Screening for Species-Specific AFLP Markers in the Saccharum Complex

Sugarcane bioenergy introgression programs have used wild sugarcane accessions and related genera as parents in crosses with commercial varieties to introgress favorable genes for fiber and biomass. The development of SCAR markers derived from AFLP species-specific markers for S. spontaneum and S. robustum can allow the rapid identification of hybrids derived from these crosses. A preliminary screening for species-specific AFLP markers in the Saccharum Complex was conducted with five selective primer pairs combinations (EcoRI/MspI) of which four were selected to produce DNA fingerprints for a group of 60 genotypes (10 sugarcane commercial varieties, 5 S. robustum, 5 S. barberi, 23 S. spontaneum, 12 S. officinarum and 5 Erianthus accessions). A total of 203 well clear defined polymorphic fragments was genotyped, of which 13, 17, 7, 1 and 24 were restricted to S. robustum, S. spontaneum, S. barberi, S. officinarum and E. arundinaceus accessions, respectively. The average genetic diversity within each species group ranged from 0.267 (S. spontaneum) to 0.498 (S.robustum). The dendrogram gave rise to five main clusters, with most of the accessions clearly assigned to the respective species and with the E. arundinaceus accessions clustered together and distant from the other species. The highest average genetic similarity was within the group of commercial varieties (82.7%) and the lowest (44.6%) within the S. spontaneum group. The proportion of membership for each accession estimated by the Structure software allowed the identification of accessions showing different proportions of species which need to be taken into consideration in the identification of species-specific markers.