High-Throughput Phenotyping in Plants: Methods and Protocols PDF
Preview High-Throughput Phenotyping in Plants: Methods and Protocols
M M B ™ ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 wwwwwwwwww High-Throughput Phenotyping in Plants Methods and Protocols Edited by Jennifer Normanly University of Massachusetts, Amherst, MA, USA Editor Jennifer Normanly University of Massachusetts Amherst, MA, USA Please note that additional material for this book can be downloaded from h ttp://extras.springer.com ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-61779-994-5 ISBN 978-1-61779-995-2 (eBook) DOI 10.1007/978-1-61779-995-2 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2012942930 © Springer Science+Business Media, LLC 2012 This work is subject to copyright. 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Printed on acid-free paper Humana Press is a brand of Springer Springer is part of Springer Science+Business Media (www.springer.com) Preface Genetic approaches to understanding plant growth and development have always benefi tted from screens that are simple, quantitative, and fast. Visual screens and morphometric analysis have yielded a plethora of interesting mutants and traits that have provided insight into complex regulatory pathways. Still, many genes within any given plant genome remain unde fi ned. The premise underlying this book is that the higher the resolution of the phenotype analysis the more likely that new genes and complex interactions will be revealed. Recent advances in automation and highly sensitive analytical techniques have substantially expanded the plant biologist’s toolbox with which to screen for mutants a nd traits and identify new genes. There are now centers and institutes dedicated to high-throughput phenotyping of plants, and it has been the subject of at least three international conferences to date. As always, the value of the data obtained through high-throughput phenotyping methods depends upon the experimental design, which is discussed here. The methods described in this book can be generally classifi ed as either quantitative pro fi ling of cellular components, ranging from ions to small molecule metabolites and nuclear DNA, or image capture that ranges in resolution from chlorophyll fl uorescence from leaves and time-lapse images of seedling shoots and roots to individual plants within a population at a fi eld site. The sort of high-throughput analytical analysis described in these chapters will be relevant to plant researchers who rely on phenotype analysis to defi ne gene function and characterize genome responses to the environment; this includes bio- chemists, molecular geneticists, ecologists, evolutionary biologists, and population geneti- cists. As robotics, computing, and imaging technologies all continue to advance at a rapid rate, the list of quantifi able assays that can be carried out in high-throughput and at high resolution will continue to expand, providing more tools to understand plant growth and development. Amherst, MA J ennifer Normanly v wwwwwwwwww Contents Preface ..................................................................................................................... v Contributors ............................................................................................................. ix 1 Image-Based Analysis of Light-Grown Seedling Hypocotyls in Arabidopsis ............. 1 Benjamin J. Cole and Joanne Chory 2 High-Throughput Phenotyping of Plant Shoots ...................................................... 9 Bettina Berger, Bas de Regt, and Mark Tester 3 High-Throughput Phenotyping of Root Growth Dynamics .................................... 21 Nima Yazdanbakhsh and Joachim Fisahn 4 LEAF GUI: Analyzing the Geometry of Veins and Areoles Using Image Segmentation Algorithms ............................................................................. 41 Charles A. Price 5 Remote Chlorophyll Fluorescence Measurements with the Laser-Induced Fluorescence Transient Approach ....................................... 51 Roland Pieruschka, Denis Klimov, Joseph A. Berry, C. Barry Osmond, Uwe Rascher, and Zbigniew S. Kolber 6 Leaf Hue Measurements: A High-Throughput Screening of Chlorophyll Content .......................................................................................... 61 László Sass, Petra Majer, and Éva Hideg 7 High-Resolution, Time-Lapse Imaging for Ecosystem-Scale Phenotyping in the Field ......................................................................................... 71 Tim Brown, Christopher Zimmermann, Whitney Panneton, Nina Noah, and Justin Borevitz 8 High-Throughput Phenotyping of Plant Populations Using a Personal Digital Assistant ..................................................................................... 97 Raju Naik Vankudavath, Reddaiah Bodanapu, Yellamaraju Sreelakshmi, and Rameshwar Sharma 9 High-Throughput Fractionation of Natural Products for Drug Discovery ............... 117 Ying Tu and Bing Yan 10 Conducting Molecular Biomarker Discovery Studies in Plants ................................. 127 Christian Schudoma, Matthias Steinfath, Heike Sprenger, Joost T. van Dongen, Dirk Hincha, Ellen Zuther, Peter Geigenberger, Joachim Kopka, Karin Köhl, and Dirk Walther 11 Highly Sensitive High-Throughput Profiling of Six Phytohormones Using MS-Probe Modification and Liquid Chromatography–Tandem Mass Spectrometry ................................................................................................. 151 Mikiko Kojima and Hitoshi Sakakibara 12 Qualitative and Quantitative Screening of Amino Acids in Plant Tissues .................. 165 Will I. Menzel, Wen-Ping Chen, Adrian D. Hegeman, and Jerry D. Cohen vii viii Contents 13 Arabidopsis thaliana Membrane Lipid Molecular Species and Their Mass Spectral Analysis ............................................................................. 179 Thilani Samarakoon, Sunitha Shiva, Kaleb Lowe, Pamela Tamura, Mary R. Roth, and Ruth Welti 14 Inductively Coupled Plasma–Mass Spectrometry as a Tool for High-Throughput Analysis of Plants .................................................................. 