Abstract
DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.
Highlights
Floral fragrance is one of the most important ornamental traits of horticultural plants (Schiestl, 2010)
We revealed the functions of those differentially methylated genes (DMGs) by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis
The results clearly showed that DMGs were widely involved in almost all steps in the phenylpropanoid biosynthesis process, including the dominant and key components, and the low (FPKM value < lower quartile) or none (FPKM value < 1) part in P. mume fragrance
Summary
Floral fragrance is one of the most important ornamental traits of horticultural plants (Schiestl, 2010). The diverse combinations of floral volatiles emitted confer the unique floral fragrances among different aromatic plants (Knudsen et al, 2006; Muhlemann et al, 2014). Genes related to the biosynthesis of substances conferring floral aromas have been comprehensively studied in model plants (Tzin and Galili, 2010), such as Clarkia breweri, Antirrhinum majus, Rosa ssp., and Petunia hybrida (Boatright et al, 2004; Fraser and Chapple, 2011; Dudareva et al, 2013; Muhlemann et al, 2014; Widhalm and Dudareva, 2015). Some important genes for the biosynthesis of phenylpropanes have been confirmed in petunia (Boatright et al, 2004; Moerkercke et al, 2009)
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