Dragon fruit pigments, genomes and breeding

Peel and pulp colour

The red and purple colours of many dragon fruits are associated with betalains. This group includes red-violet betacyanins and yellow betaxanthins. Their precursors derive from tyrosine. Peel and pulp can differ in colour, so studies analyse these tissues separately. This distinction helps connect the visible trait with metabolites and gene activity. [Pucker and Brockington 2022, Pucker i Brockington 2022 p. 1–3, Zaman et al. 2025 p. 14–18][Zaman et al. 2025, Pucker i Brockington 2022 p. 1–3, Zaman et al. 2025 p. 14–18]

A comparison of fruit from the Andaman and Nicobar Islands included four genotypes of three species. The authors measured phenolic compounds, flavonoids, carotenoids and extract activity in DPPH and ABTS assays. Results varied between genotypes and tissues. A chemical assay describes a sample’s capacity to react under the assay conditions, whereas the effects of consuming the fruit require separate investigation. [Abirami et al. 2021, p. 2–8]

Establishing pigment identity

Naming a pigment requires appropriate chemical identification. In 2022, Pucker and Brockington reanalysed data used to infer the presence of anthocyanins in dragon fruit. They emphasized comparisons with authentic standards and examination of fragmentation spectra. A similar analytical signal can lead to incorrect compound assignment when identification relies on too limited a set of characteristics. [Pucker and Brockington 2022, pp. 1–3]

The authors compared metabolomic data with expression of flavonoid-pathway genes. Low transcript abundance at the key DFR and ANS steps, together with a weak relationship between the proposed anthocyanins and pulp colour, challenged the earlier identification. The atlas therefore describes dragon fruit pigments primarily through documented betalains. Anthocyanins remain a disputed assignment requiring strong identification evidence. [Pucker and Brockington 2022, pp. 2–3]

Yellow dragon fruit and four chromosome sets

Selenicereus megalanthus is tetraploid, with studies reporting 2n = 4x = 44. This denotes four chromosome sets in a somatic cell. In 2025, Zaman and colleagues presented a reference genome assembly for the species. They combined long DNA reads with data on spatial chromatin contacts, DNA accessibility and gene expression. [Cohen and Tel-Zur 2012, Cohen and Tel-Zur 2012 p. 345–347, Zaman et al. 2025 p. 1, 18–22][Zaman et al. 2025, Cohen and Tel-Zur 2012 p. 345–347, Zaman et al. 2025 p. 1, 18–22]

The final assembly of approximately 1.79 Gb was organized into eleven reference chromosomes. It represents sequences after removal of redundant haplotypes, closely similar sequence variants. The chromosome count in this representation concerns assembly organization. The tetraploid plant retains the forty-four-chromosome complement reported in the study. [Zaman et al. 2025, p. 4–5, 20]

Chromatin and colour-associated candidates

Nuclear DNA forms a spatial network of contacts. Hi-C estimates which regions are more often close to each other. ATAC-seq describes chromatin accessibility, while RNA-seq provides information on transcript abundance. Combining these methods connects sequence, spatial organization and gene activity in the plants being compared. [Zaman et al. 2025, p. 18–23]

The authors compared Selenicereus megalanthus with S. undatus and identified candidates associated with the betalain pathway and regulatory regions. Expression differences co-occurred with differences in chromatin organization and fruit colour. The study supplies a resource for breeding and mechanistic hypotheses. The authors identified candidate functions and causal relationships with pigmentation as questions for further experiments. [Zaman et al. 2025, p. 14–18]

Polyploidization and the breeding system

Cohen and Tel-Zur studied lines obtained by chromosome doubling. From diploid Selenicereus monacanthus, they produced tetraploids that formed fruit after self-pollination. This was accompanied by changes in pollen size, pollen viability and seed traits. The result shows that chromosome-set number can alter pollen–pistil compatibility. [Cohen and Tel-Zur 2012, p. 346–353]

