Genetic diversity analysis of Pandanus amaryllifolius using EST-SSR and iPBS markers

Abstract

Abstract Pandanus amaryllifolius, a tropical fragrant screw pine, is commonly used in cooking and traditional medicine. Despite the fact that various studies have been conducted on the metabolite, transcriptome and proteome profiles of P. amaryllifolius, there is a scarcity of molecular markers suitable for genetic improvement. Therefore, this research aimed to analyse the genetic diversity of P. amaryllifolius using EST-SSR markers derived from transcriptome dataset and iPBS marker system. Using the leaf transcriptomes of three biological replicates, we successfully generated 157,467 unigenes from P. amaryllifolius, with an average length of 1,084 base pairs. Of these, 66,820 EST-SSRs were identified, presenting one SSR for every 2.6 kb of distribution density. The most common SSRs were dinucleotides (45.54%), followed by mononucleotides (32.65%). Out of 48,816 developed EST-SSR markers, we randomly selected 30 for the genetic diversity analysis among 24 P. amaryllifolius accessions, together with sixteen iPBS markers for P. amaryllifolius diversity study. Only two EST-SSR and three iPBS markers showed polymorphic bands, indicating a low polymorphism level among 24 P. amaryllifolius accessions. Diversity analysis using EST-SSR markers revealed 3 polymorphic bands with an average polymorphic information content (PIC) value of 0.26. Meanwhile, the iPBS markers generated10 polymorphic bands with an average PIC value of 0.16. The UPGMA cluster analysis differentiated accessions into 5 clusters with iPBS markers and 2 clusters with EST-SSR markers, indicating that iPBS marker system is more effective in identifying the polymorphism of this species. The present work provides a great resource for identifying genes and developing markers in P. amaryllifolius.