Sugar Tech

, Volume 8, Issue 4, pp 246–256 | Cite as

Highly polymorphic microsatellite dna markers for sugarcane germplasm evaluation and variety identity testing

  • Yong-Bao PanEmail author
Research Article


The objective of this study was to evaluate the entire set of 221 sugarcane microsatellite (SSR) markers from the International Sugarcane Microsatellite Consortium for their utility on molecular characterization of elite U.S. germplasm. Five elite U.S. sugarcane clones were tested, including two cultivars LCP 85-384 and HoCP 96-540 from Louisiana, two cultivars CP 72-1210 and CP 85-1308 from Florida, and Green German, an active parental clone used in both states. The 5’ ends of all forward primers were labeled with the fluorescent phosphoramidite dye, FAM and PCR-amplified DNA fragments detected using a semi-automatic capillary electrophoresis system. The sizes of DNA fragments were computed accurately by running genotyping software calibrated against 16 fluorescence-labeled DNA size standard fragments. Evaluation criteria included PCR robustness, extent of the presence of irregular peaks, and the polymorphism information content (PIC). Sixty-seven SSR markers (30% of the total) were found to be highly robust, with PIC values ranging from 56% to 80%. Of these, 40 (60%) markers contained dinucleotide repeats, 11 (16%) markers contained trinucleotide repeats, and 16 (24%) markers contained composite repeats. A total of 467 alleles were scored, of which 350 were polymorphic, averaging five polymorphic alleles per marker, with their sizes ranging from 80 to 460 bp. Several of these highly polymorphic SSR markers have proven useful in sugarcane germplasm evaluation, variety identity tests, cross fidelity assessment, and polycross paternity analysis.


