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From phenotype to genotype: whole tissue profiling for plant breeding

Goodacre, Royston; Roberts, Luned; Ellis, David I.; Thorogood, Danny; Reader, Stephen M.; Ougham, Helen; King, Ian


Royston Goodacre

Luned Roberts

David I. Ellis

Danny Thorogood

Stephen M. Reader

Helen Ougham


Fourier transform infrared spectroscopy (FT-IR) was used to obtain ‘holistic’ metabolic fingerprints from a wide range of plants to differentiate species, population, single plant genotype, and chromosomal constitution differences. Sample preparation simply entailed the maceration of fresh leaves with water, and these samples were then dried and analysed by reflectance FT-IR where spectral acquisition was typically 10 s. All samples gave reproducible, characteristic biological infrared absorption spectra and these were analysed by chemometric methods. FT-IR is not biased to any particular chemical species and thus the whole tissue profiles produced measure the total biochemical makeup of the test sample; that is to say it represents a plant phenotype. We show that by simple cluster analysis these phenotypic measurements can be related to the genotypes of the plants and can reliably differentiate closely related individuals. We believe that this approach provides a valuable new tool for the rapid metabolomic profiling of plants, with applications to plant breeding and the assessment of substantial equivalency for genetically-modified plants.


Goodacre, R., Roberts, L., Ellis, D. I., Thorogood, D., Reader, S. M., Ougham, H., & King, I. (2007). From phenotype to genotype: whole tissue profiling for plant breeding. Metabolomics, 3(4), 489-501. doi:10.1007/s11306-007-0062-6

Journal Article Type Article
Acceptance Date Apr 23, 2007
Online Publication Date Jun 19, 2007
Publication Date 2007-12
Deposit Date Dec 6, 2018
Journal Metabolomics
Print ISSN 1573-3882
Electronic ISSN 1573-3890
Publisher BMC
Peer Reviewed Peer Reviewed
Volume 3
Issue 4
Pages 489-501
Public URL
Publisher URL