lead to insightful discoveries of novel gene–metabolite associations involved in plants’ regulatory systems toward the changing environments.
Acknowledgements
This work was in part supported by the PlantaSYST project by the
European Union’s Horizon 2020 research and innovation
programme (SGA-CSA No 664621 and No 739582 under FPA
No. 664620).
References
1. Rai A, Saito K, Yamazaki M (2017) Integrated
omics analysis of specialized metabolism in
medicinal plants. Plant J 90(4):764–787
2. Fernie AR et al (2004) Metabolite profiling:
from diagnostics to systems biology. Nat Rev
Mol Cell Biol 5(9):763–769
3. Weng JK, Philippe RN, Noel JP (2012) The
rise of chemodiversity in plants. Science 336
(6089):1667–1670
4. Fraenkel GS (1959) The raison d‘etre of secondary plant substances; these odd chemicals
arose as a means of protecting plants from
insects and now guide insects to food. Science
129(3361):1466–1470
5. Alseekh S, Fernie AR (2018) Metabolomics
20 years on: what have we learned and what
hurdles remain? Plant J 94(6):933–942
6. Fang C, Luo J (2019) Metabolic GWAS-based
dissection of genetic bases underlying the
diversity of plant metabolism. Plant J 97
(1):91–100
7. Luo J (2015) Metabolite-based genome-wide
association studies in plants. Curr Opin Plant
Biol 24:31–38
8. Biais B et al (2012) Precautions for harvest,
sampling, storage, and transport of crop plant
metabolomics samples. In: Hardy NW, Hall
RD (eds) Plant metabolomics: methods and
protocols. Humana Press, Totowa, pp 51–63
9. Gibon Y, Rolin D (2012) Aspects of experimental design for plant metabolomics experiments and guidelines for growth of plant
material. Methods Mol Biol 860:13–30
10. Sysi-Aho M et al (2007) Normalization
method for metabolomics data using optimal
selection of multiple internal standards. BMC
Bioinform 8:93
11. van der Kloet FM et al (2009) Analytical error
reduction using single point calibration for
accurate and precise metabolomic phenotyping. J Proteome Res 8(11):5132–5141
12. van der Greef J et al (2007) The art and practice of systems biology in medicine: mapping
patterns of relationships. J Proteome Res 6
(4):1540–1559
13. Dunn WB et al (2008) Metabolic profiling of
serum using ultra performance liquid chromatography and the LTQ-Orbitrap mass spectrometry system. J Chromatogr B Anal
Technol Biomed Life Sci 871(2):288–298
14. Bijlsma S et al (2006) Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. Anal Chem 78
(2):567–574
15. Chen MJ et al (2014) A modified data normalization method for GC-MS-based metabolomics
to
minimize
batch
variation.
Springerplus 3:439
16. Fiehn O et al (2001) Metabolite profiling for
plant functional genomics (vol 187, pg 1157,
2000). Nat Biotechnol 19(2):173–173
17. Fiehn O et al (2000) Metabolite profiling for
plant functional genomics. Nat Biotechnol 18
(11):1157–1161
18. Lisec J et al (2006) Gas chromatography mass
spectrometry-based metabolite profiling in
plants. Nat Protoc 1(1):387–396
19. Wen W et al (2015) Genetic determinants of
the network of primary metabolism and their
relationships to plant performance in a maize
recombinant inbred line population. Plant Cell
27(7):1839–1856
20. Nunes-Nesi A et al (2019) Identification and
characterization of metabolite quantitative trait
loci in tomato leaves and comparison with
those reported for fruits and seeds. Metabolomics 15(4):46
21. de Oliveira Silva FM et al (2018) The genetic
architecture of photosynthesis and plant
Metabolomic Analysis of Natural Variation in Arabidopsis
409
Acknowledgements
This work was in part supported by the PlantaSYST project by the
European Union’s Horizon 2020 research and innovation
programme (SGA-CSA No 664621 and No 739582 under FPA
No. 664620).
References
1. Rai A, Saito K, Yamazaki M (2017) Integrated
omics analysis of specialized metabolism in
medicinal plants. Plant J 90(4):764–787
2. Fernie AR et al (2004) Metabolite profiling:
from diagnostics to systems biology. Nat Rev
Mol Cell Biol 5(9):763–769
3. Weng JK, Philippe RN, Noel JP (2012) The
rise of chemodiversity in plants. Science 336
(6089):1667–1670
4. Fraenkel GS (1959) The raison d‘etre of secondary plant substances; these odd chemicals
arose as a means of protecting plants from
insects and now guide insects to food. Science
129(3361):1466–1470
5. Alseekh S, Fernie AR (2018) Metabolomics
20 years on: what have we learned and what
hurdles remain? Plant J 94(6):933–942
6. Fang C, Luo J (2019) Metabolic GWAS-based
dissection of genetic bases underlying the
diversity of plant metabolism. Plant J 97
(1):91–100
7. Luo J (2015) Metabolite-based genome-wide
association studies in plants. Curr Opin Plant
Biol 24:31–38
8. Biais B et al (2012) Precautions for harvest,
sampling, storage, and transport of crop plant
metabolomics samples. In: Hardy NW, Hall
RD (eds) Plant metabolomics: methods and
protocols. Humana Press, Totowa, pp 51–63
9. Gibon Y, Rolin D (2012) Aspects of experimental design for plant metabolomics experiments and guidelines for growth of plant
material. Methods Mol Biol 860:13–30
10. Sysi-Aho M et al (2007) Normalization
method for metabolomics data using optimal
selection of multiple internal standards. BMC
Bioinform 8:93
11. van der Kloet FM et al (2009) Analytical error
reduction using single point calibration for
accurate and precise metabolomic phenotyping. J Proteome Res 8(11):5132–5141
12. van der Greef J et al (2007) The art and practice of systems biology in medicine: mapping
patterns of relationships. J Proteome Res 6
(4):1540–1559
13. Dunn WB et al (2008) Metabolic profiling of
serum using ultra performance liquid chromatography and the LTQ-Orbitrap mass spectrometry system. J Chromatogr B Anal
Technol Biomed Life Sci 871(2):288–298
14. Bijlsma S et al (2006) Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. Anal Chem 78
(2):567–574
15. Chen MJ et al (2014) A modified data normalization method for GC-MS-based metabolomics
to
minimize
batch
variation.
Springerplus 3:439
16. Fiehn O et al (2001) Metabolite profiling for
plant functional genomics (vol 187, pg 1157,
2000). Nat Biotechnol 19(2):173–173
17. Fiehn O et al (2000) Metabolite profiling for
plant functional genomics. Nat Biotechnol 18
(11):1157–1161
18. Lisec J et al (2006) Gas chromatography mass
spectrometry-based metabolite profiling in
plants. Nat Protoc 1(1):387–396
19. Wen W et al (2015) Genetic determinants of
the network of primary metabolism and their
relationships to plant performance in a maize
recombinant inbred line population. Plant Cell
27(7):1839–1856
20. Nunes-Nesi A et al (2019) Identification and
characterization of metabolite quantitative trait
loci in tomato leaves and comparison with
those reported for fruits and seeds. Metabolomics 15(4):46
21. de Oliveira Silva FM et al (2018) The genetic
architecture of photosynthesis and plant
Metabolomic Analysis of Natural Variation in Arabidopsis
409