Skip to main content

Main menu

  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
  • About
    • Editorial Board and Staff
    • About the Journal
    • Terms & Privacy
  • More
    • Alerts
    • Contact Us
  • Submit a Manuscript
    • Instructions for Authors
    • Submit a Manuscript
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Teaching Tools in Plant Biology
    • ASPB
    • Plantae

User menu

  • My alerts
  • Log in

Search

  • Advanced search
Plant Cell
  • Other Publications
    • Plant Physiology
    • The Plant Cell
    • Plant Direct
    • The Arabidopsis Book
    • Teaching Tools in Plant Biology
    • ASPB
    • Plantae
  • My alerts
  • Log in
Plant Cell

Advanced Search

  • Home
  • Content
    • Current Issue
    • Archive
    • Preview Papers
  • About
    • Editorial Board and Staff
    • About the Journal
    • Terms & Privacy
  • More
    • Alerts
    • Contact Us
  • Submit a Manuscript
    • Instructions for Authors
    • Submit a Manuscript
  • Follow PlantCell on Twitter
  • Visit PlantCell on Facebook
  • Visit Plantae
OtherGenomics Article
You have accessRestricted Access

Growth Stage–Based Phenotypic Analysis of Arabidopsis

A Model for High Throughput Functional Genomics in Plants

Douglas C. Boyes, Adel M. Zayed, Robert Ascenzi, Amy J. McCaskill, Neil E. Hoffman, Keith R. Davis, Jörn Görlach
Douglas C. Boyes
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adel M. Zayed
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert Ascenzi
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amy J. McCaskill
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Neil E. Hoffman
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Keith R. Davis
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jörn Görlach
Department of Plant Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site

Published July 2001. DOI: https://doi.org/10.1105/TPC.010011

  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Figure 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 1.

    Scheme of the Chronological Progression of Principal Growth Stages in Arabidopsis.

    Horizontal bars indicate the period during wild-type Col-0 plant development when the indicated trait can be used in growth stage determination. Numbers in parentheses correspond to principal growth stages listed in Table 1.

  • Figure 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 2.

    Arabidopsis Growth Stages.

    (A) Stage 0.1, imbibition.

    (B) Stage 0.5, radicle emergence.

    (C) Stage 0.7, hypocotyl and cotyledons emerged from seed coat.

    (D) Stage 1.0, cotyledons opened fully.

    (E) Stage 1.02, two rosette leaves >1 mm in length.

    (F) Stage 1.04, four rosette leaves >1 mm in length.

    (G) Stage 1.10, ten rosette leaves >1 mm in length.

    (H) Stage 5.10, first flower buds visible (indicated by arrow in inset).

    (I) Stage 6.00, first flower open.

    (J) Stage 6.50, midflowering.

    (K) Stage 6.90, flowering complete.

    (L) Stage 9.70, senescent and ready for seed harvest.

    (A) to (F) were determined in the early analysis platform. (G) to (L) were determined in the soil-based platform.

  • Figure 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 3.

    Representative Data from Wild-Type Col-0 Plants.

    (A) Number of rosette leaves >1 mm in length produced over time.

    (B) Maximum rosette radius (i.e., length of the longest rosette leaf) over time.

    (C) Plant height over time.

    Arrows indicate the time at which growth stages 5.10, 6.00, and 6.50 occur. Data are given as averages ±sd for >300 individual plants. Days are given relative to date of sowing, including a 3-day stratification at 4°C to synchronize seed germination.

  • Figure 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 4.

    Growth Stage Progression for Wild-Type (Col-0) and Five Mutant Lines.

    (A) Progression as determined in the plate-based early analysis platform.

    (B) Progression as determined in the soil-based analysis platform.

    Arrows define the time (days after sowing) at which Col-0 plants reached the growth stages indicated. Boxes represent the time elapsed between the occurrence of successive growth stages. Junctions between boxes of different shading indicate the occurrence of a growth stage. In (B), overlapping boxes for fae1-1 indicate that growth stage 5.10 was reached before stage 1.10. Days are given relative to date of sowing, including a 3-day stratificaton at 4°C to synchronize seed germination.

