es a gibberellin 3-oxidase, catalyzing the final step of bioactive GA synthesis [11]. In our

es a gibberellin 3-oxidase, catalyzing the final step of bioactive GA synthesis [11]. In our RNA-seq analysis, FGFR4 Inhibitor site DWARF1 was down-regulated by 6.43fold in dnl2. The ent-kaurene oxidase (Zm00001d046342, KO), GA 20-oxidase (Zm00001d034898, GA20ox), and DWARF3 (Zm00001d045563) genes, which participate in the early steps of GA synthesis [12,13], were up-regulated by two.eight o ten.5-fold within the dnl2 mutant. GA2oxidase (Zm00001d017294, GA20ox1), catalyzing the deactivation of bioactive GA or its precursors [49], was up-regulated inside the dnl2 mutant, which may well have contributed to the decrease in endogenous GA content. As for the GA signal transduction, two GIBBERELLIN INSENSITIVE DWARF genes (Zm00001d010308, Zm00001d038165) encoding GA receptors were up-regulated in dnl2 (Figure 13B and Table S4).Int. J. Mol. Sci. 2022, 23,12 ofFigure 13. DEGs involved in phytohormone biosynthesis and signaling. (A) DEGs involved in auxin biosynthesis and signaling. (B) DEGs involved in gibberellin synthesis and signaling. Around the log2 scale, dark blue and dark red colors represent decrease and larger expression, respectively.Moreover, genes related to ETH, ABA, CK, BR, and JA were also identified to be differentially expressed between the dnl2 CYP2 Inhibitor site mutant as well as the wild-type plants (Table S5). Ethylene has been recognized as a growth inhibitor. We identified 25 ethylene-responsive transcription factors (AP2-EREBP), two reversion-to-ethylene sensitivity (RTE), and 1 ethylene insensitive 3 (EIN3) proteins exhibited enhanced expression levels in dnl2. Nearly all of the genes connected to ABA, CK, JA, and BR were up-regulated in dnl2 in comparison with the wild-type. The altered expression level of these genes may well disturb hormone synthesis and signaling homeostasis in the dnl2 mutant, resulting in development inhibition. 2.9. Altered Expression of Genes Associated with Cell Wall Development within the dnl2 Mutant The plant cell wall not only gives mechanical strength and support, but additionally controls cell development and differentiation. Because the secondary cell wall structure is altered inside the dnl2 mutant, we evaluated the expression levels of DEGs related to cell wall deposition and remodeling. Our transcriptome analysis identified a lot more than 130 DEGs associated to cell wall synthesis, remolding, and signaling, and 66.7 with the DEGs were down-regulated in the dnl2 mutant in comparison with the wild-type plants. These DEGs have been further divided into numerous classes in line with the functional annotation, and the majority of them have been classified as secondary cell wall-related. Cellulose synthase (CesA) participates in cellulose synthesis throughout main and secondary cell wall deposition. The maize genome contains a minimum of 12 CesA genes, and CesA1 are believed to be involved in primary cell wall formation, whilst CesA102 are involved in secondary wall deposition [50]. Our RNA-seq outcomes revealed that 4 CesA genes, including CesA7 (Zm00001d005775), CesA10 (Zm00001d032776), CesA11 (Zm00001d043477),Int. J. Mol. Sci. 2022, 23,13 ofand CesA12 (Zm00001d020531), were all down-regulated within the dnl2 mutant. The Brittle stalk 2 (Zm00001d047276), and an additional COBRA-like protein (Zm00001d022082), which participate in the cellulose synthesis on the secondary cell wall [51], also exhibited decreased expression levels in dnl2 (Figure 14A and Table S6). Xylan will be the second-most abundant polysaccharide in plant secondary walls [52]. Various enzymes have already been implicated in xylan synthesis and substitution, including glycosyl transferase (