MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings

The Plant Journal : for Cell and Molecular Biology
Isabel Betegón-PutzeAna I Caño-Delgado

Abstract

Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R2  = 0.997). When compared with previous developed software with similar features (BRAT and EZ-Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use ...Continue Reading

References

Oct 30, 1995·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·G JürgensT Laux
Jan 1, 1995·Plant Physiology·H Ishikawa, M L Evans
Sep 13, 2001·Plant Physiology·J LiJ Chory
Apr 22, 2008·Nature Cell Biology·Susana Ubeda-TomásMalcolm J Bennett
Nov 13, 2008·The Plant Journal : for Cell and Molecular Biology·Patrick ArmengaudAnna Amtmann
Jan 2, 2009·Current Opinion in Plant Biology·Anjali Iyer-PascuzziPhilip N Benfey
Jun 12, 2009·Plant Physiology·Andrew FrenchTony Pridmore
Jan 29, 2011·Development·Mary-Paz González-GarcíaAna I Caño-Delgado
Aug 16, 2012·Methods in Molecular Biology·Nima Yazdanbakhsh, Joachim Fisahn
Jan 22, 2013·Plant Physiology·Daniela RistovaGloria M Coruzzi
Jun 15, 2013·Plant Physiology·Michael P PoundTony Pridmore
Oct 11, 2013·Plant Methods·Guillaume LobetClaire Périlleux
Jan 30, 2014·Journal of Experimental Botany·Hirotomo Takatsuka, Masaaki Umeda
Jun 13, 2014·The Plant Cell·Radka SlovakWolfgang Busch
Jan 24, 2015·Plant Physiology·Guillaume LobetAndrea Schnepf
Jun 14, 2015·Journal of Experimental Botany·René C P KuijkenHarro J Bouwmeester
Aug 1, 2015·Journal of Experimental Botany·Jinhai CaiStanley J Miklavcic
Jun 3, 2017·Trends in Plant Science·Guillaume Lobet

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Citations

Nov 17, 2020·Frontiers in Plant Science·Chen ShenLimin Shao
Jun 17, 2021·Molecular Systems Biology·Isabel Betegón-PutzeAna I Caño-Delgado

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Methods Mentioned

BETA
imaging techniques
transgenic

Software Mentioned

BRAT
ROOT
linSVM
EZ
MATLAB Runtime
Hypocotyl
MyROOT
Rhizo
HypocotylDetection
rsml

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