title: Detection of a gravitropism phenotype in glutamate receptor-like 3.3 mutants of Arabidopsis thaliana using machine vision and computation.
abstract: Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca(2+)-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function.
authors.affiliation: Department of Mathematics, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Miller
authors.forename: Tessa L
authors.initials: TL
authors.lastname: Durham Brooks
authors.forename: Amir H
authors.initials: AH
authors.lastname: Assadi
authors.forename: Edgar P
authors.initials: EP
authors.lastname: Spalding
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000502:physiology*; D015220:Calcium Channels; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D005838:Genotype; D018522:Gravitropism / Q000235:genetics* / Q000502:physiology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D009154:Mutation; D010641:Phenotype; D018517:Plant Roots / Q000235:genetics / Q000502:physiology; D017470:Receptors, Glutamate / Q000235:genetics* / Q000502:physiology*; D036226:Seedlings / Q000033:anatomy & histology / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction; D058067:Wavelet Analysis
chemical_list: D029681:Arabidopsis Proteins; D015220:Calcium Channels; C516468:GLR3.3 protein, Arabidopsis; D017470:Receptors, Glutamate