269 Javier Seravalli 15 The Plant Volatilome: Methods of Analysis ............................................................. 289 Carlo Bicchi and Massimo Maffei 16 High-Throughput Monitoring of Plant Nuclear DNA Contents Via Flow Cytometry ............................................................................................... 311 David W. Galbraith and Georgina M. Lambert 17 Transient RNAi Assay in 96-Well Plate Format Facilitates High-Throughput Gene Function Studies in Planta ................................................ 327 Shu-Zon Wu and Magdalena Bezanilla 18 A High-Throughput Biological Conversion Assay for Determining Lignocellulosic Quality ........................................................................................... 341 Scott J. Lee, Thomas A. Warnick, Susan B. Leschine, and Samuel P. Hazen 19 Carbohydrate Microarrays in Plant Science .............................................................. 351 Jonatan U. Fangel, Henriette L. Pedersen, Silvia Vidal-Melgosa, Louise I. Ahl, Armando Asuncion Salmean, Jack Egelund, Maja Gro Rydahl, Mads H. Clausen, and William G.T. Willats Index ....................................................................................................................................... 363 Contributors LOUISE I. AHL • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark BETTINA BERGER • The Plant Accelerator, University of Adelaide, Urrbrae , SA , Australia JOSEPH A. BERRY • Department of Global Ecology , Carnegie Institution of Washington, Stanford , CA , USA MAGDALENA BEZANILLA • Department of Biology, University of Massachusetts, Amherst , MA , USA CARLO BICCHI • Dipartimento di Scienza e Tecnologia del Farmaco, University of Turin, Turin , Italy REDDAIAH BODANAPU • School of Life Sciences, University of Hyderabad, Hyderabad, India JUSTIN BOREVITZ • Department of Ecology and Evolution, University of Chicago, Chicago , IL , USA TIM BROWN • Time Science, Salt Lake City, UT , USA WEN-PING CHEN • Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota-Twin Cities, St. Paul, MN , USA JOANNE CHORY • Plant Biology Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla , CA , USA MADS H. CLAUSEN • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark JERRY D. COHEN • Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota-Twin Cities, St. Paul, MN , USA BENJAMIN J. COLE • Plant Biology Laboratory , Salk Institute for Biological Studies, La Jolla , CA , USA ; Division of Biological Sciences, University of California – San Diego, La Jolla , CA , USA BAS DE REGT • The Plant Accelerator, University of Adelaide, Urrbrae, SA , Australia JACK EGELUND • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark JONATAN U. FANGEL • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark JOACHIM FISAHN • Max Planck Institute of Molecular Plant Physiology, Potsdam , Germany DAVID W. GALBRAITH • School of Plant Sciences, University of Arizona, Tucson , AZ , USA PETER GEIGENBERGER • Department Biologie I, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany SAMUEL P. HAZEN • Department of Biology, University of Massachusetts, Amherst , MA , USA ADRIAN D. HEGEMAN • Department of Horticultural and Microbial and Plant Genomics Institute, D epartment of Plant Biology , University of Minnesota-Twin Cities , St. Paul, MN , USA ÉVA HIDEG • Institute of Biology, Faculty of Sciences, University of Pécs, Pécs , Hungary DIRK HINCHA • Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany ix x Contributors DENIS KLIMOV • Monterey Bay Aquarium Research Institute, Moss Landing, CA , USA KARIN KÖHL • Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany MIKIKO KOJIMA • RIKEN Plant Science Center, Tsurumi, Yokohama, Japan ZBIGNIEW S. KOLBER • University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA , USA JOACHIM KOPKA • Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany GEORGINA M. LAMBERT • School of Plant Sciences, University of Arizona, Tucson , AZ , USA SCOTT J. LEE • Plant Biology Graduate Program, University of Massachusetts, Amherst , MA , USA SUSAN B. LESCHINE • Department of Microbiology, University of Massachusetts, Amherst , MA , USA KALEB LOWE • Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, KS , USA MASSIMO MAFFEI • Unità di Fisiologia Vegetale, Dipartimento di Biologia Vegetale, University of Turin, Turin , Italy PETRA MAJER • Institute of Plant Physiology, Biological Research Centre, Szeged, Hungary WILL I. MENZEL • Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota-Twin Cities, St. Paul, MN , USA NINA NOAH • Department of Ecology and Evolution, University of Chicago, Chicago , IL , USA C. BARRY OSMOND • Plant Sciences Division, Research School of Biology, Australian National University, Canberra, Australia WHITNEY PANNETON • Department of Ecology and Evolution, University of Chicago, Chicago , IL , USA HENRIETTE L. PEDERSEN • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark ROLAND PIERUSCHKA • Forschungszentrum Jülich, IBG: 2 Plant Sciences, Jülich , Germany CHARLES A. PRICE • School of Plant Biology, University of Western Australia, Crawley, Perth , Australia UWE RASCHER • Forschungszentrum Jülich, IBG: 2 Plant Sciences, Jülich , Germany MARY R. ROTH • Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, KS , USA MAJA GRO RYDAHL • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark HITOSHI SAKAKIBARA • RIKEN Plant Science Center, Tsurumi, Yokohama, Japan ARMANDO ASUNCION SALMEAN • Department of Plant Biology and Biotechnology, University of Copenhagen, Frederiksberg, Denmark THILANI SAMARAKOON • Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, KS , USA LÁSZLÓ SASS • Institute of Plant Physiology , Biological Research Centre, Szeged, Hungary CHRISTIAN SCHUDOMA • Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany JAVIER SERAVALLI • Redox Biology Center and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE , USA RAMESHWAR SHARMA • School of Life Sciences, University of Hyderabad, Hyderabad, India
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