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Roots are the primary sites of water stress perception in plants. The aim of this work was to study differential expression of proteins and transcripts in amaranth roots (Amaranthus hypochondriacus L.) when the plants were grown under drought stress. Changes in protein abundance within the roots were examined using two-dimensional electrophoresis and LC/ESI-MS/MS, and the differential expression of transcripts was evaluated with suppression subtractive hybridisation (SSH). Induction of drought stress decreased relative water content in leaves and increased solutes such as proline and total soluble sugars in roots. Differentially expressed proteins such as SOD(Cu-Zn) , heat shock proteins, signalling-related and glycine-rich proteins were identified. Up-regulated transcripts were those related to defence, stress, signalling (Ser, Tyr-kinases and phosphatases) and water transport (aquaporins and nodulins). More noteworthy was identification of the transcription factors DOF1, which has been related to several plant-specific biological processes, and MIF1, whose constitutive expression has been related to root growth reduction and dwarfism. The down-regulated genes/proteins identified were related to cell differentiation (WOX5A) and secondary metabolism (caffeic acid O-methyltransferase, isoflavone reductase-like protein and two different S-adenosylmethionine synthetases). Amaranth root response to drought stress appears to involve a coordinated response of osmolyte accumulation, up-regulation of proteins that control damage from reactive oxygen species, up-regulation of a family of heat shock proteins that stabilise other proteins and up-regulation of transcription factors related to plant growth control.

Salt stress is one of the major factors limiting crop productivity worldwide. Amaranth is a highly nutritious pseudocereal with remarkable nutraceutical properties; it is also a stress-tolerant plant, making it an alternative crop for sustainable food production in semiarid conditions. A two-dimensional electrophoresis gel coupled with a liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) approach was applied in order to analyze the changes in amaranth root protein accumulation in plants subjected to salt stress under hydroponic conditions during the osmotic phase (1 h), after recovery (24 h), and during the ionic phase of salt stress (168 h). A total of 101 protein spots were differentially accumulated in response to stress, in which 77 were successfully identified by LC-MS/MS and a database search against public and amaranth transcriptome databases. The resulting proteins were grouped into different categories of biological processes according to Gene Ontology. The identification of several protein isoforms with a change in pI and/or molecular weight reveals the importance of the salt-stress-induced posttranslational modifications in stress tolerance. Interestingly stress-responsive proteins unique to amaranth, for example, Ah24, were identified. Amaranth is a stress-tolerant alternative crop for sustainable food production, and the understanding of amaranth's stress tolerance mechanisms will provide valuable input to improve stress tolerance of other crop plants.