  • Figure 5.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Figure 5.

    Detection of Phenotypic Differences between Mutants and Wild-Type Col-0 Plants.

    (A) Comparison of leaf initiation between hls1-1 and Col-0. The number of leaves >1 mm were measured on day 14. Data are averages of 40 or >100 plants for hls1-1 and Col-0, respectively.

    (B) Comparison of shoot growth between fae1-1 and Col-0. Total exposed leaf area was determined via a computerized analysis of digital images of intact rosettes (see Methods). Data are averages of 10 or >100 plants for fae1-1 and Col-0, respectively.

    (C) Comparison of root growth between adg1-1 and Col-0. Both measurements were taken on day 14 (11 days after transfer to the growth chamber) and represent 20 seedlings grown on two plates.

    (D) Comparison of silique area and the number of seed per half-silique between adg1-1 and Col-0. Silique area was determined via computerized analysis of digital images of mature filled siliques (see Methods). The number of seed per half-silique was observed after removal of the outer layer of one valve of a mature filled silique. Both measures were averaged from three siliques per plant and are reported as the average of 10 or >300 plants for adg1-1 and Col-0, respectively.

    (E) Comparison of silique number and yield per plant between adg1-1 and Col-0. The final number of siliques per plant was determined after the completion of flower production (stage 6.90). Yield is reported as the desiccated mass (mg) of seed produced per plant. Data are averages and standard deviations of 10 or >300 plants for adg1-1 or Col-0, respectively.

    (A) to (C) were obtained in the plate-based assay, and (D) and (E) were obtained in the soil-based assay.

    Error bars indicate ±sd.

Tables

  • Figures
    • View popup
    Table 1.

    Arabidopsis Growth Stages for the Plate-Based Phenotypic Analysis Platform

    Col-0 Data
    StageDescriptionDaysasdCVb
    Principal growth stage 0Seed germination
    0.10Seed imbibition3.0NAcNA
    0.50Radicle emergence4.30.410.3
    0.7Hypocotyl and cotyledon emergence5.50.611.2
    Principal growth stage 1Leaf development
    1.0Cotyledons fully opened6.00.58.5
    1.022 rosette leaves >1 mm10.30.65.8
    1.044 rosette leaves >1 mm14.40.53.4
    Stage R6More than 50% of the seedlings have primary roots ≥6 cm in lengthNDdNDND
    • a Average day from date of sowing, including a 3-day stratification at 4°C to synchronize germination.

    • b CV, coefficient of variation, calculated as (sd/days) × 100.

    • c NA, not applicable.

    • d ND, not determined (see text for details).

    • View popup
    Table 2.

    Arabidopsis Growth Stages for the Soil-Based Phenotypic Analysis Platform

    Col-0 Data
    StageDescriptionDaysasdCVb
    Principal growth stage 1Leaf development
    1.022 rosette leaves >1 mm in length12.51.310.7
    1.033 rosette leaves >1 mm in length15.91.59.5
    1.044 rosette leaves >1 mm in length16.51.69.8
    1.055 rosette leaves >1 mm in length17.71.810.2
    1.066 rosette leaves >1 mm in length18.41.89.8
    1.077 rosette leaves >1 mm in length19.42.211.1
    1.088 rosette leaves >1 mm in length20.02.211.2
    1.099 rosette leaves >1 mm in length21.12.310.8
    1.1010 rosette leaves >1 mm in length21.62.310.9
    1.1111 rosette leaves >1 mm in length22.22.511.2
    1.1212 rosette leaves >1 mm in length23.32.611.3
    1.1313 rosette leaves >1 mm in length24.83.212.8
    1.1414 rosette leaves >1 mm in length25.52.610.2
    Principal growth stage 3Rosette growth
    3.20Rosette is 20% of final size18.93.016.0
    3.50Rosette is 50% of final size24.04.117.0
    3.70Rosette is 70% of final size27.44.115.0
    3.90Rosette growth complete29.33.512.0
    Principal growth stage 5Inflorescence emergence
    5.10First flower buds visible26.03.513.3
    Principal growth stage 6Flower production
    6.00First flower open31.83.613.3
    6.1010% of flowers to be produced have opened35.94.913.6
    6.3030% of flowers to be produced have opened40.14.912.3
    6.5050% of flowers to be produced have opened43.54.911.2
    6.90Flowering complete49.45.811.7
    Principal growth stage 8Silique ripening
    8.00First silique shattered48.04.59.3
    Principal growth stage 9Senescence
    9.70Senescence complete; ready for seed harvestNDcNDND
    • a Average day from date of sowing, including a 3-day stratification at 4°C to synchronize germination.

