*2.5. Identification of Cis-Acting Elements of* PLP\_deC *Genes*

Plant growth and development are regulated by different cis-elements in genes. Therefore, we used the PlantCARE database to identify and analyze cis-elements in the *PLP\_deC* genes and identified three categories of cis-elements: plant growth and development, phytohormone response, and biotic and abiotic stress response. The cis-acting elements in the growth and development category included the CAT-box for meristem expression, O2-site for zein metabolic regulation, MRE and Box 4 for light response, and others. We identified 35 Box-4 motifs, which compose the largest portion of the growth and development category. All the *PLP\_deC* genes contained Box-4 elements (Figure 5a), indicating that the expression of all these genes is closely related to light. In the phytohormone response category, TCA elements for SA response and P-boxes and TATC-boxes for gibberellic acid response were identified. Notably, TGACG motifs for MeJA response accounted for 47% of the phytohormone response category (Figure 5c), while ABRE elements for ABA response accounted for 33%. The last category was biotic and abiotic-stress-response elements, including AREs and GC motifs for anerobic response, TC-rich repeats for defence and stress response, and MBSs and LTRs for low temperature response. Our data suggested that the *PLP\_deC* genes may respond to abiotic stresses in *D. o*ffi*cinale*.

**Figure 5.** Numbers of cis-acting elements in all the *PLP\_deC* genes of *D. o*ffi*cinale* and *P. equestris*. (**a**) The different colors and numbers in the grid indicate the numbers of different promoter elements in each *PLP\_deC* gene. (**b**) The different colored histogram represents the numbers of cis-acting elements in the different categories. The red, blue, and green indicate plant growth and devolepment, phytohormone response, and biotic and abiotic stress, respectively. (**c**) The pie charts indicate the percentages of different promoter elements in the different categories.
