Multi-omics study reveals how pitaya peels acquire their colors

A research team has revealed that pitaya peel color arises from coordinated changes in several pigment pathways rather than from a single coloring compound. Betalains—particularly red betacyanins—were the main determinants of red peel, whereas carotenoids and flavonoids made larger contributions to yellow peel, especially in the cultivar ‘Yanwoguo’. Meanwhile, reduced chlorophyll production and accelerated chlorophyll degradation helped expose these pigments as the fruit matured. By identifying the metabolites and genes associated with contrasting peel colors, the findings provide a scientific foundation for breeding pitaya cultivars with more diverse, stable, and commercially attractive appearances.

Pitaya peel color is an important indicator of fruit quality and market value. Previous research has established that betalains give many pitaya cultivars their characteristic red coloration, while carotenoids, flavonoids, and chlorophyll also influence color in plant tissues. Studies have identified individual betalain-related genes and transcription factors, but they have generally examined one regulatory component at a time or focused primarily on fruit pulp. Consequently, scientists have lacked a systematic explanation of why different cultivars develop red or yellow peels and how multiple pigment pathways interact during ripening. Understanding these processes requires integrated analysis of gene activity and metabolite accumulation across contrasting cultivars and developmental stages.

A study (DOI: 10.48130/tp-0026-0013) published in Tropical Plants on 28 May 2026 by Hua Tang's team, Hainan University, shows that betalain biosynthesis dominates red-peel formation, while carotenoid and flavonoid accumulation, together with chlorophyll degradation, drives yellow coloration.

The researchers examined four cultivars representing contrasting peel and pulp combinations: the red-peel/red-pulp ‘Jinduyihao’, red-peel/white-pulp ‘Yuenanbairou’, and two yellow-peel/white-pulp cultivars, 'Wucihuanglong' and 'Yanwoguo'. Peel tissues were collected at the green-fruit, color-transition, and mature stages, with three biological replicates for each treatment, producing 36 samples. The team combined untargeted liquid chromatography–mass spectrometry metabolomics with Illumina RNA sequencing, pathway-enrichment analysis, and quantitative real-time polymerase chain reaction validation. Transcriptome sequencing generated 29.59 gigabases of clean data and identified 5,195 previously unrecognized genes, of which 1,890 received functional annotations. Metabolomic analysis detected 2,682 peaks and annotated 2,670 metabolites. The researchers then linked differentially expressed genes with metabolites involved in betalain, flavonoid, carotenoid, and chlorophyll metabolism. In red-peel cultivars, the betacyanins betanidin, gomphrenin-I, and lampranthin II accumulated during ripening, particularly in ‘Jinduyihao’. This pattern closely matched the increased expression of key betalain-biosynthesis genes, including CYP76AD1, DODA, and several glycosyltransferase genes. ‘Wucihuanglong’ also activated this pathway, but less strongly, suggesting that its peel color reflects contributions from several pigment classes. By contrast, ‘Yanwoguo’ maintained low betalain concentrations and weak expression of betalain-related genes despite having abundant tyrosine, the pathway’s precursor. This indicates that its limited betalain production probably results from inefficient precursor conversion rather than insufficient raw material. The cultivar instead accumulated substantially more carotenoid and flavonoid metabolites. Across all samples, the researchers identified 61 flavonoids, five carotenoid-pathway metabolites, and numerous associated genes; 25 flavonoids were especially abundant in ‘Yanwoguo’. Carotenoid-related genes such as PSY, LCYB, and LCYE, and flavonoid-related genes including CHS, CHI, F3H, and FLS, showed strong activity in yellow peels. At the same time, chlorophyll-biosynthesis genes such as HEMA, POR, and DVR generally declined during maturation, while degradation genes including SGR and PAO increased, removing the green background and revealing the accumulating pigments.

Overall, the study presents pitaya coloration as a dynamic, multi-pigment process. Coordinated betalain production generates red peel, whereas enhanced carotenoid and flavonoid metabolism supports yellow coloration, with chlorophyll loss facilitating both transitions. The results identify promising candidate genes for molecular breeding and may help breeders develop cultivars with distinctive peel colors and improved visual appeal. Because the analysis measured relative metabolite abundance rather than the absolute concentration and color contribution of each pigment, the researchers recommend targeted pigment quantification and functional validation to confirm the roles of the candidate genes.

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References

DOI

10.48130/tp-0026-0013

Original Source URL

https://doi.org/10.48130/tp-0026-0013

Funding information

This work was supported by the Hainan Provincial Natural Science Foundation high-level Talents Project (320RC487), the Hainan Major Science and Technology project (ZDKJ2021014), the Natural Science Fund of Hainan Province (311025), the Hainan Province Science and Technology Special Fund (ZDYF2022XDNY199), and the earmarked fund for Tropical High-efficiency Agricultural Industry Technology System of Hainan University (Project No. THAITS-5).

About Tropical Plants

Tropical Plants (e-ISSN 2833-9851) is the official journal of Hainan University and published by Maximum Academic Press. Tropical Plants undergoes rigorous peer review and is published in open-access format to enable swift dissemination of research findings, facilitate exchange of academic knowledge and encourage academic discourse on innovative technologies and issues emerging in tropical plant research.