    • b CV, coefficient of variation, calculated as (sd/days) × 100.

    • c ND, not determined (see text for details).

    • View popup
    Table 3.

    Measurements Performed during the Plate-Based Phenotypic Analysis

    First-Phase Measurements
    Measurement/QueryGrowth Stage Defined
    Has radicle emergence been reached or passed?Stage 0.5
    Are the hypocotyl and cotyledons visible?Stage 0.7
    Have the cotyledons opened fully?Stage 1.0
    Number of rosette leaves >1 mmPrincipal growth stage 1
    Length of primary root ≥6 cmStage R6
    • View popup
    Table 4.

    Measurements Performed during the Soil-Based Phenotypic Analysis

    First-Phase Measurements
    Measurement/QueryGrowth Stage Defined
    Rosette radiusPrincipal growth stage 3
    Are flower buds visible?Stage 5.10
    Is first flower open?Stage 6.00
    Length of stemStage 6.50a
    Number of open flowersPrincipal growth stage 6
    Number of senescent flowersPrincipal growth stage 6
    Number of filled siliquesPrincipal growth stages 6 and 7
    Number of shattered siliquesPrincipal growth stage 8
    Is flower production complete?Stage 6.90
  • Col-0 Data
    MeasurementUnitGrowth StageAveragesdCVa
    Number of rosette leavesCount1.0b3.30.513.7
    Length of primary rootmm1.0b45.24.19.0
    Number of secondary rootsCountR6c10.51.413.2
    Rosette, total exposed leaf areamm2R6c22.22.611.9
    Rosette, perimetermmR6c42.15.212.2
    Rosette, sd of radiusNoneR6c39.23.17.9
    Rosette, major axismmR6c7.90.79.1
    Rosette, minor axismmR6c5.90.69.5
    Rosette, eccentricityNoneR6c0.630.057.2
    • a CV, coefficient of variation, calculated as (sd/days) × 100.

    • b Data collection initiated at stage 1.0 and continued until the end of the experiment.

    • c R6 or 14 days after sowing, whichever comes first.

