Chapter 19
Metabolomic Analysis of Natural Variation in Arabidopsis
Si Wu, Saleh Alseekh, Yariv Brotman, and Alisdair R. Fernie
Abstract
Methodological advances in coupled-mass spectrometry (gas chromatography and liquid chromatography;
GC-MS and LC-MS) have rendered the profiling of highly complex plant extracts relatively facile and
allowed that their high-throughput use aids the investigation of a range of biological questions. Among
these is the elucidation of the genetic factors underlying metabolite abundance. For this purpose genomewide association studies (GWAS) are being widely adopted in Arabidopsis with the resultant quantitative
trait loci being subjected to cross-validation by the use of recombinant inbred lines, introgression lines, and
T-DNA insertional knockout lines.
Key words Metabolomics, QTL analysis, Genome-wide association mapping, Gas-chromatography
mass-spectrometry, Liquid-chromatography mass-spectrometry
1 Introduction
The metabolites extant in the plant kingdom are extremely diverse;
a commonly quoted estimate is that plants produce somewhere in
the order of 200,000 unique chemical structures [1], with upward
of 5000 being present in any given species [2]. Of these, some 1000
or so are primary metabolites which are essential for everyday
cellular function and growth but the vast majority are specialized
metabolites [3, 4] that are nonessential for growth and therefore
not constitutively present in every cell type at every developmental
stage. Recently, there has been an increasing use in analytical technologies such as metabolomics for comprehensive profiling of
metabolites in biological samples in many different fields of biology
including the characterization of natural variance in the plant model
species Arabidopsis thaliana. Given the diversity of structural classes of metabolites, ranging from primary metabolites such as carbohydrates, amino acids, and organic acids to very complex
secondary metabolites such as the Brassicacea-specific glucosinolates as well as phenolics, alkaloids, and terpenoids, there is no
single methodology that can measure the complete metabolome
Jose J. Sanchez-Serrano and Julio Salinas (eds.), Arabidopsis Protocols, Methods in Molecular Biology, vol. 2200,
https://doi.org/10.1007/978-1-0716-0880-7_19, © Springer Science+Business Media, LLC, part of Springer Nature 2021
393
Metabolomic Analysis of Natural Variation in Arabidopsis
Si Wu, Saleh Alseekh, Yariv Brotman, and Alisdair R. Fernie
Abstract
Methodological advances in coupled-mass spectrometry (gas chromatography and liquid chromatography;
GC-MS and LC-MS) have rendered the profiling of highly complex plant extracts relatively facile and
allowed that their high-throughput use aids the investigation of a range of biological questions. Among
these is the elucidation of the genetic factors underlying metabolite abundance. For this purpose genomewide association studies (GWAS) are being widely adopted in Arabidopsis with the resultant quantitative
trait loci being subjected to cross-validation by the use of recombinant inbred lines, introgression lines, and
T-DNA insertional knockout lines.
Key words Metabolomics, QTL analysis, Genome-wide association mapping, Gas-chromatography
mass-spectrometry, Liquid-chromatography mass-spectrometry
1 Introduction
The metabolites extant in the plant kingdom are extremely diverse;
a commonly quoted estimate is that plants produce somewhere in
the order of 200,000 unique chemical structures [1], with upward
of 5000 being present in any given species [2]. Of these, some 1000
or so are primary metabolites which are essential for everyday
cellular function and growth but the vast majority are specialized
metabolites [3, 4] that are nonessential for growth and therefore
not constitutively present in every cell type at every developmental
stage. Recently, there has been an increasing use in analytical technologies such as metabolomics for comprehensive profiling of
metabolites in biological samples in many different fields of biology
including the characterization of natural variance in the plant model
species Arabidopsis thaliana. Given the diversity of structural classes of metabolites, ranging from primary metabolites such as carbohydrates, amino acids, and organic acids to very complex
secondary metabolites such as the Brassicacea-specific glucosinolates as well as phenolics, alkaloids, and terpenoids, there is no
single methodology that can measure the complete metabolome
Jose J. Sanchez-Serrano and Julio Salinas (eds.), Arabidopsis Protocols, Methods in Molecular Biology, vol. 2200,
https://doi.org/10.1007/978-1-0716-0880-7_19, © Springer Science+Business Media, LLC, part of Springer Nature 2021
393