Longjack (E. longifolia Jack) is one of the important medicinal plants, distributed naturally in the mountainous and sandy areas of Vietnam. The main objective of this study was to evaluate the genetic diversity within and among four longjack populations in Thua Thien Hue with a total of 276 individuals based on the markers as random amplified polymorphic DNA (RAPD), start codon targeted (SCoT), and branch point single sequences (BPS). The analysis of polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI), and resolving power (Rp) showed markers SCoT and BPS are more informative than RAPD markers. Combining the data of these markers indicated that genetic diversity (He) and Shannon index (I) are relatively low, at only 0.17 and 0.28, respectively. The analysis of molecular variance (AMOVA) revealed that genetic variation was greater within populations than between them, 89% vs 11%. A Bayesian cluster analysis (STRUCTURE) showed the number of genetic groups was two (K = 2), similar to the results of Principle Coordinate Analysis (PCoA) and Ward’s method. The Mantel test also exhibited a positive correlation of the geographical, elevational factors, morphological characteristics with the genetic variation.
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