Abstract
Metabolites reflect the integration of gene expression, protein interaction and other different regulatory processes and are therefore closer to the phenotype than mRNA transcripts or proteins alone. Amongst all –omics technologies, metabolomics is the most transversal and can be applied to different organisms with little or no modifications. It has been successfully applied to the study of molecular phenotypes of plants in response to abiotic stress in order to find particular patterns associated to stress tolerance. These studies have highlighted the essential involvement of primary metabolites: sugars, amino acids and Krebs cycle intermediates as direct markers of photosynthetic dysfunction as well as effectors of osmotic readjustment. On the contrary, secondary metabolites are more specific of genera and species and respond to particular stress conditions as antioxidants, Reactive Oxygen Species (ROS) scavengers, coenzymes, UV and excess radiation screen and also as regulatory molecules. In addition, the induction of secondary metabolites by several abiotic stress conditions could also be an effective mechanism of cross-protection against biotic threats, providing a link between abiotic and biotic stress responses. Moreover, the presence/absence and relative accumulation of certain metabolites along with gene expression data provides accurate markers (mQTL or MWAS) for tolerant crop selection in breeding programs.
Highlights
Metabolites reflect the integration of gene expression, protein interaction and other different regulatory processes and are closer to the phenotype than mRNA transcripts or proteins alone
These compounds are synthesized through the shikimate pathway leading to phenylanaline which is the substrate of phenylalanine ammonia lyase (PAL) which is the key enzyme in the phenolic biosynthesis pathway
The study of the metabolome represents the integration of the genetic background and the influence of the environmental conditions, describing more accurately the phenotype of a given plant species
Summary
The phenotype of an organism is the result of the combination of multiple intertwined, dynamic and linear/non-linear interactions among different elements (DNA, RNA, proteins and metabolites) with the environment (developmental stages and/or adverse conditions such as salinity, temperature and water or nutrient availability). The sum of these three aspects does not provide a clear picture of the actual phenotype of a given organism but a sequential characterization of the elements one by one This approach lacks the emerging properties that characterize biological organisms; there is an increasing need for the integration of all these aspects [1,2,3]. This is of especial relevance when the objective is to understand how plants respond to environmental cues. The physiological and biochemical effects of different abiotic stress conditions and how metabolite markers can be used for the selection of cultivars and/or rootstocks with improved yield/abiotic stress tolerance will be reviewed
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