Calligonum leucocladum (Schrenk) Bunge populations: genomic and population genetics analyses for assessing genetic diversity

Calligonum leucocladum (Schrenk) Bunge is an ecologically significant desert shrub adapted to the arid and semi-arid environments of Central Asia. For the first time, this study provides an integrative assessment of its genetic diversity, population structure, and phytochemical variation using high-resolution SNP genotyping and chemometric profiling. We analyzed 150 individuals from three geographically distinct populations (P1, P2, and P3) in the Kyzylkum Desert and adjacent regions. Linkage disequilibrium (LD) decay analysis showed that P1 had the highest recombination rate (with r² declining sharply at 10 kb), while P2 exhibited strong LD across longer distances, indicating moderate genetic isolation. P3 displayed intermediate genomic characteristics. Principal Coordinates Analysis (PCoA) explained 76.55% of total genetic variation and supported the clear differentiation of P1, whereas P2 and P3 showed closer genetic relationships. Minimum Spanning Tree (MST) analysis further confirmed these patterns. Phytochemical profiling revealed, for the first time, significant population-level differences in total phenolic and flavonoid content, as well as antioxidant capacity, which were consistent with the genetic structure. These findings suggest that geographic isolation, habitat fragmentation, and environmental stressors contribute to population divergence in C. leucocladum . The high genetic and biochemical diversity found in P1 identifies it as a potential reservoir of adaptive traits. This work provides a valuable foundation for conservation planning and ecological restoration of desert flora.