Table Of ContentM 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
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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
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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
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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
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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
