De novo transcriptome assembly and development of EST-SSR derived functional domain markers for Pandanus amaryllifolius

Abstract

Pandanus amaryllifolius, a tropical fragrant screw pine, is commonly used in cooking and traditional medicine. Although studies have analysed its metabolite, transcriptome, and proteome profiles, molecular markers for genetic improvement remain scarce. This study aimed to develop EST-SSR markers from the P. amaryllifolius transcriptome and utilise them to analyse their genetic diversity. We obtained 157,467 unigenes with an average length of 1,084 base pairs. From these, 66,820 EST-SSRs were identified, with dinucleotides being the most common (45.5%). Following functional domain marker (FDM) analysis, 7,208 markers were used for in silico PCR, which revealed 8,843 polymorphic bands (86.9%), with an average polymorphic information content (PIC) of 0.41, gene diversity of 0.54, and a Shannon index of 0.91. The dendrogram and PCA plot clearly separated samples from Malaysia and India. These findings provide a new alternative for EST-SSR marker validation and a foundation for genetic improvement and conservation strategies for P. amaryllifolius.

Keywords: Pandanus amaryllifolius; expressed sequence tag (EST)-simple sequence repeats (SSR); RNA-seq; functional domain marker (FDM); in silico PCR