A CACTA transposon in the Anthocyanidin Synthase 1 gene is putatively responsible for apricot fruit colour in the raspberry (Rubus ideaus) cultivar Varnes. Rubus idaeus cultivar:Varnes

Cultivated raspberries (Rubus idaeus L.) most commonly bear small, red, highly aromatic fruits, which when ripe are rich in nutrients. Their colour is derived predominantly from anthocyanins, water soluble polyphenolic pigments, but as well as red forms, there exist cultivars that display yellow- and apricot-coloured fruits. In this investigation, we used a multi-omics approach to elucidate the genetic basis of the apricot fruit colour in raspberry. Using metabolomics, we quantified the concentration of anthocyanins in red and apricot raspberry fruits and demonstrated that, in contrast to yellow fruited raspberries, which do not product any anthocyanin pigments, fruits of the apricot cultivar Varnes contain low concentrations of several anthocyanin compounds. By performing RNASeq, we revealed differential expression patterns in the apricot-fruited Varnes for genes in the anthocyanin biosynthesis pathway and following whole genome sequencing using long-read Oxford Nanopore Technologies sequencing, we identified a CACTA transposon in the second exon of the Anthocyanidin synthase (Ans) gene that caused a truncated predicted ANS protein. PCR confirmed the presence in heterozygous form of the transposon in an unrelated, red-fruited cultivar Veten, indicating apricot fruit colour is recessive to red and that it may be widespread in raspberry germplasm, potentially explaining why apricot forms appear at regular intervals in modern raspberry breeding populations.