Transcriptomics Reveals Genes Involved in Purple Tuber Colour Development in Potato

Red/purple coloured potato is beneficial for human health. This study aimed to identify genes associated with coloured potato. Hence, transcriptome sequencing was performed using Illumina platform in the tuber and leaf tissues of purple, red, and yellow flesh tuber potato genotypes compared to white flesh (control). The purple genotype recorded maximum anthocyanins (11.73 mg/100 g FW) than other potatoes. Transcriptome analysis resulted in 2.93–5.30 Gb high-quality data (QV > 25) and 77.8–83.6% reference mapping. In tubers and leaf tissues, significant (p < 0.05) differentially expressed genes (DEGs) were identified in purple (up-regulated, > 2 log₂ fold change: 146 and 412; and down-regulated, <  − 2 log₂ fold change: 262 and 363), red (up-regulated: 414 and 428; and down-regulated: 352 and 370), and yellow (up-regulated: 196 and 390; and down-regulated: 267 and 356), respectively. Common DEGs were identified by Venn diagram analysis and gene expression markers were developed for the genes like patatin-3-Kuras 1, patatin-01, and asparagine synthetase for early stage identification. DEGs were functionally annotated with gene ontology (GO) domains with a predominance of molecular function (2294), and major KEGG pathways were signal transduction, translation, and carbohydrate metabolism. A phylogeny tree showed distinctness among 25 amino acid sequences belonging to 22 genes associated with red/purple genotypes. Common three motifs were also identified using MEME tools. Selected genes were confirmed by real-time qPCR. Overall, we identified anthocyanin biosynthesis pathways genes in purple/red potatoes such as anthocyanin 5-O-glucosyltransferase, anthocyanin acyltransferase, chalcone synthase 2, chalcone isomerise, flavonoid 3',5'-hydroxylase, transcription factors (e.g. R2R3-MYB, WRKY, AP2/ERF, BHLH), and phytohormones (e.g. SAUR family protein, gibberellin 3-oxidase). Our study provides an overview of genes involved in purple/red colour potatoes for further research.