Comparison of AFLP, TRAP and SSRs in the estimation of genetic relationships in sugarcane

The Sugarcane Breeding Programme of the Instituto Agronomico de Campinas has been using routinely different types of molecular markers for the characterization of their breeding clones and varieties. In the present work we compared the genetic relationships among 82 sugarcane clones/varieties based on three types of molecular markers; AFLP, TRAP and Microsatellites (SSRs). Five AFLP selective primer combinations, 10 SSRs and four TRAP fixed primers, designed from candidate genes involved in the drought tolerance response metabolism, were used in combination with three arbitrary primers. The pair-wise genetic similarity based on the Jaccard’s coefficient, the dedrogram and matrix comparison were done using NTSYS Software. A total of 410 polymorphic markers were obtained: 145 AFLPs, 103 SSRs, and 160 TRAPs. Although the average genetic similarity estimates based on AFLP (0,675) and TRAP (0,655) was closer to each other than to SSRs (0,522), the correlation between TRAP and SSRs was higher (r= 0.24). The coefficient of variation was lower for AFLP and TRAP (∼6.55%) than for SSRs (13%). These results indicate that the choice of molecular markers should be considered carefully, based on the purpose of the application in the breeding programme, as it is not possible to select a marker system that fits all the requirements for germplasm characterization.