  • Col-0 Data
    MeasurementUnitGrowth StageAverage sdCVb
    Number of cotyledonsCount1.042.00.15.0
    Rosette, total exposed leaf areamm21.10580.0202.234.9
    Rosette, perimetermm1.10418.0119.128.5
    Rosette, sd of radiusNone1.1045.73.27.0
    Rosette, major axismm1.1040.48.019.8
    Rosette, minor axismm1.1034.67.521.7
    Rosette, eccentricityNone1.100.50.120.0
    Rosette, total exposed leaf areamm26.003225.01088.333.7
    Rosette, perimetermm6.00808.1181.322.4
    Rosette, sd of radiusNone6.0036.73.59.5
    Rosette, major axismm6.0082.315.318.6
    Rosette, minor axismm6.0073.113.418.3
    Rosette, eccentricityNone6.000.40.125.0
    Rosette, dry weightmg6.00117.445.939.1
    Number of stem branches on main boltCount6.503.40.617.6
    Number of side bolts >1 cmCount6.504.21.228.6
    Length of peduncle of second flower on main boltmm6.5011.51.613.9
    Distance across face of open flowermm6.503.90.37.7
    Sepal lengthmm6.502.20.29.1
    Pollen grain, areaμm26.50589.0132.022.4
    Pollen grain, perimeterμm6.50114.513.011.2
    Pollen grain, sd of radiusNone6.509.12.527.5
    Pollen grain, major axisμm6.5030.63.310.8
    Pollen grain, minor axisμm6.5024.33.012.3
    Pollen grain, eccentricityNone6.500.60.116.7
    Silique, areamm26.5010.61.917.9
    Silique, perimetermm6.5040.96.114.9
    Silique, sd of radiusNone6.5055.80.50.9
    Silique, major axismm6.5017.21.79.9
    Silique, minor axismm6.501.20.216.7
    Silique, eccentricityNone6.501.00.00.0
    Total number of seeds per silique valveCount6.5029.92.89.4
    Number of abnormal seeds per silique valveCount6.500.20.4200
    Dry weight of stemmg6.50188.839.320.8
    Dry weight of rosettemg6.50163.752.031.8
    Total number of siliquesCount6.90160.460.737.8
    Seed, areamm29.700.140.017.1
    Seed, perimetermm9.701.950.042.1
    Seed, sd of radiusNone9.7016.920.945.6
    Seed, major axismm9.700.530.035.7
    Seed, minor axismm9.700.330.026.1
    Seed , eccentricityNone9.700.780.022.6
    Seed yield per plant (desiccated)mg9.70127.952.741.2
    • a Used to define the working definition of stage 6.50 as described in the text.

    • b CV, coefficient of variation, calculated as (sd/days) × 100.

PreviousNext
Back to top

Table of Contents

Print
Download PDF
Email Article

Thank you for your interest in spreading the word on Plant Cell.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Growth Stage–Based Phenotypic Analysis of Arabidopsis
(Your Name) has sent you a message from Plant Cell
(Your Name) thought you would like to see the Plant Cell web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Growth Stage–Based Phenotypic Analysis of Arabidopsis
Douglas C. Boyes, Adel M. Zayed, Robert Ascenzi, Amy J. McCaskill, Neil E. Hoffman, Keith R. Davis, Jörn Görlach
The Plant Cell Jul 2001, 13 (7) 1499-1510; DOI: 10.1105/TPC.010011

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Request Permissions
Share
Growth Stage–Based Phenotypic Analysis of Arabidopsis
Douglas C. Boyes, Adel M. Zayed, Robert Ascenzi, Amy J. McCaskill, Neil E. Hoffman, Keith R. Davis, Jörn Görlach
The Plant Cell Jul 2001, 13 (7) 1499-1510; DOI: 10.1105/TPC.010011
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
    • Abstract
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • METHODS
    • Acknowledgments
    • References
  • Figures & Data
  • Info & Metrics
  • PDF

In this issue

The Plant Cell Online: 13 (7)
The Plant Cell
Vol. 13, Issue 7
Jul 2001
  • Table of Contents
  • About the Cover
  • Index by author
View this article with LENS

More in this TOC Section

  • Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis
  • Laser-Capture Microdissection, a Tool for the Global Analysis of Gene Expression in Specific Plant Cell Types: Identification of Genes Expressed Differentially in Epidermal Cells or Vascular Tissues of Maize
  • A High-Throughput Arabidopsis Reverse Genetics System
Show more GENOMICS ARTICLE

Similar Articles

Our Content

  • Home
  • Current Issue
  • Plant Cell Preview
  • Archive
  • Teaching Tools in Plant Biology
  • Plant Physiology
  • Plant Direct
  • Plantae
  • ASPB

For Authors

  • Instructions
  • Submit a Manuscript
  • Editorial Board and Staff
  • Policies
  • Recognizing our Authors

For Reviewers

  • Instructions
  • Peer Review Reports
  • Journal Miles
  • Transfer of reviews to Plant Direct
  • Policies

Other Services

  • Permissions
  • Librarian resources
  • Advertise in our journals
  • Alerts
  • RSS Feeds
  • Contact Us

Copyright © 2021 by The American Society of Plant Biologists

Powered by HighWire