiology and modelling. Yield advance by genetic improvement continues to require prediction of phenotype based on genotype, and this remains challenging for complex traits despite recent advances in genotyping and phenotyping. Crop models that capture physiological knowledge and can robustly predict phenotypic consequences of genotype-by-environment-by-management (G×E×M) interactions have demonstrated potential as an integrating tool. But does this biological reality come with a degree of complexity that restricts applicability in crop improvement? Simple, high-speed, parsimonious models are required for dealing with the thousands of genotypes and environment combinations in modern breeding programs utilizing genomic prediction technologies. In contrast, it is often considered that greater model complexity is needed to evaluate potential of putative variation in specific traits in target environments as knowledge on their underpinning biology advances. Is this a contradiction leading to divergent futures? Here it is argued that biological reality and parsimony do not need to be independent and perhaps should not be. Models structured to readily allow variation in the biological level of process algorithms, while using coding and computational advances to facilitate high-speed simulation, could well provide the structure needed for the next generation of crop models needed to support and enhance advances in crop improvement technologies. Beyond that, the trans-scale and transdisciplinary dialogue among scientists that will be required to construct such models effectively is considered to be at least as important as the models.","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/insilicoplants/diz010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61382773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Positional variation rather than salt stress dominates changes in three-dimensional leaf shape patterns in cucumber canopies","authors":"Dominik Schmidt, K. Kahlen","doi":"10.1093/insilicoplants/diz011","DOIUrl":"https://doi.org/10.1093/insilicoplants/diz011","url":null,"abstract":"Leaf shape plays a key role in the interaction of a plant with its environment, best-known in the plant’s light harvest. Effects of the environment on the interplay of canopy architecture and physiological functioning can be estimated using functional-structural plant models (FSPMs). In order to reduce the complexity of canopy simulations, leaf shape models used in FSPMs are often simple prototypes scaled to match current leaf area. L-Cucumber is such an FSPM, whose leaf prototype mimics average real leaf shape of unstressed cucumber plants well. However, adaptation processes or stress responses may lead to non-proportional changes in leaf geometries, which, for example, could affect length to width ratios or curvatures. The current leaf shape model in L-Cucumber is static and hence does not incorporate changes in leaf shape within or between plants. Thus, the aim of this study was to estimate leaf shape variation and exemplarily study its effects on FSPM simulations. Three-dimensional leaf coordinate data from a salt stress study were analysed with a robust Bayesian mixed-effects model for estimating leaf shape depending on rank, size and salinity. Results showed that positional and size variation rather than salinity levels dominated 3D leaf shape patterns of cucumber. Considering variable leaf shapes in relation to this main sources of variation in L-Cucumber simulations, only minor effects compared to a realistic, yet static average shape were found. However, with similar computational demands variation in shapes other studies highly sensitive to shape dynamics, for example, pesticide spraying might be affected more strongly.","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/insilicoplants/diz011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61382335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developing the nuts, bolts, theoretical frameworks and community infrastructures to support global plant systems biology research","authors":"Xinguang Zhu","doi":"10.1093/INSILICOPLANTS/DIZ002","DOIUrl":"https://doi.org/10.1093/INSILICOPLANTS/DIZ002","url":null,"abstract":"The rate of progress in biological science today can be compared with that of physical science at the beginning of the 20th century. With so many new discoveries emerging on a daily basis, are these discoveries simply the application or manifestation of basic scientific principles such as the central dogma of molecular biology, the fundamental theorems of genetics, or the basic genetic principles of epigenetics, or will they have a larger impact? Are there grand challenges to be found in biological science research beyond the current stage of fact observation and the elucidation of the underlying mechanistic basis of individual cases using the basic principles discovered long ago? The answer is ‘yes’. In the field of plant science, though there is ever-increased resolution of the mechanistic details of the plant growth and development, we are far from being able to predict the growth and development of plants of particular genotypes under different environments, let alone predict changes in plant growth and development for an altered genotype and under a changed environment. This is one major reason why we label biology as an ‘experimental’ science, which is essentially another way of saying that models for whole plants are far from being mechanistic, sufficiently robust and satisfactorily predictive. Is there any hope of developing such models given the complexity of biological systems? There are good reasons to be optimistic. Pioneering researchers have developed many models that enable the accurate quantitative prediction of biological performances, such as the prediction of photosynthetic CO2 uptake rates under either steadystate (Farquhar et al. 1980) or dynamic conditions (Zhu et al. 2013). Models simulating many other physiological plant processes have also been developed (see reviews in Zhu et al. 2015; Chang and Zhu 2017). It is foreseeable that, as modules for individual processes become available, robust and complete models for plant growth and development will be within reach. This will not be a simple task. Even for the model organism Arabidopsis thaliana, there are about 30 000 genes, whose action and interaction among them and with their micro-environments, underlie growth and develop. Creating highly robust models to predict the behaviour of such a complex system with detailed descriptions of the mechanisms of all underlying genetic, biochemical, biophysical, and associated physical and chemical processes represent a huge challenge ahead. If such models are developed, they can be used to support plant science research, such as to study the mechanistic basis of natural variations of plant structure and function, to study the responses, acclimation, adaption and evolutionary trajectories of plants under environmental changes, in addition to the currently widely appreciated roles of plant models in guiding crop engineering, breeding or cultivation (Zhu et al. 2015; Marshall-Colon et al. 2017; Xiao et al. 2017). There are a few resear","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/INSILICOPLANTS/DIZ002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47893102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An explanatory model of temperature influence on flowering through whole-plant accumulation of <i>FLOWERING LOCUS T</i> in <i>Arabidopsis thaliana</i>.","authors":"Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim","doi":"10.1093/insilicoplants/diz006","DOIUrl":"10.1093/insilicoplants/diz006","url":null,"abstract":"<p><p>We assessed mechanistic temperature influence on flowering by incorporating temperature-responsive flowering mechanisms across developmental age into an existing model. Temperature influences the leaf production rate as well as expression of <i>FLOWERING LOCUS T</i> (<i>FT</i>), a photoperiodic flowering regulator that is expressed in leaves. The <i>Arabidopsis</i> Framework Model incorporated temperature influence on leaf growth but ignored the consequences of leaf growth on and direct temperature influence of <i>FT</i> expression. We measured <i>FT</i> production in differently aged leaves and modified the model, adding mechanistic temperature influence on <i>FT</i> transcription, and causing whole-plant <i>FT</i> to accumulate with leaf growth. Our simulations suggest that in long days, the developmental stage (leaf number) at which the reproductive transition occurs is influenced by day length and temperature through <i>FT</i>, while temperature influences the rate of leaf production and the time (in days) the transition occurs. Further, we demonstrate that <i>FT</i> is mainly produced in the first 10 leaves in the Columbia (Col-0) accession, and that <i>FT</i> accumulation alone cannot explain flowering in conditions in which flowering is delayed. Our simulations supported our hypotheses that: (i) temperature regulation of <i>FT</i>, accumulated with leaf growth, is a component of thermal time, and (ii) incorporating mechanistic temperature regulation of <i>FT</i> can improve model predictions when temperatures change over time.</p>","PeriodicalId":36138,"journal":{"name":"in silico Plants","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9534314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33491126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}