Analysis of the population genetics and the ecological characteristics of the endangered narrow endemic Soda grandis (Freitag, Vural & N. Adıgüzel) Akhani from Türkiye

Soda grandis (Freitag, Vural & N. Adıgüzel) Akhani, from the Amaranthaceae family, is a halophyte plant with significant promise and genetic potential in agriculture, especially as a source of genes. It is narrowly distributed only in gypsum and marly soils and a critically endangered annual species endemic to Türkiye. The level and pattern of genetic diversity in 92 individuals from four natural populations of the species were investigated using inter-simple sequence repeat (ISSR) markers. Physical and chemical analyses of soil samples and bioclimatic data of the study areas were conducted. At the species level, the percentage of polymorphic bands was 22.5%. Nei’s gene diversity was 0.085, and Shannon’s information index was 0.126. At populations level, the percentage of polymorphic bands = 2.12%, Nei’s gene diversity = 0.007, and Shannon’s information index = 0.011. The genetic differentiation coefficient indicated that the majority of the total genetic variability occurred among populations (91.9%). Analysis of molecular variance (AMOVA) revealed that 93% of the genetic variance was attributable to differences among populations, while the remaining 7% occurred within populations. The gene flow was very low (Nm = 0.044). The Mantel test revealed a significant, positive, and weak correlation between genetic and geographic distance (r = 0.296, p < 0.001). The dendrograms were created using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), and the results were supported through Principal Coordinate Analyses (PCoA). STRUCTURE analysis indicated three distinct genetic groups (ΔK = 3). Given the high genetic differentiation among populations, it is crucial to evaluate sub-speciation and implement in situ conservation efforts.