## 3 Discussion
Ascorbate peroxidase (spot #2908) and manganese peroxide dismutase (spot #3658) are the main enzymes of the antioxidant defense system of plants. Many plants cope with oxidative stress via the over-expression of ascorbate peroxidase and superoxide dismutase genes [41]. Expressions of these enzymes did not change in tall mutant plants in comparison to the control, indicating that tall mutants can also fight against adverse environmental conditions. Allene oxide cyclase (spot # 2401) is involved in the jasmonate biosynthetic pathway, catalyzing the most critical step [42]. Jasmonates (JAs) are involved in the regulation of a wide range of metabolic activities, from stress responses to development [43]. The JA acts as a signaling molecule in response to wounds and pathogenesis [44]. It also works as a stress hormone and promotes the synthesis of various primary and secondary metabolites in plants [45; 46; 47]. In our study, the expression of this protein was higher in the dwarf mutant line than in the tall and semi-dwarf mutant lines and the control. The up-regulation of this protein in dwarf mutants could be correlated with the higher level of thymoquinone content in the seeds of these mutants (Supplementary Table S2). It has been reported that the overexpression of the allene oxide cyclase gene (_HnAOC_) in tobacco led to the up regulation of genes from the nicotine biosynthetic pathway. This resulted in a 4.8-fold enhancement in the nicotine level over the control [46]. Transgenic _Artemisia annua_, overexpressing allene oxide cyclase(_AaAOC_), synthesized higher levels of endogenous JA and resulted in an increased biosynthesis of artemisinin [42]. Microtubules are the principal component of the cytoskeleton; microtubules continuously assemble and disassemble within the cell. The microtubules determine the cell's shape. Tubulin is the major constituent of microtubules. The tubulin alpha-6 chain (spot #1268) in our study is up-regulated in tall mutants and down-regulated in the dwarf mutant. Reduced expression of the \(\alpha\)-tubulin gene in _A. thaliana_ caused cellular defects that resulted in poor growth and abnormal morphology of the root. A low level of a-tubulin proteins resulted in microtubule disassembly, causing a reduction in growth [48]. The down-regulation of this protein in dwarf mutants in our study could also be correlated with the reduced growth of these plants. In this study, the auxin-repressed protein (spot #6801) was up-regulated in dwarf mutant lines but did not show any change in other mutants compared to the control. Salicylic acid signaling is mediated by an auxin-repressed protein, which is induced by indole acetic acid [49]. Reports demonstrate the induction of auxin-repressed proteins by abiotic stresses, causing an arrest in growth, possibly by inhibiting cell elongation [50]. Transcription factor PRE1 has been found to regulate extensive developmental processes in plants. In this study, spot #4518 was up-regulated in tall mutant lines but down-regulated in the dwarf mutant lines of _N. sativa_. Plant height and seed size are directly affected by cell length. PRE1 has been reported to work in association with the ACE protein (cell elongation regulator) and AtIBH1 protein (cell elongation inhibitor) [51]. While the ACE induces cell elongation, AtIBH1 inhibits the activity of ACE. PRE1 has been found to promote elongation by indirectly interfering with the activity of AtIBH1. Final cell length is determined by the balance between the three proteins. These proteins are the transcription factors controlling the functions of several genes [51]. It is suggested that mutagens affect the expression of the PRE1 protein. Up-regulation of this protein produced tall mutant lines and down-regulation generated dwarf mutant lines. Polycomb proteins have been found to regulate extensive developmental processes in plants [52]. In the present study, spot #4006 was identified as the polycomb group protein FIE1. This protein was up-regulated in tall and semi-dwarf mutant lines. [PERSON] et al.