Assessment of genetic variance, phylogenetic relationship and population structures using multiple molecular marker systems in popular varieties of citrus

<title>Abstract</title> <p>Citrus is one of the most important fruit crops worldwide and belongs to Rutaceae family. Numerous molecular marker systems have been utilized for the characterization of citrus germplasm. However, information on the combined utilization and comparative efficiency of different marker systems in citrus remains limited. Therefore, ten each neutral systems (RAPD and ISSR) along with 36 SCoT and 25 CBDP markers were evaluated to identify the most suitable marker system(s) for the characterization of 19 popular citrus varieties. Among the marker systems evaluated SCoT exhibited the highest mean polymorphic information content (PIC) value (0.42), whereas ISSR showed lowest (0.35). Likewise, the SCoT marker exhibited comparatively higher level of polymorphism than the other marker systems. UPGMA clustering analysis classified the citrus varieties into two major groups with Fairchild and Pearl Tangelo forming an outlier cluster, reflecting their interspecific hybrid nature. Population structure analysis based on RAPD and CBDP markers delineated 19 varieties into three populations, while ISSR and SCoT markers resolved them into eight populations. Analysis of molecular variance (AMOVA) revealed a majority of genetic variation (≥ 90%) resided within populations, while only a small proportion (≤ 5%) was attributed to variation among populations. Although, RAPD and CBDP markers were found to be effective for genotype discrimination, the SCoT marker systems emerged as the most efficient on marker efficiency parameters compared with other markers systems analyzed. The identified markers in this study may serve as valuable tools for citrus germplasm characterizations and effectively utilized in future citrus crop improvement programmes.</p>