Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis.
The detection of phenotypic alterations of mutants and variants is one of the bottlenecks that hinder systematic gene functional studies of the model plant Arabidopsis. In an earlier study, we have addressed this problem by proposing a novel methodology for phenome analysis based on in silico analysis of polygon models that are acquired by 3-dimensional (3D) measurement and which precisely reconstruct the actual plant shape. However, 3D quantitative descriptions of morphological traits are rare, whereas conventional 2D descriptions have already been studied but may lack the necessary precision. In this report, we focus on six major leaf morphological traits, which are commonly used in the current manual mutant screens, and propose new 3D quantitative definitions that describe these traits. In experiments to extract the traits, we found significant differences between two variants of Arabidopsis with respect to blade roundness and blade epinasty. Remarkably, the detected difference between variants in the blade roundness trait was undetectable when using conventional 2D descriptions. Thus, the result of the experiment indicates that the proposed definitions with 3D description may lead to new discoveries of phenotypic alteration in gene functional studies that would not be possible using conventional 2D descriptions.
Kaminuma
Eli
E
Bioinformatics Group, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan. eli@gsc.riken.jp
Heida
Naohiko
N
Tsumoto
Yuko
Y
Nakazawa
Miki
M
Goto
Nobuharu
N
Konagaya
Akihiko
A
Matsui
Minami
M
Toyoda
Tetsuro
T
D000465:Algorithms; D017360:Arabidopsis / Q000033:anatomy & histology* / Q000145:classification*; D001185:Artificial Intelligence; D016208:Databases, Factual; D007090:Image Interpretation, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008953:Models, Anatomic; D010641:Phenotype; D018515:Plant Leaves / Q000033:anatomy & histology* / Q000145:classification*