A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar "Varnes"
Sargent, D.J. , et al. (2025). A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar "Varnes." PLoS ONE 20(2), e0318692. DOI: 10.1371/journal.pone.0318692
This study explores the factors influencing apricot fruit coloration in the raspberry cultivar "Varnes" using genetic, biochemical, and molecular approaches to understand its pigmentation mechanisms. Raspberries (Rubus idaeus L.) typically bear red fruit due to anthocyanins, water-soluble pigments that influence plant coloration and stress responses. However, some cultivars, such as "Varnes", display apricot-colored fruit, likely due to variations in anthocyanin biosynthesis.
Metabolomic profiling showed that "Varnes" produces lower anthocyanin levels compared to red-fruited cultivars. Red raspberries typically contain ten anthocyanins, but "Varnes" accumulates only cyanidin-3-sophoroside and cyanidin-3-glucoside in reduced concentrations. Principal Component Analysis (PCA) indicated a distinct metabolic profile in "Varnes" compared to red-fruited cultivars. RNA sequencing (RNA-Seq) further revealed differential expression of anthocyanin biosynthesis genes, with Anthocyanidin synthase (Ans) exhibiting significantly lower expression levels in "Varnes", correlating with reduced anthocyanin accumulation.
Whole-genome sequencing using Oxford Nanopore Technologies and Illumina short-read sequencing identified a CACTA-like transposable element (TE) insertion in the second exon of the Ans gene in "Varnes". This TE insertion introduced a premature stop codon, truncating the ANS protein and reducing its function in anthocyanin synthesis. The mutation was homozygous in "Varnes", whereas PCR analysis revealed heterozygosity in the red-fruited cultivar "Veten", suggesting a recessive inheritance pattern for apricot coloration.
Further validation involved the Wizard® SV Gel and PCR Clean-Up Kit and the pGEM®-T Easy Vector System, which were used for PCR purification and cloning to confirm genetic variations. Comparative analysis with the yellow-fruited cultivar "Anne" showed that while both contain mutations in Ans, the mutation in "Varnes" retains partial anthocyanin production, explaining its apricot rather than yellow coloration. "Anne" carries a distinct, complete loss-of-function mutation, underscoring the diversity of regulatory mechanisms affecting anthocyanin biosynthesis in raspberries.
This study highlights the role of transposable elements in fruit pigmentation and the regulation of anthocyanin biosynthesis in raspberries. The discovery of a CACTA-like TE insertion disrupting Ans function in "Varnes" demonstrates how structural genetic variations contribute to fruit color diversity. Understanding these genetic mechanisms allows breeders to selectively introduce or suppress color traits, enhancing fruit marketability and appeal.
Keywords: Rubus idaeus, anthocyanins, anthocyanidin synthase, fruit pigmentation, CACTA transposable element, gene expression, raspberry breeding, metabolomics, transcriptomics, genetic variation
