Genetic differentiation and conservation insights into Salicornia iranica subsp. sinus-persica from Musa Bay using SCoT markers and DNA barcodes

Abstract

Understanding genetic diversity is essential for the conservation and management of halophyte species, especially in ecologically sensitive and industrially impacted regions. In this study, 52 accessions of Salicornia iranica subsp. sinus-persica were collected from diverse microhabitats across Musa Bay, including coastal zones, islands, and petrochemical sites. Following comprehensive morphological assessments showing high phenotypic similarity, and to ensure broad ecological coverage, 16 accessions representing all major microhabitats were selected for molecular analysis. SCoT markers and DNA barcoding (ITS and trnH-psbA regions) were employed to investigate their genetic structure. The SCoT markers revealed considerable polymorphism and partial genetic differentiation, especially between accessions from petrochemical and natural saline habitats. ITS sequencing identified five haplotypes without forming a monophyletic clade, indicating shallow divergence and possible ancestral polymorphism. In contrast, no variation was detected in the plastid region trnH-psbA. These results represent the first global report of ITS and trnH-psbA haplotypes for this subspecies. While the findings are preliminary due to limited sample size and marker coverage, they provide a critical baseline for future studies employing high-resolution genomic tools. Our findings underscore the influence of habitat fragmentation and anthropogenic pressures on genetic patterns and emphasize the importance of conserving genetically distinct accessions in ecologically vulnerable habitats to support the long-term survival and sustainable utilization of this coastal halophyte.