ARS | Publication request: Genetic diversity and phylogenetic relationships among sugarcane and related species determined from microsatellite DNA data

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: May 14, 2007
Publication Date: June 11, 2007
Citation: Pan, Y.-B. 2007. Genetic diversity and phylogenetic relationships among sugarcane and related species determined from microsatellite DNA data [abstract]. Journal of the American Society of Sugar Cane Technologists. 27:57.

Technical Abstract: Genetic diversity and phylogenetic relationships were assessed among 105 clones of commercial sugarcane hybrids and related Saccharum species using 22 microsatellite (SSR) DNA markers. These included 17 sugarcane cultivars from the U.S. mainland, 23 S. officinarum clones, 16 S. robustum clones, 15 S. barberi clones, 10 S. sinense clones, 22 S. spontaneum clones, and two S. edule clones. Total genomic DNA samples extracted from leaf tissue were subjected to PCR with fluorescence-labeled SSR primers. Amplified SSR DNA fragments were fractionated by capillary electrophoresis (CE) along with DNA size standards, and resulting CE run files were analyzed with the GeneMapper™ software (www.appliedbiosystems.com). Five hundred and sixteen polymorphic SSR fragments were identified and presence or absence of each of the 516 fragments was recorded for each clone. The 516 data matrices were subjected to cluster analysis using NTSYSpc (www.exetersoftware.com) and DNAMAN® (www.lynnon.com) programs. Both analyses produced almost identical homology trees, but the DNAMAN® program also produced a phylogenetic tree with bootstrap values. Six major groups/clusters of clones were identified that mostly supported the classical Saccharum taxonomy. One exception was that the two S. edule clones did not group together but were found within the S. robustum cluster. The greatest diversity was displayed among S. spontaneum clones, which were also more distantly related to the other species, suggesting greater potential for their utilization in sugarcane improvement through breeding. Less diversity was found both within and between the other four species (S. officinarum, S. robustum, S. barberi, and S. sinense) as well as the cultivars. As for the U.S. cultivars, the Florida cultivars were generally separated from the Louisiana and Texas cultivars, which appeared to be similar to one another genetically. The results placed 10 wild species clones (about 10%) outside their normal groups/clusters, due either to taxonomical misclassification or mis-labeling during shipment and handling.