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Natural Variation For Growth In Arabidopsis Thaliana
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Book Synopsis Ecological Genomics by : Christian R. Landry
Download or read book Ecological Genomics written by Christian R. Landry and published by Springer Science & Business Media. This book was released on 2013-11-25 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.
Book Synopsis Natural Variation for Growth in Arabidopsis Thaliana by : Daniela-Loredana Vlad
Download or read book Natural Variation for Growth in Arabidopsis Thaliana written by Daniela-Loredana Vlad and published by . This book was released on 2009 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: Not only do plants represent an essential food source, but they are also an important source of renewable materials and molecules. In this context, plant growth, and consequently yield, is an important parameter of tomorrow's agriculture and society in many ways. Also fundamental to our understanding of evolution, plant growth is an extremely complex process under the influence of many factors from virtually any aspects of plant biology. The genetic analysis of natural variation allows the discovery of allelic variants at previously known genes or new genes affecting quantitative traits. We aimed at identifying genes underlying natural variation for shoot growth using a quantitative genetics approach (QTL mapping). The analysis of shoot growth variation from a Bur-0 x Col-0 Recombinant Inbred Line (RIL) set, led to the identification of two loci, SG1 (Shoot Growth-1) mapped at the top of chromosome 5 and SG3 (Shoot Growth-3) results from allelic variation in the genomic region underlying a QTL predicted between 14 and 15 Mb on chromosome 4. SG3 was not visible in the RIL population due to an epistatic interaction with another locus SG3i (SG3-interactor), and because it was very likely counter-selected. Fine-mapping and complementation revealed the gene responsible for the phenotype, a stromal oxidoreductase affecting photosynthetic electron transfer rate, which was duplicated in Bur-0 but not in Col-0. We show that natural variation at the SG3 locus is explained by the divergent evolution of a (dispersed) single gene duplication causing the transposition of the functional copy of the gene in Bur (compared to Col). The presence of the Col allele at SG1 has severe phenotypic consequences. The candidate region for SG1 has been reduced to ~ 8 kb containing only one gene of unknown function and no major sequence polymorphism. On the other hand, the two alleles at SG1 show important DNA-methylation contrast. Even though we tend to think that SG1 is the effect of an epiallele, so far the genetic mechanism is not understood. The analysis of these QTLs revealed new genes affecting plant growth, and allows us to draw an always more complex picture of the architecture of quantitative traits.
Book Synopsis Decoding the Complexity of Natural Variation for Shoot Growth and Response to the Environment in Arabidopsis Thaliana by : Charlotte Trontin
Download or read book Decoding the Complexity of Natural Variation for Shoot Growth and Response to the Environment in Arabidopsis Thaliana written by Charlotte Trontin and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz's team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.
Book Synopsis The Genetic and Molecular Basis of Natural Variation for Plant Growth and Related Traits in Arabidopsis Thaliana by : Bjorn Pieper
Download or read book The Genetic and Molecular Basis of Natural Variation for Plant Growth and Related Traits in Arabidopsis Thaliana written by Bjorn Pieper and published by . This book was released on 2009 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genes that Underlie Natural Variation in Growth Rate and Flowering Time in Local Accessions of Arabidopsis Thaliana by : Zafar Iqbal Malik
Download or read book Genes that Underlie Natural Variation in Growth Rate and Flowering Time in Local Accessions of Arabidopsis Thaliana written by Zafar Iqbal Malik and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Natural Variation in Arabidopsis Thaliana Root Growth Behavior by : Laura M. Vaughn
Download or read book Natural Variation in Arabidopsis Thaliana Root Growth Behavior written by Laura M. Vaughn and published by . This book was released on 2010 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Natural Variation in Arabidopsis Thaliana Growth in Response to Ambient Temperatures by : Asif Khattak
Download or read book Natural Variation in Arabidopsis Thaliana Growth in Response to Ambient Temperatures written by Asif Khattak and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :James R. Ehleringer Publisher :Springer Science & Business Media ISBN 13 :9780387220697 Total Pages :560 pages Book Rating :4.2/5 (26 download)
Book Synopsis A History of Atmospheric CO2 and Its Effects on Plants, Animals, and Ecosystems by : James R. Ehleringer
Download or read book A History of Atmospheric CO2 and Its Effects on Plants, Animals, and Ecosystems written by James R. Ehleringer and published by Springer Science & Business Media. This book was released on 2005-01-27 with total page 560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Trees, CO2 concentration, climate change, herbivores, temperature.
