Genotyping by Sequencing (GBS) uncovers genetic diversity and population structure for salicornia breeding programs in Iran

Salicornia, a succulent halophyte flourishing in coastal and mangrove ecosystems, holds significant economic and ecological promise. Establishing sustainable cultivation systems requires a profound understanding of its geographical distribution, genetic potential, and the identification of agronomically superior populations. Despite this potential, comprehensive genomic investigations into the genus remain scarce. This study utilized genome-wide markers to elucidate the genetic diversity and population structure of Iranian Salicornia germplasm, a region recognized as a center of origin for several species. Sampling comprised 200 individuals from 26 geographically defined populations spanning 13 provinces. High-throughput genotyping-by-sequencing (GBS) generated an average of 9.8 million raw reads per sample. From an initial pool of 253,630 raw single-nucleotide polymorphisms (SNPs), 84,215 high-confidence markers were retained following stringent quality control. Across the 26 population-level diversity summaries, mean observed heterozygosity was 0.081 (range = 0.0076–0.3734), with the highest values in Tashk, Shahr Babak, and Noq. Pairwise FST values ranged from 0.05 to 0.66 (mean = 0.241), indicating moderate to high differentiation. K-means clustering identified four primary genetic cohorts, while DAPC and co-ancestry analyses indicated substantial shared genetic background among parts of the germplasm. Formal migration analyses further resolved the temporal pattern of connectivity. Historical migration was the strongest between the Azerbaijan and Central-North units (M = 1.670 from Azerbaijan to Central-North; M = 1.528 in the reverse direction), whereas the weakest historical exchange occurred between Gwadar and Chabahar (M = 0.174–0.188). Contemporary migration was substantially lower than historical connectivity, with self-assignment ranging from 0.810 to 0.960 and the highest values in Chabahar (0.950) and Gwadar (0.960). Spatial analysis and ecological niche modeling further delineated current habitats and projected suitable regions for future expansion. Together, these population-genomic, migration, and spatial results provide a framework for conservation prioritization, germplasm management, and Salicornia breeding in saline and marginal environments of Iran.