A rapid, simple method for the genetic discrimination of intact Arabidopsis thaliana mutant seeds using metabolic profiling by direct analysis in real-time mass spectrometry

Suk Weon Kim,Yong Kook Kwon,Young Pyo Jang,Jang R Liu,Myung Suk Ahn,Jong Hyun Kim,Hye Jin Kim

doi:10.1186/1746-4811-7-14

Abstract

BackgroundEfficient high throughput screening systems of useful mutants are prerequisite for study of plant functional genomics and lots of application fields. Advance in such screening tools, thanks to the development of analytic instruments. Direct analysis in real-time (DART)-mass spectrometry (MS) by ionization of complex materials at atmospheric pressure is a rapid, simple, high-resolution analytical technique. Here we describe a rapid, simple method for the genetic discrimination of intact Arabidopsis thaliana mutant seeds using metabolic profiling by DART-MS.ResultsTo determine whether this DART-MS combined by multivariate analysis can perform genetic discrimination based on global metabolic profiling, intact Arabidopsis thaliana mutant seeds were subjected to DART-MS without any sample preparation. Partial least squares-discriminant analysis (PLS-DA) of DART-MS spectral data from intact seeds classified 14 different lines of seeds into two distinct groups: Columbia (Col-0) and Landsberg erecta (Ler) ecotype backgrounds. A hierarchical dendrogram based on partial least squares-discriminant analysis (PLS-DA) subdivided the Col-0 ecotype into two groups: mutant lines harboring defects in the phenylpropanoid biosynthetic pathway and mutants without these defects. These results indicated that metabolic profiling with DART-MS could discriminate intact Arabidopsis seeds at least ecotype level and metabolic pathway level within same ecotype.ConclusionThe described DART-MS combined by multivariate analysis allows for rapid screening and metabolic characterization of lots of Arabidopsis mutant seeds without complex metabolic preparation steps. Moreover, potential novel metabolic markers can be detected and used to clarify the genetic relationship between Arabidopsis cultivars. Furthermore this technique can be applied to predict the novel gene function of metabolic mutants regardless of morphological phenotypes.

Highlights

Efficient high throughput screening systems of useful mutants are prerequisite for study of plant functional genomics and lots of application fields
These results indicated that metabolic profiling with Direct analysis in real-time (DART)-mass spectrometry (MS) spectral data could discriminate two Arabidopsis ecotypes even though there were no visible, distinctive characteristics in the seed morphology
In this study, we demonstrate that Direct analysis in real-time mass spectrometry (DART-MS) combined by multivariate analysis allows for rapid screening and metabolic characterization of lots of Arabidopsis mutant seeds without complex metabolic preparation steps

Summary

Introduction

Efficient high throughput screening systems of useful mutants are prerequisite for study of plant functional genomics and lots of application fields. Global metabolic profiling coupled with statistical analysis is often used for diverse plant biotechnology applications including rapid discrimination between plant species [1,2,3], differentiation of cultivars or ecotypes [4,5,6], identification of genetically modified plants [7,8,9,10,11,12,13], and metabolic evaluation of commercial food stocks or medicinal herbs [14,15,16,17,18] These techniques have been successfully applied to plant functional genomics [19,20,21,22]. Plant metabolomics combined with transcriptomics has been used to characterize systemic physiological stress responses [23,24,25,26]

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Results

Conclusion