## 2 Materials and Methods
### Data Analysis  
The Rp index (resolving power index) was calculated to estimate the ability of the nine RAPD primers to differentiate between genotypes following the formulation below [32]:  
\[\text{Rp}=\sum\text{I}_{\text{b}}\]  
\[\text{I}_{\text{b}}=1-(2\times|0.5-\text{p}|)\]  
\(\text{I}_{\text{b}}\): amplicon's informativeness; p: percentage of individuals containing amplicon I. \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Component** & \multicolumn{2}{c}{**Initial**} & **Final** & \\  & **Concentration** & **Concentration** & **Volume/Sample (\(\upmu\)L)** \\ \hline
2X PCR master mix & MgC\({}_{\text{I2}}\) & 3 mM & \\ (Promega, USA) & dNTPs & 400 \(\upmu\)M each dNTP & 1\(\times\) & 12.5 \(\upmu\)L \\ Primer Operon & 2 \(\upmu\)M & 0.1 \(\upmu\)M & 0.5 \\ GoTaq DNA polymerase (Promega, USA) & 5 unit/\(\upmu\)L & 1 unit/\(\upmu\)L & 0.2 \\ DNA & - & 30 ng/\(\upmu\)L & 2 \\ \(\text{H}_{2}\)O nuclease-free & & & 11.8 \\ \hline \hline \end{tabular}
\end{table} 
Table 4: PCR reaction mix composition. \begin{table}
\begin{tabular}{c c} \hline \hline
**Name of Primer** & **Primer Sequence (5’-3’)** & **References** \\ \hline OPF-03 & CCTGATCACC & \\ OPJ-10 & AAGCCCGAGG & \\ OPJ-01 & CCCGGCATAA & [31; 34] \\ OPE-17 & CTACTGCCCG & [31; 33; 34] \\ OPJ-20 & ACCCCGGTAC & \\ OPD-10 & GGTTACACC & \\ OPH-13 & GACGCCACAC & \\ OPG-12 & CAGCTCACGA & \\ OPG-14 & GGATGAGACC & \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Used RAPD polymorphic primer sequences. \begin{table}
\begin{tabular}{c c c} \hline \hline
**Number of Cycles** & **Temp (\({}^{\circ}\)C)** & **Time** \\ \hline \(1\) & Initial denaturation & 94 & 4 min \\ \hline \multirow{3}{*}{35} & Denaturation & 95 & 25 s \\ \cline{2-3}  & Hybridization & Annealing t\({}^{\circ}\)(c) & 25 s \\ \cline{2-3}  & Extension & 72 & 1 min \\ \hline \(1\) & Post-extension & 35 & 5 min \\ \hline \hline \end{tabular}
\end{table} 
Table 5: PCR program for amplification of RAPD primers. Moreover, the PIC index (polymorphism information content) was determined to assess the efficacy of each RAPD primer in identifying polymorphic loci both within and across populations using the following equation:  
\[\text{PIC}=1-\sum\text{Pi}^{2}\]  
Pi is the ith allele's frequency [35]. The usefulness per marker was evaluated indirectly via the indices: PPB (the proportion of polymorphic bands or amplicon), MI (marker index) and EMR (effective multiplex ratio), as described by [36]. The binary data matrix resulting from the RAPD polymorphism was processed through the PopGene software (Version 1.31) based on the assumption of Hardy-Weinberg equilibrium [37]. This analysis provided a structure of measurement for the population's genetic diversity degree, including [PERSON]'s genetic diversity index (H) [38], PPB and the Shannon (I) information index. [PERSON]'s gene diversity statistics [39] were utilized to determine the amount of gene or interpopulation differentiation for several loci (G\({}_{\text{ST}}\)). The method outlined by [40] was employed to estimate gene flow (Nm) following the formula below:  
\[\text{N}_{\text{m}}=\frac{0.5\times(1-\text{G}_{\text{ST}})}{\text{G}_{\text{ ST}}}\]  
Furthermore, a molecular variation analysis within broomrape species (AMOVA) was conducted to determine RAPD's statistical variance components. This analysis divided the variation both within and between species using the GenAlEx 6.5 software [41]. A non-parametric test was used to estimate \(p\)-value significance after 1000 random permutations. The neighbor-joining (NJ) method was selected to construct a dendrogram. To assess the dependability of the clusters, a bootstrapping analysis was carried out with 1000 resamples using the DARwin software, version 5.0.158 [42]. The diversity and differentiation between individuals (genetic relationships) were evaluated through principal coordinate analysis (PCoA) using PAST version 2.17c [43]. The genetic structure of the population was inferred through Bayesian methods of clustering implemented in STRUCTURE version 2.3.4 [44].