Book Synopsis Natural Variation for Loci Controlling Metabolism and Development in Arabidopsis Thaliana by : S. Gill
Download or read book Natural Variation for Loci Controlling Metabolism and Development in Arabidopsis Thaliana written by S. Gill and published by . This book was released on 2003 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Annual Plant Reviews, Seed Development, Dormancy and Germination by : Kent Bradford
Download or read book Annual Plant Reviews, Seed Development, Dormancy and Germination written by Kent Bradford and published by John Wiley & Sons. This book was released on 2008-04-15 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The formation, dispersal and germination of seeds are crucial stages in the life cycles of gymnosperm and angiosperm plants. The unique properties of seeds, particularly their tolerance to desiccation, their mobility, and their ability to schedule their germination to coincide with times when environmental conditions are favorable to their survival as seedlings, have no doubt contributed significantly to the success of seed-bearing plants. Humans are also dependent upon seeds, which constitute the majority of the world’s staple foods (e.g., cereals and legumes). Seeds are an excellent system for studying fundamental developmental processes in plant biology, as they develop from a single fertilized zygote into an embryo and endosperm, in association with the surrounding maternal tissues. As genetic and molecular approaches have become increasingly powerful tools for biological research, seeds have become an attractive system in which to study a wide array of metabolic processes and regulatory systems. Seed Development, Dormancy and Germination provides a comprehensive overview of seed biology from the point of view of the developmental and regulatory processes that are involved in the transition from a developing seed through dormancy and into germination and seedling growth. It examines the complexity of the environmental, physiological, molecular and genetic interactions that occur through the life cycle of seeds, along with the concepts and approaches used to analyze seed dormancy and germination behavior. It also identifies the current challenges and remaining questions for future research. The book is directed at plant developmental biologists, geneticists, plant breeders, seed biologists and graduate students.
Book Synopsis Genetic Basis of Natural Variation in Photoprotection in Arabidopsis by : Tepsuda Rungrat
Download or read book Genetic Basis of Natural Variation in Photoprotection in Arabidopsis written by Tepsuda Rungrat and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Light is a necessary factor for most living organism on Earth; however it can also become one of the most important abiotic environmental stresses limiting plant growth. As natural environments are extremely variable, plant has developed several mechanisms to cope with excess light energy such as adjusting leaf angle, chloroplast position, thermal dissipation, and detoxification of the reactive oxygen species resulting from stress. Among those mechanisms, thermal dissipation or Non-Photochemical Quenching (NPQ) seem to be the most rapid photoprotective response in higher plants. To investigate the natural variation of NPQ, different sets of Arabidopsis thaliana (Arabidopsis) including a genetically balanced set of natural accessions, Recombinant Inbred Intercross (RIXs), and photoprotective mutants were studied using simulated natural environments. In natural habitats, natural genetic variation is selected on to result in adaptive allelic variation. The Genome-Wide Association Study (GWAS) has been successful in identifying natural allelic variants underlying natural variation in many traits and in different plant species such as Arabidopsis, rice and maize. In order to expand the current knowledge of the genetic basis of NPQ, which may also be affected by environment, two main approaches were taken in this thesis. Firstly, the natural variation in NPQ under simulated natural environments was explored. Secondly, two mapping approaches, RIXs and GWAS, were applied to reveal candidate genes/loci underlying variation in the NPQ trait. This study investigated the physiological and molecular changes that occur in response to diurnal and seasonal growth conditions which plant experiences in the field. Two dynamic natural environments were simulated: coastal-autumn; which had moderate temperatures and light intensities, and inland-autumn; where plants were exposed to greater temperature variations and higher light intensities. Inland plants presented evidence of rapid NPQ in response to sudden higher light exposure, a decline of steady state NPQ and a decrease in chlorophyll content, indicating long-term acclimation. In contrast, coastal plants had a slower induction of NPQ followed by a slow increase in NPQ over time. This provides a better understanding on how plants have different NPQ kinetics responses under different environments; furthermore the responses are varied between accessions. The findings presented in this thesis demonstrated that natural genetic variation in NPQ phenotype is influenced not only by genetic factor but also environmental effects. TheGWAS and RIX results for the NPQ trait revealed a total of 27 QTL, of which RIX-QTL5-3, QTL5-2, and QTL5-3 overlapped between the two different mapping approaches. One of the most significant findings from this study is the identification of QTL1-4, which was found predominantly in the coastal condition. This QTL was directly over the PSII protein subunit PsbS gene, of which the loss of function mutant, non-photochemical quenching 4 (npq4), has been shown to lack Energy-dependent quenching (qE). The identification of this a priori gene is significant as although it a known NPQ gene it has not been identified in previous NPQ mapping studies. This suggests that the novel use of climate chambers and GWAS in this study allowed the genetic basis of variation in NPQ specific to certain environments and certain plant developmental stages to be identified. Taken together, the findings presented here have provided meaningful insight into the naturally occurring genetic variation in Arabidopsis accessions during stressful condition, providing the opportunity to identify more genes that are involved in the regulation of photoprotection in response to the natural environment.
