Integrative analysis of transcriptome and phytohormones reveals new genes network involved in shoot apical meristem development in maize under blue and red light

Blue and red light play a significant role in regulating transcriptional expression, phytohormone levels, and gene signal network reconstruction in the shoot apical meristem. To further elucidate the effects of red and blue light on transcriptional characteristics and phytohormone expression, and to explore signaling pathways and novel genes, we conducted comparative experiments under different light quality treatments. The results are as follows: a total of 22,327 genes were found to be effectively expressed, with a considerable number of alternative splicing events occurring concurrently. Furthermore, 1063 differentially expressed genes were identified, primarily associated with transcriptional variations resulting from the transition from blue light to red light. These differentially expressed genes are predominantly involved in KEGG annotations related to photosynthesis, DNA replication and carbon metabolism. The findings from targeted metabolism analysis reveal significant variations in 45 phytohormones, including ABA, auxin, CK, ETH, GA, JA, and SA. Correlation analysis between transcription and metabolism further indicates that IAA.Glc, IAA.Glu, TRP, mT9G, and GA53 show the strongest correlation with differentially expressed genes, with genes ssu1, ssu2, pep1, me3, and hsp90 displaying a significant relationship. Additionally, in the protein-protein interaction network, three novel genes (LOC100286132, LOC100510780, and LOC103653934) were identified as significant responding to the regulation of blue and red light. Following protein function analysis, the proteins were provisionally identified as ubiquitin conjugating enzyme-like, OXIDATIVE STRESS 3LIKE 2-like, and Ribosomal L 18p/L5e, respectively. Conclusively, it is depicted that the most significant impact of transitions between red light, blue light, and two light qualities lies in the transcriptional process of shot apical meristem of the C4 plant maize. This process is intricately linked to nitrogen availability, carbon dioxide assimilation capacity, and the stimulatory effects of auxin, cytokinin, and gibberellin. The expression of the putative L 18/ L5e in blue and BTR light conditions may enhance transcript and synthesis capabilities of ribosome. (c) 2024 SAAB. Published by Elsevier B.V. All rights are reserved, including those for text and data mining, AI training, and similar technologies.