There is very limited genetic information on Plum species (Esmenjaud and Dirlewanger 2007) required for plum breeding which happens to be slow due to high degree of heterozygosity, self-incompatibility and long juvenile phase (Guerra and Rodrigo 2015). In this study resolving power of RAPD, ISSR and SCoT was used to confirm the genetic relatedness in Plum cvs. Santa Rosa and Frontier. The relationship within and between two cultivars was drawn by cluster analysis from binary data generated through these marker systems. For RAPD analysis eighteen RAPD primers out of 28 resulted in 33 scorable bands ranging from minimum of 1 in primers OPA 08, OPB 01, OPB 02, OPB 06, OPB 07, OPB 08, OPB 10, OPB 14, OPE 04 and OPE 14 to a maximum of 5 in OPC 02. All the amplified products ranged from 100–1500 bp. Genetic similarity between the two cultivars ranged from 0.74 to 0.94 having an average of 0.84 (Fig. 1a) indicating very low level of polymorphism, similarly the Nei’s gene diversity ranged from 0 to 0.37 depicting very high similarity between the two cultivars. The highest PIC value of RAPD primers was 0.78, indicating the efficiency of these primers in genetic diversity studies. Shimada et al (1999) reported a polymorphism of 24% while studying the genetic variations in plum commercial genotypes through RAPD markers which is nearly similar to our studies.
During ISSR analysis all of 15 ISSR primers used for the study amplified the genomic DNA generating 73 detectable bands which ranged from 3 to 8. Minimum of 3 bands were amplified by ISSR 825, ISSR 841, ISSR 845 and ISSR 873 whereas, maximum of 8 bands was produced through ISSR 807, having an average of 4.86 bands per primer ranging from 100- 3000bp size. The similarity coefficient between the two cultivars ranged from 0.62 to 0.67 (Fig. 1b) and Shannon’s information index was between 0 to 0.67 depicting low genetic diversity. Previously, ISSR markers were utilized for studying the genetic variability of many plum varieties of Southern China through by Wu et al. (2019). In SCoT analysis seven out of 26 primers resulted in amplification of genomic DNA ranging from 200 to 2000bp having genetic similarity of 0.67 to 0.89 (Fig. 1c) and Nei’s gene diversity index ranging from 0 to 0.25.
All the three markers were effective in distinguishing the two genotypes as majority of the amplicons generated were polymorphic (0.75%) amongst both the genotypes. However, the dendrogram pertaining to the above data broadly divided these two cultivars into two major clusters containing in vitro shoots, their progenies and mother trees of respective cultivars which depicted a genetic similarity of 0.65 to 0.84 between plum cvs. Santa Rosa and Frontier. Amongst all the three markers used for the study SCoT were found to be more efficient having highest PIC (0.88) and Rp value (15.09) followed by ISSR having highest PIC value of 0.86. Many RAPD primers had the lowest PIC and Rp values. On the contrary low polymorphism has been reported by SCoT markers in date palm (Qurainy et al., 2015)
Plums are self-incompatible, therefore it becomes tough to decide if cultivars are pure species. Many of the varieties cultivated today are hybrids with unknown parents. Previously a close genetic relationship between Plum cvs Golden Japan and Santa Rosa was derived by Hend et al., (2009) with the aid of RAPD markers the information regarding which can be utilized for the improvement of this crop. Santa Rosa is a complex hybrid developed by Luther Burbank (Athanasiadis et al., 2013) and is a parent to many other varieties of plum including Frontier (Jonathan, 1993) that is justified by our studies showing a molecular relatedness between them indicating a common lineage.