High-Throughput Phenotyping in Plants Methods and Protocols

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 Biology™ 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.

1. Image-Based Analysis of Light-Grown Seedling Hypocotyls in Arabidopsis

            Benjamin J. Cole and Joanne Chory

2. High Throughput Phenotyping of Plant Shoots

            Bettina Berger, Bas de Regt, and Mark Tester

3. High Throughput Phenotyping of Root Growth Dynamics

            Nima Yazdanbakhsh and Joachim Fisahn

4. LEAF GUI: Analyzing the Geometry of Veins and Areoles Using Image Segmentation Algorithms

            Charles A. Price

5. Remote Chlorophyll Fluorescence Measurements with the Laser Induced Fluorescence Transient (LIFT) Approach

            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

            László Sass, Petra Majer, and Éva Hideg

7. High Resolution, Time-Lapse Imaging for Ecosystem-Scale Phenotyping in the Field

            Tim Brown, Christopher Zimmermann, Whitney Panneton, Nina Noah, and Justin Borevitz

8. High Throughput Phenotyping of Plant Populations Using a Personal Digital Assistant

            Raju Naik Vankudavath, Reddaiah Bodanapu, Yellamaraju Sreelakshmi, and Rameshwar Sharma

9. High Throughput Fractionation of Natural Products for Drug Discovery

            Ying Tu and Bing Yan

10. Conducting Molecular Biomarker Discovery Studies in Plants

            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

            Mikiko Kojima and Hitoshi Sakakibara

12. Qualitative and Quantitative Screening of Amino Acids in Plant Tissues

            Will I. Menzel, Wen-Ping Chen, Adrian D. Hegeman, and Jerry D. Cohen

13. Arabidopsis thaliana Membrane Lipid Molecular Species and Their Mass Spectral Analysis

            Thilani Samarakoon, Sunitha Shiva, Kaleb Lowe, Pamela Tamura, Mary R. Roth, and Ruth Welti

14. ICP-MS as a Tool For High Throughput Analysis of Plants

            Javier Seravalli

15. The Plant Volatilome: Methods of Analysis

            Carlo Bicchi and Massimo Maffei

16. High Throughput Monitoring of Plant Nuclear DNA Contents via Flow Cytometry

            David W. Galbraith and Georgina M. Lambert

17. Transient RNAi Assay in 96-Well Plate Format Facilitates High Throughput Gene Function Studies in planta

            Shu-Zon Wu and Magdalena Bezanilla

18. A High Throughput Biological Conversion Assay for Determining Lignocellulosic Quality

Scott J. Lee, Thomas A. Warnick, Susan B. Leschine, and Samuel P. Hazen

19. Carbohydrate Microarrays in Plant Science

            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