SCoT and ISSR based conservation genetics of Calligonum polygonoides Linn.: An endangered species of Thar desert

Calligonum polygonoides, an endangered species of desert due to poor regeneration and overexploitation, which requires immediate conservation attention. Genetic diversity analysis is crucial for effective conservation and management initiatives, for elite genotypes. Therefore, in the present study, SCoT (start codon target) and ISSR (inter simple sequence repeat) markers were used to investigate the genetic variability in 120 individuals of Calligonum polygonoides. A total of 300 amplicons were produced (164 by SCoT and 136 by ISSR), of which 292 were polymorphic, exhibiting an overall 97.33 % polymorphism. The Nei's gene diversity (h) ranged from 0.0698 to 0.193, with 0.252 overall diversity at the species level. Shannon's information index (I) varied from 0.105 to 0.282, with 0.393 total diversity. Genetic variation within population (56.28 %) was higher than among population (25.49 %), as revealed by the results of analysis of molecular variance (AMOVA). Pair-wise distances were calculated using the agglomerative data from each marker. Results of Mantel's test revealed there is no correlation found between geographical distance and genetic distance (R² = 0.0958; P > 0.05), which indicates the adaptation of this species to climatic conditions. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram separates 120 genotypes into 7 main clusters. Findings of UPGMA dendrogram were further validated by using population structure analysis. The low gene flow value (Nm = 0.471), high coefficient of genetic differentiation (G_ST = 0.515), and high fixation index (F_ST = 0.514) indicate populations are not in Hardy-Weinberg proportions. All the studied parameters revealed that individuals of populations Bmr (Barmer) A and Chr (Churu) A showed the highest diversity. This information would be helpful to select the suitable elite germplasm for development of conservation strategies for this endangered plant species.