Analysis of genetic diversity and population structure of Iranian Artemisia annua L. accessions using IRAP-based molecular markers and revealing retroelement insertional polymorphism

Abstract

Retrotransposons (RTNs) are a primary source of structural evolution in plant genomes, propagating through a copy-and-paste mechanism. This makes them widely utilized in plants as effective molecular markers for DNA fingerprinting, genetic mapping, and assessing genetic variability. Inter-retrotransposon amplified polymorphisms (IRAPs) were employed to evaluate genetic variability and structure in a collection of 118 Artemisia annua (sweet wormwood) accessions, identifying and amplifying 849 loci with 32 IRAP primers derived from Rosaceae, Gramineae, and Solanaceae retroelements. The single IRAP primer Tnt1.OL16, based on RTNs, produced the highest number of markers. The percentage of polymorphic loci (PPL), mean expected heterozygosity (He), number of effective alleles (Ne), and Shannon's information index (I) in the studied collection were 95.80%, 0.30, 1.48, and 0.46, respectively. Although the analysis of molecular variance (AMOVA) revealed no significant genetic structure among populations, the four populations clustered into three groups in the neighbor joining (NJ) dendrogram, indicating relatively higher genetic variation within each population. In conclusion, low genetic diversity was detected in Iranian sweet wormwood, suggesting it forms a distinct population ideal for the uniform extraction of artemisinin. Breeding efforts could be enhanced by introducing exotic or improved germplasm to mitigate potential inbreeding depression effects.