Leaf color in ornamental plants is largely shaped by anthocyanins, pigments that create red, purple, and blue hues and also contribute to stress responses. In woody hybrids, however, color traits can be unstable because parental genomes, environmental signals, and developmental timing interact in complex ways. DNA methylation can regulate gene activity without changing the deoxyribonucleic acid (DNA) sequence, while alternative splicing can generate different transcript forms from the same gene. In P. mume ‘Meiren’, young leaves emerge purple but later turn green, reducing the ornamental value of the cultivar. Due to these challenges, an in-depth investigation into the genetic and epigenetic regulation of leaf color change is needed.
A research team from Beijing Forestry University, Beijing, China, reported (DOI: 10.1093/hr/uhag039) the study in Horticulture Research on February 18, 2026. The article titled examines why this hybrid ornamental tree shows unstable purple foliage. Using whole-genome bisulfite sequencing (WGBS), ribonucleic acid sequencing (RNA-seq), and molecular assays, the authors analyzed leaves across five developmental stages and focused on how methylation and alternative splicing affect anthocyanin biosynthesis.
The study found that CHH-context methylation increased markedly during leaf development, especially when purple leaves began turning green. Genes with hypermethylated CHH regions generally showed lower expression, suggesting that DNA methylation contributes to transcriptional repression during leaf color fading. The team also detected a stable CG-context methylation imbalance between the two haplotypes of ‘Meiren’: haplotype M (HM) and haplotype C (HC). The HM subgenome showed higher methylation levels, particularly in promoter regions, and this ASM was negatively associated with ASE. Among anthocyanin-related genes, PmMYB10.5 showed strong promoter methylation differences between alleles. The researchers further identified two alternative splicing variants of PmMYB10.5b, named PmMYB10.5b1 and PmMYB10.5bP. These variants contained insertion–deletion (InDel) changes that disrupted the R2 domain of the MYB protein. Functional assays showed that the altered proteins lost their ability to promote anthocyanin biosynthesis and may instead compete with PmMYB10.5b for interaction with PmbHLH3, thereby weakening anthocyanin biosynthesis genes (ABGs).
The authors said the work shows that leaf color fading in ‘Meiren’ is not caused by a simple loss of pigment, but by a coordinated molecular shift. They said DNA methylation appears to reduce the activity of key anthocyanin-related genes as leaves mature, while alternative splicing changes the behavior of a central MYB regulator. Instead of driving pigment formation, the altered forms of PmMYB10.5b may act like molecular brakes. This gives researchers a clearer way to understand why purple foliage can be strong in young leaves but unstable later in development.
These findings may help breeders develop ornamental trees with more stable and lasting foliage color. Molecular markers linked to methylation patterns, allele-specific regulation, or PmMYB10.5b splicing variants could support earlier selection of cultivars with improved purple-leaf performance. The study also broadens understanding of how hybrid genomes regulate visible traits through both inherited allele differences and flexible epigenetic responses. Beyond P. mume, the results may inform research on other ornamental and fruit crops in which anthocyanin-based coloration affects market value. Future work on temperature and light responses could further clarify how environmental signals reshape these regulatory layers.
###
References
DOI
10.1093/hr/uhag039
Original Source URL
https://doi.org/10.1093/hr/uhag039
Funding information
This work is supported by the National Natural Science Foundation of China (32572116), the Fundamental Research Funds for the Central Universities (QNTD202503), and Beijing High-Precision Discipline Project, Discipline of Ecological Environment of Urban and Rural Human Settlements.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.