The Poplar Genome
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The Poplar Genome
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Author : Ilga Porth
language : en
Publisher: Springer Nature
Release Date :
The Poplar Genome written by Ilga Porth and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on with categories.
Genetics Genomics And Breeding Of Poplar
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Author : C. P. Joshi
language : en
Publisher: CRC Press
Release Date : 2011-03-29
Genetics Genomics And Breeding Of Poplar written by C. P. Joshi and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-03-29 with Science categories.
Written by researchers representing six countries and 28 institutions, this book highlights the development of the genus Populus as a model organism for tree genomics. Reflecting an impressive depth of coverage, the contributors' thorough reviews and analyses of Populus genomics provide insight into future discoveries about the basic biology of thi
Genetics And Genomics Of Populus
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Author : Stefan Jansson
language : en
Publisher: Springer
Release Date : 2010-03-02
Genetics And Genomics Of Populus written by Stefan Jansson and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-03-02 with Science categories.
Genetics and Genomics of Populus provides an indepth description of the genetic and genomic tools and approaches for Populus, examines the biology that has been elucidated using genomics, and looks to the future of this unique model plant. This volume is designed to serve both experienced Populus researchers and newcomers to the field. Contributors to the volume are a blend of researchers, some who have spent most of their research career on Populus and others that have moved to Populus from other model systems. Research on Populus forms a useful complement to research on Arabidopsis. In fact, many plant species found in nature are – in terms of the life history and genetics – more similar to Populus than to Arabidopsis. Thus, the genetic and genomic strategies and tools developed by the Populus community, and showcased in this volume, will hopefully provide inspiration for researchers working in other, less well developed, systems.
Glyphosate Resistant Poplar An Effort To Improve The Poplar Genome
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Author : Brandon Michael Brett
language : en
Publisher:
Release Date : 2003
Glyphosate Resistant Poplar An Effort To Improve The Poplar Genome written by Brandon Michael Brett and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with categories.
Genome Enabled Discovery Of Carbon Sequestration Genes In Poplar
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Author :
language : en
Publisher:
Release Date : 2007
Genome Enabled Discovery Of Carbon Sequestration Genes In Poplar written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
The goals of the S.H. Strauss laboratory portion of 'Genome-enabled discovery of carbon sequestration genes in poplar' are (1) to explore the functions of candidate genes using Populus transformation by inserting genes provided by Oakridge National Laboratory (ORNL) and the University of Florida (UF) into poplar; (2) to expand the poplar transformation toolkit by developing transformation methods for important genotypes; and (3) to allow induced expression, and efficient gene suppression, in roots and other tissues. As part of the transformation improvement effort, OSU developed transformation protocols for Populus trichocarpa 'Nisqually-1' clone and an early flowering P. alba clone, 6K10. Complete descriptions of the transformation systems were published (Ma et. al. 2004, Meilan et. al 2004). Twenty-one 'Nisqually-1' and 622 6K10 transgenic plants were generated. To identify root predominant promoters, a set of three promoters were tested for their tissue-specific expression patterns in poplar and in Arabidopsis as a model system. A novel gene, ET304, was identified by analyzing a collection of poplar enhancer trap lines generated at OSU (Filichkin et. al 2006a, 2006b). Other promoters include the pGgMT1 root-predominant promoter from Casuarina glauca and the pAtPIN2 promoter from Arabidopsis root specific PIN2 gene. OSU tested two induction systems, alcohol- and estrogen-inducible, in multiple poplar transgenics. Ethanol proved to be the more efficient when tested in tissue culture and greenhouse conditions. Two estrogen-inducible systems were evaluated in transgenic Populus, neither of which functioned reliably in tissue culture conditions. GATEWAY-compatible plant binary vectors were designed to compare the silencing efficiency of homologous (direct) RNAi vs. heterologous (transitive) RNAi inverted repeats. A set of genes was targeted for post transcriptional silencing in the model Arabidopsis system; these include the floral meristem identity gene (APETALA1 or AP1), auxin response factor gene (ETTIN), the gene encoding transcriptional factor of WD40 family (TRANSPARENTTESTAGLABRA1 or TTG1), and the auxin efflux carrier (PIN-FORMED2 or PIN2) gene. More than 220 transgenic lines of the 1st, 2nd and 3rd generations were analyzed for RNAi suppression phenotypes (Filichkin et. al., manuscript submitted). A total of 108 constructs were supplied by ORNL, UF and OSU and used to generate over 1,881 PCR verified transgenic Populus and over 300 PCR verified transgenic Arabidopsis events. The Populus transgenics alone required Agrobacterium co-cultivations of 124.406 explants.
Comparative And Evolutionary Genomics Of Angiosperm Trees
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Author : Andrew Groover
language : en
Publisher: Springer
Release Date : 2017-11-21
Comparative And Evolutionary Genomics Of Angiosperm Trees written by Andrew Groover and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-11-21 with Science categories.
