Comparative assessment of SSR, ISSR and AFLP markers for characterization of selected genotypes of Himalayan Chir pine (Pinus roxburghii Sarg.) based on resin yield

A set of 19 SSR (Simple Sequence Repeats), 9 ISSR (Inter-Simple Sequence Repeats) and 5 AFLP (Amplified Fragment Length Polymorphism) primer combinations were used to evaluate the variability among 53 genotypes of Pinus roxburghii selected based on resin yield from the natural zone of occurrence of this species in Uttarakhand, India. The selected trees of pine varied in resin yield from 0.25 to 8 kg/year/tree. Based on the comparative assessment of SSR, ISSR and AFLP markers, SSR markers were found most polymorphic with an average PIC value of 0.327 and 2.42 alleles per marker, while ISSR markers showed the highest effective multiplex ratio (15.536) and marker index (4.958). AFLP markers showed the maximum resolving power (8.099) which was comparable to the resolving power (8.059) of ISSR markers. UPGMA-based dendrogram using SSR markers revealed more distinct grouping of genotypes on the basis of resin yield as compared to ISSR and AFLP markers. AMOVA by collection site revealed no significant variation among the populations. Whereas, AMOVA by resin yield using SSR, ISSR and AFLP markers revealed F-ST values to be 0.1096, 0.0483 and 0.2422 indicating moderate, low and great genetic differentiation among the groups. This clearly indicated that the variation at the molecular level was attributed to the resin yield and not the site of collection.