How sweet alyssum turned purple: scientists trace the domestication of flower color
image: Genomic features and floral traits of L. maritima. (A) Photo of different cultivars of L. maritima. (B) Photo of the sample used in genome sequencing. (C) Circos plot illustrating the genomic characteristics across various versions of the L. maritima genome. (I) The innermost circle depicts the individual chromosomes of each genome. The bars labeled Lma01–12 represent the chromosomes of LmG v1.0, while the bars labeled Chr1–12 represent the chromosomes of LmG v2.0. (II) Gene density. (III) GC content. Within the inner circle, colored sections represent synteny blocks between two version genomes. All distributions are generated using a window size of 100 Kb.
Credit: Horticulture Research
Flower color in ornamental plants not only enhances their aesthetic appeal but also reflects complex evolutionary histories. In Lobularia maritima (sweet alyssum), researchers have unraveled how domestication shaped its striking color diversity—from its ancestral white flowers to the cultivated purple hues adored worldwide. Through chromosome-level genome assembly and population genomic analyses, the study identified a key regulatory gene, PAP1, whose mutation and differential activation of downstream genes such as CHS and DFR drive the purple coloration. This discovery illuminates the genetic pathway of flower pigmentation and reveals how human selection during domestication directed the emergence of new color phenotypes in ornamental plants.
Flower color diversity arises mainly from variations in anthocyanin pigments, which are regulated by MYB, bHLH, and WD40 transcription factors. In many species, shifts in these regulators have created a kaleidoscope of ornamental traits. Lobularia maritima, native to the Mediterranean, was once exclusively white-flowered in the wild but is now cultivated globally in shades of pink, lavender, and purple. Its transformation provides a unique case for understanding how selection and mutation interplay to shape floral traits. However, the genetic and evolutionary pathways driving this transition remain largely unresolved. Due to these questions, researchers conducted a comprehensive genomic study to uncover the origins and genetic mechanisms of color diversification.
Chengdu, China, April 1, 2025 — A research team from Sichuan University and collaborators from Lanzhou University and the Botanical Institute of Barcelona have published a new study (DOI: 10.1093/hr/uhae355) in Horticulture Research revealing how domestication altered the flower color of Lobularia maritima. By sequencing and assembling a high-quality genome and analyzing populations from across the Mediterranean Basin, the team discovered that all modern cultivars originated from a single domestication event in Tunisia and that mutations in the anthocyanin regulator PAP1 generated the purple flower varieties familiar in gardens today.
The researchers produced a gold-standard genome (284 Mb, BUSCO 99.2%) using PacBio HiFi and Hi-C sequencing and performed resequencing on 84 wild and cultivated samples. Population genetic analyses identified two wild lineages—Tunisia (TS) and Northwestern Mediterranean (NM)—and one cultivated lineage (CU), confirming a single domestication origin from the Tunisian wild population approximately 5,000 years ago. Interestingly, the divergence between white and purple cultivars occurred only about 700 years ago, coinciding with the flourishing of ornamental horticulture in medieval North Africa and Spain.
Genomic scans and genome-wide association studies pinpointed PAP1, a MYB transcription factor, as the determinant of purple pigmentation. Two distinct haplotypes, PAP1-Hap1 (white) and PAP1-Hap2 (purple), were identified. Dual-luciferase assays showed that the purple-associated PAP1 variant more strongly activates CHS and DFR, key genes in anthocyanin biosynthesis. These mutations enhanced pigment accumulation, leading to the distinctive purple phenotype. The study also revealed that other genes related to flowering and stress responses were selected during domestication, reflecting adaptation to cultivation and aesthetic preferences.
“Our study decodes the genetic origin of color diversity in sweet alyssum, bridging ornamental plant breeding with evolutionary genomics,” said Professor Quanjun Hu, senior author of the paper. “The discovery that a single mutation in PAP1 reshaped the flower’s palette demonstrates how subtle genetic shifts can drive remarkable visual changes under human selection. It also provides a valuable genomic resource for understanding how aesthetic traits evolve and how we can harness such mechanisms in breeding programs for ornamental improvement.”
This research offers more than insight into one species—it provides a blueprint for understanding the molecular evolution of ornamental traits. The identification of PAP1 haplotypes and their regulatory effects opens possibilities for breeding new varieties with customized hues through molecular design rather than traditional crossbreeding. Moreover, tracing the domestication origin to Tunisia highlights how human culture, climate, and trade shaped floral diversity. The findings lay a foundation for using wild germplasm to enrich modern cultivars and for advancing genome-assisted breeding strategies across ornamental and horticultural plants.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae355
Funding information
This research was supported by the National Natural Science Foundation of China (32171606).
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.