Age-Related Alterations in DNA Methylation and APETALA2 (AP2) Levels in Herbaceous Peony (Paeonia lactiflora Pall.)

Abstract

The ornamental and commercial values of herbaceous peony (Paeonia lactiflora Pall.) are directly related to its flower pattern. However, the molecular mechanisms underlying the type formation of P. lactiflora flowers have not been studied in great detail. Previous studies identified, using integrated multipleomics analysis, revealed that APETALA2 (AP2) is an important candidate gene that modulates type formation of P. lactiflora flowers. To further reveal the expression mechanism of AP2 in P. lactiflora petals, we examined the profile of AP2 expression in the inner and outer petals of ‘ZiFengyu’ at various developmental stages using qRT-PCR and BSP+Miseq methylation analysis. Based on our data, the AP2 levels in the outer petals were obviously increased, relative to the inner petals. In addition, the S3 levels at the bloom stage were significantly higher than at the flower-bud stage S1, thereby promoting bloom stage S2, while declining stage S4. Using chromosome walking, the 2000 bp of the 5′-end upstream promoter region was achieved. This region harbored a CpG island (−665∼−872 bp), with multiple essential transcription factor binding sites (TFBS) such as NF-kappa B, GATA-1, Sp1, and C/EBP. Methylation sequencing revealed 7 methylated CpG sites in the CpG island region of the AP2 promoter, thereinto, the methylation ratio of the CpG-3 site in the inner petals was significantly higher than in the outer petals. Correlation analysis revealed a negative association between the level of methylation (CpG-3, CpG-6), and AP2 mRNA expression. CpG-3 was located on the Sp1 transcription factor binding site. Thus, we speculated that the CpG-3 methylation may inhibit transcription factor Sp1 binding to the gene promoter, thereby regulating AP2 expression. Herein, we examined the role of AP2 in the determination of flower patterns in P. lactiflora. Our conclusion will provide theoretical guidance for the molecular breeding of the flower pattern in P. lactiflora.