De novo transcriptome assembly and development of EST-SSR derived functional domain markers for Pandanus amaryllifolius
Document Type
Article
Publication Date
1-1-2024
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
Divisions
cebar
Funders
Universiti Malaya (RU006-2019),MOHE-Top 100 grant (TU002B-2018)
Publication Title
Crop Breeding and Applied Biotechnology
Volume
24
Issue
4
Publisher
Brazilian Society of Plant Breeding
Publisher Location
UNIV FEDERAL VICOSA, VICOSA-MG, 36 571-000, BRAZIL