Book Synopsis Exploring Natural Variation in Flowering Time in Arabidopsis Thaliana by : Jonathan David Werner
Download or read book Exploring Natural Variation in Flowering Time in Arabidopsis Thaliana written by Jonathan David Werner and published by . This book was released on 2004 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis High-Throughput Phenotyping in Plants by : Jennifer Normanly
Download or read book High-Throughput Phenotyping in Plants written by Jennifer Normanly and published by Humana Press. This book was released on 2017-04-30 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic approaches to understanding plant growth and development have always benefitted from screens that are simple, quantitative and rapid. Visual screens and morphometric analysis have yielded a plethora of interesting mutants and traits that have provided insight into complex regulatory pathways, and yet many genes within any given plant genome remain undefined. The premise underlying High Throughput Phenotyping in Plants: Methods and Protocols is that the higher the resolution of the phenotype analysis the more likely that new genes and complex interactions will be revealed. The methods described in this volume can be generally classified as quantitative profiling of cellular components, ranging from ions to small molecule metabolites and nuclear DNA, or image capture that ranges in resolution from chlorophyll fluorescence from leaves and time-lapse images of seedling shoots and roots to individual plants within a population at a field site. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, High Throughput Phenotyping in Plants: Methods and Protocols serves as an invaluable guide to plant researchers and all scientists who wish to better understand plant growth and development.
Book Synopsis Genetic and Enironmental Effects on Natural Variation in Arabidopsis Thaliana Seed Size by : Sebastian Christopher Gnan
Download or read book Genetic and Enironmental Effects on Natural Variation in Arabidopsis Thaliana Seed Size written by Sebastian Christopher Gnan and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Annual Plant Reviews, Insect-Plant Interactions by : Claudia Voelckel
Download or read book Annual Plant Reviews, Insect-Plant Interactions written by Claudia Voelckel and published by John Wiley & Sons. This book was released on 2014-05-02 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: This latest volume in Wiley Blackwell’s prestigious Annual Plant Reviews brings together articles that describe the biochemical, genetic, and ecological aspects of plant interactions with insect herbivores.. The biochemistry section of this outstanding volume includes reviews highlighting significant findings in the area of plant signalling cascades, recognition of herbivore-associated molecular patterns, sequestration of plant defensive metabolites and perception of plant semiochemicals by insects. Chapters in the genetics section are focused on genetic mapping of herbivore resistance traits and the analysis of transcriptional responses in both plants and insects. The ecology section includes chapters that describe plant-insect interactions at a higher level, including multitrophic interactions, investigations of the cost-benefit paradigm and the altitudinal niche-breadth hypothesis, and a re-evaluation of co-evolution in the light of recent molecular research. Written by many of the world’s leading researchers in these subjects, and edited by Claudia Voelckel and Georg Jander, this volume is designed for students and researchers with some background in plant molecular biology or ecology, who would like to learn more about recent advances or obtain a more in-depth understanding of this field. This volume will also be of great use and interest to a wide range of plant scientists and entomologists and is an essential purchase for universities and research establishments where biological sciences are studied and taught. To view details of volumes in Annual Plant Reviews, visit: www.wiley.com/go/apr Also available from Wiley: Plant Defense Dale Walters 9781405175890 Herbicides and Plant Physiology, 2nd Edn Andrew Cobb & John Reade 9781405129350
Book Synopsis Genetic Characterization of Natural Variation Regulating Thermal Responses in Plant Development by : Wangsheng Zhu
