Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence

0359493 - ÚVGZ 2012 RIV NL eng J - Journal Article
Codrea, C. C. - Hakala-Yatkin, M. - Karlund-Marttila, A. - Nedbal, Ladislav - Aittokallio, T. - Nevalainen, O. S. - Tyystjärvi, E.
Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence.
Photosynthesis Research. Roč. 105, č. 3 (2010), s. 273-283. ISSN 0166-8595. E-ISSN 1573-5079
Institutional research plan: CEZ:AV0Z60870520
Keywords : arabidopsis thaliana * chlorophyll fluorescence * fluorescence imaging * mutant detection * outlier detection
Subject RIV: EH - Ecology, Behaviour
Impact factor: 2.410, year: 2010
http://www.springerlink.com/content/x3586512462pn006/

Rapid nondestructive screening of mutants is a common step in many research projects in plant biology. Here we report the development of a method that uses kinetic imaging of chlorophyll fluorescence to detect phenotypes that differ from wild-type plants. The method uses multiple fluorescence features simultaneously in order to catch different types of photosynthesis-related mutants with a single assay. The Mahalanobis distance was used to evaluate the degree of similarity in fluorescence features between the wild-type and test plants, and plants differing strongly from the wild-type were classified as mutants. The method was tested on a collection of photosynthesis-related mutants of Arabidopsis thaliana. The plants were evaluated from images in which the color of each pixel depended on the Mahalanobis distance of the fluorescence features. Two parameters of the color-coding procedure were used to adjust the trade-off between detection of true mutants and erratic classification of wild-type plants as mutants. We found that a large percentage of photosynthesis-related mutants can be detected with this method. Scripts for the free statistics software R are provided to facilitate the practical application of the method.
Permanent Link: http://hdl.handle.net/11104/0197274