A comparison of UP ‐ PCR and RAPD markers to study genetic diversity of F usicladium effusum (G. Winter), cause of pecan scab

Summary Fusicladium effusum infects pecan causing yield loss, but no information is available on the genetic diversity of F. effusum . Randomly amplified polymorphic DNA s ( RAPD s) and universally primed polymerase chain reaction ( UP ‐ PCR ) were compared to detect polymorphisms on a group of 20 isolates of F. effusum from 11 geographical locations in the southeastern USA . Two tests (run 1 and 2) of both the RAPD and UP ‐ PCR s were conducted to assess the repeatability of the methods, and the markers scored on agarose gels. In addition, the UP ‐ PCR markers from run 1 were scored using an automated capillary system. Both RAPD s and UP ‐ PCR markers detected a high level of polymorphism among the scored markers (92 and 91% of RAPD markers, and 86 and 87% of manually scored UP ‐ PCR markers in run 1 and 2 were polymorphic, respectively; 93% of UP ‐ PCR markers were polymorphic when scored using the automated system). Unweighted paired group method of arithmetic averages ( UPGMA ) analysis showed both RAPD s and UP ‐ PCR markers individually identified each isolate, producing three groupings, but only the groupings based on run 1 and 2 of the UP ‐ PCR contained the same isolates. Bootstrap analysis based on the Dice coefficient produced phenograms from the UP ‐ PCR data with weak to moderate node support (≥54) for the primary branch, but no support for the RAPD s data (≤34). A Mantel test of runs 1 and 2 using RAPD s or UP ‐ PCR showed good agreement ( r  = 0.8761 and 0.8289, p < 0.0001), but poor agreement between RAPD s and UP ‐ PCR . UP ‐ PCR results based on the interisolate Dice coefficients showed a weak to strong association with distance. Based on these results, both RAPD s and UP ‐ PCR markers were capable of demonstrating polymorphisms and identifying relationships among isolates of F. effusum ; however, UP ‐ PCR markers appear to be more reliable.