Download or read book Genetic Characterization of Natural Variation Regulating Thermal Responses in Plant Development written by Wangsheng Zhu and published by . This book was released on 2014 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: Temperature affects several aspects of plant growth and development. The predicted rises in global temperature is expected to have an impact on worldwide crop productivity. Plants alter their physiological and developmental strategies in order to survive day to day and seasonal fluctuation in their growth temperature. In order to predict the impact of temperature on plants and to develop varieties that can cope with varied temperatures, we need to have a better knowledge of temperature response in plants at the molecular level. It is currently unclear as to how plants perceive and respond to varying temperatures. In this thesis, I employed model plant Arabidopsis thaliana as a tool to identify new factors involved in this process in plants. In this thesis, I have screened for natural variation in Arabidopsis accessions in temperature-response, followed by gene identification and characterization. First, Cvi-0, collected from Cape Verde Island, was identified to be insensitive to higher temperature. Using Quantitative Trait Loci (QTL) mapping with recombinant inbred lines derived from a cross between Cvi-0 and the reference strain Col-0 (CviColRILs), I showed that a QTL tightly linked to the blue light receptor CRYTOCHROMOME 2 (CRY2) contributes to natural variation in hypocotyl elongation and flowering response to temperature. The role for the CviCRY2 allele in response to temperature was supported by quantitative knockdown experiment with artificial microRNAs (amiRNAs) in Cvi-0. In addition, transgenic complementation experiments with CviCRY2 allele in the Ler-0, Col-0 and cry2 mutant backgrounds suggest that the role of CRY2 in regulating temperature response is dependent on the genetic background indicating the presence of modifiers for this response. Second, I discovered that Sij4 strain, collected from central Asia, is insensitive to temperature-induced hypocotyl elongation, and displays a temperature-dependent growth defect in their first leaves (thus named "abnormal first leaves (afl)"). Both traits show high genetic correlation (afl) (rG=0.88) indicating common genetic basis. Using Sij4ColF2 and Sij4LerF2 populations, I fine mapped the AFL locus to a 6 kb fragment, which includes a previously uncharacterized gene At2g31580. I demonstrate At2g31580 is AFL through transgenic complementation and artificial microRNA mediated knock-down experiments. I show that AFL regulates cell cycle at the G2/M transition through a combination of flow cytometry, transcriptome analysis and by using the cell cycle marker CYCB1. CyclinB1,1 (CYCB1,1), a key gene in the regulation of cell cycle, was not mis-expressed on transcriptional level, but a strong pCYCB1,1-CYCB1,1-GFP signal accumulated in mutant cells suggested that inhibition of CYCB1,1 degrading during G2/M phase transition. This was associated with increased DNA content suggestive of endoreduplication. Furthermore, I have shown that plants compromised for AFL function are more prone to DNA damage, suggesting a role for AFL in DNA repair. In summary, my studies on natural genetic variation in Arabidopsis identify a new factor AFL in regulating cell elongation and cell proliferation in response to higher temperature. In this thesis I review temperature response in plants and then report novel functions for two genes, CRY2 and AFL, in higher temperature response. In the first chapter I review our understanding of temperature response in plants and the associated mechanisms. I also provide an introduction to natural variation in Arabidopsis. In the second chapter I describe the results from screen I have carried out to find natural variants with altered thermal response and then go on describe the genetic basis of the temperature insensitivity phenotype in the Cvi-0 strain of Arabidopsis thaliana. In Chapter 3, I describe the genetic and molecular basis of temperature insensitivity in Sij-4, another strain I picked up from the screen. The natural afl mutant allele in Sij4 can be used as system to address fundamental questions of AFL beyond temperature response such as cell cycle regulation in plants. My finding on CRY2 opens up avenues for studying temperature and light interactions. The implications of this study as well as future areas for research are also discusses.
Book Synopsis Genetic and Environmental Effects on Natural Variation in Arabidopsis Thaliana Seed Size by : Sebastian Christopher Gnan
Download or read book Genetic and Environmental Effects on Natural Variation in Arabidopsis Thaliana Seed Size written by Sebastian Christopher Gnan and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