In Selenicereus megalanthus, increasing ploidy from four to eight sets produced a different outcome. Fruit development aborted in all octaploid lines studied. Some yield and seed parameters also deteriorated in tetraploid S. monacanthus lines. Each line therefore requires separate assessment of reproduction, growth and fruit quality. [Cohen and Tel-Zur 2012, p. 348–353]

From a sample to an application

Dragon fruit biotechnology involves two connected directions. Pigment analysis characterizes a raw material, while genomics helps identify traits relevant to breeding. The first direction requires reproducible chemical assays and reliable pigment identification. The second calls for cultivar comparisons, gene-function validation and measurement of crop traits. [Abirami et al. 2021, zakres wyników i wniosków cytowanych prac][Pucker and Brockington 2022, zakres wyników i wniosków cytowanych prac][Zaman et al. 2025, zakres wyników i wniosków cytowanych prac]

Peel and pulp have different chemical profiles, so tissue selection changes the properties of an extract. Accurate identification of the plant, cultivar, fruit maturity and sample preparation remains part of the process description. Material documented in this way can be compared between experiments and used to assess colour stability and pigment recovery. [Abirami et al. 2021, Abirami et al. 2021 p. 8–10, Pucker i Brockington 2022 p. 1–3][Pucker and Brockington 2022, Abirami et al. 2021 p. 8–10, Pucker i Brockington 2022 p. 1–3]

From crosses to breeding lines

The programme described by Tel-Zur covered more than three decades of introduction, selection and crossing of fruiting cacti. Crosses between materials with equal or different ploidy were combined with embryo rescue in culture. Chromosome doubling and the production of gamete-derived plants provided additional approaches. Each stage supplied a different kind of material for subsequent comparisons. Cultivar value was evaluated through reproduction, ripening, fruit keeping quality, fruit characteristics and growth in cultivation. [Tel-Zur 2022, p. 1–11, tabela 1]

Earlier cytological studies documented chromosome numbers and meiotic behaviour. Lichtenzveig and colleagues examined diploid Hylocereus undatus and H. polyrhizus alongside tetraploid Selenicereus megalanthus. They related irregular chromosome segregation during meiosis in yellow pitahaya to reduced pollen viability. Their hypothesis about the species’ origin was based on the cytological and crossing data then available. The 2025 genome assembly provides a different level of resolution and its own interpretation of an autopolyploid genome. An account of research history preserves the methods and conclusions of each study. [Lichtenzveig et al. 2000, Lichtenzveig i wsp. p. 1058–1065; Zaman i wsp. 2025 p. 4–10][Zaman et al. 2025, Lichtenzveig i wsp. p. 1058–1065; Zaman i wsp. 2025 p. 4–10]

Comparing wild and cultivated fruit

Pérez-Orozco and Sosa compared betalains and sugars in fruit from five Selenicereus taxa. Material came from wild populations and cultivation in Mexico and Colombia and was collected in 2019. Peel and flesh were analysed separately, with pigment content estimated spectrophotometrically. Considerable variation was found among samples, including within S. undatus. Fruit colour and origin therefore provide a starting point for analysis, while actual pigment content is established by measurement. [Pérez-Orozco and Sosa 2022, p. 1–9, metody i tabele 1–2]

Seed proteins and IgE-binding studies

Hao and colleagues analysed seed proteins from white- and red-fleshed pitahayas using sera from five people reporting symptoms after eating these fruits. Immunoblotting revealed a strongly reactive band near 20 kDa. Proteins from this gel region were identified by liquid chromatography–tandem mass spectrometry. Immunoinformatic tools selected candidates, including cupin_1-domain proteins and HSP70. Additional measurements concerned expression of the corresponding genes. The findings describe IgE reactivity in this sample and candidate proteins. Allergy prevalence among consumers requires population-based investigation. [Hao et al. 2022, p. 2–10, metody i wyniki]