Purple foliage in ornamental plants is largely produced by the accumulation of anthocyanins, pigments that contribute both visual color and responses to environmental stress. Their production is controlled by networks of biosynthetic genes and transcription factors, including members of the B-box family. Natural genetic variations in these regulators can generate major differences in pigmentation, yet the principal locus controlling persistent purple leaves in crape myrtle had remained unresolved. Previous work had implicated several regulators, including LiHY5 and LiMYB75, but their genetic patterns could not fully explain the trait. Given these challenges, a deeper investigation was needed to identify the causal genetic variation and determine how it reshapes anthocyanin regulation in crape myrtle.
Published (DOI: 10.1093/hr/uhag179) online on April 29, 2026, in Horticulture Research, the study was led by researchers at Beijing Forestry University, with collaborators from Qingdao Agricultural University and the Beijing Academy of Science and Technology. The team combined genetic mapping, multi-omics analyses and functional experiments to identify the genetic basis of purple foliage in crape myrtle and uncover how a 32-base-pair deletion changes the activity of LiBBX16, linking anthocyanin accumulation with both leaf coloration and seedling development.
The researchers first constructed five segregating populations and showed that purple foliage behaves as a dominant, single-gene trait. Bulked segregant analysis (BSA), targeted metabolomics and ribonucleic acid sequencing (RNA-seq) narrowed the search to LiBBX16, which encodes a B-box zinc-finger transcription factor. Purple-leaf plants carried the LiBBX16p allele, distinguished by a 32-base-pair deletion in its third exon. An insertion/deletion (InDel) marker based on this sequence difference consistently separated purple- and green-leaf plants across hybrid populations and tested cultivars. Functional experiments then strengthened the genetic evidence: silencing LiBBX16 in purple crape myrtle reduced anthocyanin levels to about 61.8% of the control, whereas expression of LiBBX16p in Arabidopsis thaliana produced purple leaves and stems and approximately 9.5-fold higher anthocyanin accumulation than controls. The deletion also changes the LiBBX16p protein, removing its nuclear localization signal and Valine-Proline motif and altering its intracellular distribution. Regulatory assays further showed that LiBBX16p activates anthocyanin-related genes such as LiF3GT and LiMYB75 more strongly than the green-leaf-associated form. Intriguingly, although LiBBX16g can bind these promoters directly, LiBBX16p cannot, suggesting that the mutant protein may instead work as a co-activator recruited through protein–protein interactions.
The authors said the findings show how an exceptionally small genetic change can reshape a complex ornamental trait by changing how a regulatory protein operates rather than simply switching a gene on or off. They said the 32-base-pair deletion appears to give LiBBX16p a new regulatory behavior that strengthens anthocyanin production while also connecting leaf pigmentation with plant development. The team emphasized that the proposed co-activator mechanism still requires additional experimental testing, including studies of interacting proteins, nuclear transport and protein stability, but provides a testable framework for understanding how structural variation can create new functions in plant regulatory proteins.
Beyond explaining why some crape myrtles remain purple, the discovery offers breeders a direct route from DNA variation to plant selection. The InDel marker developed from the 32-base-pair deletion could allow purple-leaf genotypes to be identified at an early stage, reducing reliance on prolonged phenotypic screening. Importantly, the study also found that plants homozygous for LiBBX16p showed severe developmental defects and did not survive through normal seedling development, information that could help breeders design crosses while avoiding undesirable genotype combinations. More broadly, the work illustrates how structural variants can create new regulatory functions and offers LiBBX16 as a potential molecular target for improving foliage color in ornamental plants.
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References
DOI
10.1093/hr/uhag179
Original Source URL
https://doi.org/10.1093/hr/uhag179
Funding information
This work was supported by the National Key Research and Development Project of China (2023YFD1200105), Key R&D Program of Shandong Province (2025LZGC031), and the Yunnan Province Science and Technology Talent and Platform Program-Yunnan Province Zhang Qixiang Expert Workstation (202405AF140078).
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.