Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 4, 2003
Publication Date: October 20, 2004
Repository URL: http://handle.nal.usda.gov/10113/20820
Citation: Pan, Y.-B., Burner, D.M., Legendre, B.L., Grisham, M.P., White, W.H. 2004. An assessment of the genetic diversity within a collection of Saccharum spontaneum L. with RAPD-PCR. Genetic Resources and Crop Evolution. 51(8):895-903. Interpretive Summary: Saccharum spontaneum, one of sugarcane's ancestor species, is arguably the most important germplasm used in breeding programs around the world. Many desirable traits, such as vigor, cold hardiness and pest resistance, can be found in this species. While clones of S. spontaneum exhibit vast amount of genetic variability in readily observable traits, this species has not been extensively characterized at the DNA level. The objective of this study was to assess the amount of genetic variability among 33 clones of S. spontaneum and two cultivated sugarcane varieties using the DNA fingerprints called RAPD-PCR. The results from this study showed that these S. spontaneum clones had substantial DNA variability. In addition, these clones could be distinguished from one another by a minimum of two such DNA fingerprints. The information from this study helped assure that maximum genetic diversity could be maintained in a local S. spontaneum collection with limited resources. The DNA variability observed in this study also may help sugarcane breeders identify species-specific DNA markers for the selection of hybrid plants.
Technical Abstract: A local collection of 33 Saccharum spontaneum clones and two sugarcane cultivars (LCP 82-89 and LCP 85-384) were assessed for genetic variability using random amplified polymorphic DNA (RAPD)-PCR. A total of 157 polymorphic RAPD-PCR bands was scored with 17 primers. The number of RAPD-PCR products per primer ranged from four to 16. The data were analyzed with two computer programs, NTSYSpc and DNAMAN. Although these two programs yielded similar results, a bootstrapped phylogenetic tree could be generated with the DNAMAN software. A substantial degree of genetic diversity was found within the local S. spontaneum collection. Pairwise genetic homology coefficients ranged from 65% (SES 196/Tainan 2n=96) to 88.5% (IND 81-80/IND 81-144). LCP 82-89 and LCP 85-384 were more similar to each other (82%) than either one was to any clone of S. spontaneum (ranging from 60.5% to 75.2%). The 33 S. spontaneum clones were assigned to seven groups independent of their geographic origin or morphology, while the two sugarcane cultivars were assigned to an eighth group. All but two pairs of S. spontaneum clones could be distinguished by a single RAPD primer OPBB-02. The use of a second primer, either OPBE-04 or Primer 262, separated all S. spontaneum clones. One of the amplification products from the RAPD primer OPA-11, OPA-11-336, proved to be cultivar-specific and has been utilized in our breeding program. Information from this study should help conserve the genetic diversity of S. spontaneum.