Marking the change in focus of tree genomics from single species to comparative approaches, this book covers biological, genomic, and evolutionary aspects of angiosperm trees that provide information and perspectives to support researchers broadening the focus of their research. The diversity of angiosperm trees in morphology, anatomy, physiology and biochemistry has been described and cataloged by various scientific disciplines, but the molecular, genetic, and evolutionary mechanisms underlying this diversity have only recently been explored. Excitingly, advances in genomic and sequencing technologies are ushering a new era of research broadly termed comparative genomics, which simultaneously exploits and describes the evolutionary origins and genetic regulation of traits of interest. Within tree genomics, this research is already underway, as the number of complete genome sequences available for angiosperm trees is increasing at an impressive pace and the number of species for which RNAseq data are available is rapidly expanding. Because they are extensively covered by other literature and are rapidly changing, technical and computational approaches—such as the latest sequencing technologies—are not a main focus of this book. Instead, this comprehensive volume provides a valuable, broader view of tree genomics whose relevance will outlive the particulars of current-day technical approaches. The first section of the book discusses background on the evolution and diversification of angiosperm trees, as well as offers description of the salient features and diversity of the unique physiology and wood anatomy of angiosperm trees. The second section explores the two most advanced model angiosperm tree species (poplars and eucalypts) as well as species that are soon to emerge as new models. The third section describes the structural features and evolutionary histories of angiosperm tree genomes, followed by a fourth section focusing on the genomics of traits of biological, ecological, and economic interest. In summary, this book is a timely and well-referenced foundational resource for the forest tree community looking to embrace comparative approaches for the study of angiosperm trees.
Activation Tagging As A Powerful Tool For Gene Discovery In Poplar
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Author : Edward John Harrison
language : en
Publisher:
Release Date : 2007
Activation Tagging As A Powerful Tool For Gene Discovery In Poplar written by Edward John Harrison and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
Our understanding of tree growth and development has increased substantially in the last few decades and is expected to increase much more as we fully exploit newly developed genomic tools. A major milestone in tree genomics was the sequencing of the entire genome of Populus trichocarpa, and the realization that we understand the function of very few of the 45,000 predicted genes in this genome. To advance our knowledge of gene function in Populus, we have created the largest population of mutant poplars to date which will enable us to link altered phenotypes with genes that are responsible. This thesis describes this mutant population, provides preliminary results on the complexity of mutants identified and examines one distinct mutant called shriveled leaf. These results clearly demonstrate the power of this population for gene function analysis and reveal that this population will be a valuable genomic resource for tree biotechnology for many years to come.
Biology Of Populus And Its Implications For Management And Conservation
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Author : National Research Council Canada
language : en
Publisher: NRC Research Press
Release Date : 1996
Biology Of Populus And Its Implications For Management And Conservation written by National Research Council Canada and has been published by NRC Research Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996 with Nature categories.
"Poplar is increasingly recognized as an excellent model tree for the study of tree growth and its underlying physiology and genetics. By studying trees of the genus Populus (poplars, cottonwoods, aspens), which in their native ecosystems play a major role in the re-colonization of sites after disturbances, new insights have been gained into plantation culture and the development of improved cultivars. Of the 20 chapters in this publication, editored by an international group of researchers, one section deals with systematics, genetics, genetic manipulation and biotic interactions of Populus, while the other deals with stress response and the physiology of growth and productivity" --
Epigenomics Of Development In Populus
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Author :
language : en
Publisher:
Release Date : 2013
Epigenomics Of Development In Populus written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
We conducted research to determine the role of epigenetic modifications during tree development using poplar (Populus trichocarpa), a model woody feedstock species. Using methylated DNA immunoprecipitation (MeDIP) or chromatin immunoprecipitation (ChIP), followed by high-throughput sequencing, we are analyzed DNA and histone methylation patterns in the P. trichocarpa genome in relation to four biological processes: bud dormancy and release, mature organ maintenance, in vitro organogenesis, and methylation suppression. Our project is now completed. We have 1) produced 22 transgenic events for a gene involved in DNA methylation suppression and studied its phenotypic consequences; 2) completed sequencing of methylated DNA from eleven target tissues in wildtype P. trichocarpa; 3) updated our customized poplar genome browser using the open-source software tools (2.13) and (V2.2) of the P. trichocarpa genome; 4) produced summary data for genome methylation in P. trichocarpa, including distribution of methylation across chromosomes and in and around genes; 5) employed bioinformatic and statistical methods to analyze differences in methylation patterns among tissue types; and 6) used bisulfite sequencing of selected target genes to confirm bioinformatics and sequencing results, and gain a higher-resolution view of methylation at selected genes 7) compared methylation patterns to expression using available microarray data. Our main findings of biological significance are the identification of extensive regions of the genome that display developmental variation in DNA methylation; highly distinctive gene-associated methylation profiles in reproductive tissues, particularly male catkins; a strong whole genome/all tissue inverse association of methylation at gene bodies and promoters with gene expression; a lack of evidence that tissue specificity of gene expression is associated with gene methylation; and evidence that genome methylation is a significant impediment to tissue dedifferentiation and redifferentiation in vitro.
The Genome Of Black Cottonwood Populus Trichocarpa Torr Gray
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Author :
language : en
Publisher:
Release Date : 2006
The Genome Of Black Cottonwood Populus Trichocarpa Torr Gray written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.
We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.