Sugarcane germplasm microsatellite (SSR) Polymorphism information content (PIC) 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Aitken, K.S., Jackson, P.A. andMcIntyre, C.L. (2005). A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar.Theor. Appl. Genet.,110: 789–801.CrossRefGoogle Scholar
  2. Alwala, S., Suman, A., Arro, J.A., Veremis, J.C. andKimbeng, C. A. (2006). Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity in Sugarcane Germplasm Collections.Crop Sci.,46: 448–455.CrossRefGoogle Scholar
  3. Besse, P. and McIntyre, C.L. (1996). Molecular markers: Useful tools for sugarcane breeders.In Sugarcane: research towards efficient and sustainable production. J.R. Wilson, D.M. Hogarth, J.A. Campbell and A.L. Garside (Eds), pp57–58.Google Scholar
  4. Besse, P., McIntyre, C.L. andBerding, N. (1996). Ribosomal DNA variations in Erianthus, a wild sugarcane relative (Andropogoneae Saccharinae).Theor. Appl. Genet.,92: 733–743.CrossRefGoogle Scholar
  5. Besse, P., Taylor G., Carroll, B., Berding, N., Burner, D. M. andMcIntyre, C. L. (1998). Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis.Genetica,104: 143–153.CrossRefGoogle Scholar
  6. Breaux, R.D. andLegendre, B.L. (1983). The USDA Commercial breeding program in Louisiana. Proc. Inter-Amer.Sugar Cane, Sem.:Varieties and Breeding,III: 99–105.Google Scholar
  7. Burner, D.M. and Legendre, B.L. (1993). Sugarcane genome amplification for the subtropics: a twenty year effort.Sugar Cane, 5–10.Google Scholar
  8. Burner, D. M., Pan, Y-B andWebster, R. D. (1997). Genetic diversity of New World and Old World Saccharum assessed by RAPD Analysis.Genet. Res. Crop Evol.,44: 235–240.CrossRefGoogle Scholar
  9. Burnquist, W.B. (1991). Development and application of restriction fragment length polymorphism technology in sugarcane (Saccharum spp.) breeding. Ph.D. dissertation, Cornell Univ., Ithaca, NY.Google Scholar
  10. Clark, J.M. (1988). Novel non-templated nucleotide addition reactions catalyzed by prokaryotic and eukaryotic DNA polymerases.Nucleic Acids Res.,16: 9677–9686.CrossRefGoogle Scholar
  11. Cordeiro, G.M., Taylor, G.O. andHenry, R.J. (2000). Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species,Plant Sci. 155: 161–168.CrossRefGoogle Scholar
  12. Cordeiro, G.M. andHenry, R.J. (2001). Evaluation of microsatellites (Simple Sequence Repeats) as genetic markers in sugarcane.Proc. Intl. Soc. Sugar Cane Technol.,24: 627–629.Google Scholar
  13. Cordeiro, G.M., Casu, R., McIntyre, C.L., Manners, J.M. andHenry, R. J. (2001). Microsatellite markers from sugarcane (Saccharum sp.) ESTs transferable toErianthus and sorghum.Plant Sci. 160: 1115–1123.CrossRefGoogle Scholar
  14. Cordeiro, G.M., Pan, Y. B. andHenry, R.J. (2003). Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm.Plant Sci.,165: 181–189.CrossRefGoogle Scholar
  15. da Silva, J.A.G. (2001). Preliminary analysis of microsatellite markers derived from sugarcane expressed sequence tags (ESTs).Genet. Mol.Biol. 24(1–4): 155–159.CrossRefGoogle Scholar
  16. D’Hont, A., Lu, Y. H., Feldmann, P. andGlaszmann, J.C. (1993). Cytoplasmic diversity in sugar cane revealed by heterologous probes.Sugar Cane,1: 12–15.Google Scholar
  17. D’Hont, A., Rao, P.S., Feldmann, P., Grivet, L., Islam-Faridi, N., Taylor, P. andGlaszmann, J.C. (1995). Identification and characterisation of sugarcane intergeneric hybrids,Saccharum officinarum xErianthus arundinaceus, with molecular markers and DNAin situ hybridisation.Theor. Appl. Genet.,91: 320–326.Google Scholar
  18. Glaszmann, J.C., Noyer, J.L., Fautret, A., Lanaud, C. andFeldmann, P. (1989). Molecular genetic markers in sugarcane.Proc. Intl. Soc. Sugar Cane Technol.,2: 872–882.Google Scholar
  19. Glaszmann, J.C., Lu, Y.H. andLanaud, C. (1990). Variation of nuclear ribosomal DNA in sugarcane.J. Genet. Breed.,44: 191–198.Google Scholar
  20. Grivet, L., D’Hont, A., Roques, D., Feldmann, P., Lanaud, C. andGlaszmann, J.C. (1996). RFLP mapping in cultivated sugarcane (Saccharum spp.): Genome organization in a highly polyploid and aneuploid interspecific hybrid.Genetics,142: 987–1000.PubMedPubMedCentralGoogle Scholar
  21. Harvey, M. andBotha, F.C. (1996). Use of PCR-based methodologies for the determination of DNA diversity betweenSaccharum varieties.Euphytica,89: 257–265.CrossRefGoogle Scholar
  22. Jannoo, N., Forget, L. andDookun, A. (2001). Contribution of microsatellites to sugarcane breeding program in Mauritius.Proc. Intl. Soc. Sugar. Cane Technol.,24: 637–639.Google Scholar
  23. Legendre, B.L. andBreaux, R.D. (1983). The USDA basic sugarcane breeding program in Louisiana. Proc Inter-Amer Sugar Cane Sem:Varieties and Breeding,III: 96–98.Google Scholar
  24. Levinson, G. andGutman, G.A. (1987). Slipped-strand mispairing: a major mechanism for DNA sequence evolution.Mol. Biol. Evol.,4(3): 203–221.PubMedGoogle Scholar
  25. Milbourne, D., Meyer, R., Bradshaw, J.E., Baird, E., Bonar, N., Provan, J., Powell, W. andWaugh, R. (1997). Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato.Mol. Breed,. 3: 127–136.CrossRefGoogle Scholar
  26. Ming, R., Liu, S. C., Lin, Y.-R., da Silva, J., Wilson, W., Braga, D., van Deynze, A., Wenslaff, T.F., Wu, K. K., Moore, P.H., Burnquist, W., Sorrels, M.E., Irvine, J.E. andPaterson, A.H. (1998). Detailed alignment ofSaccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes.Genetics,150: 1663–1682.PubMedPubMedCentralGoogle Scholar
  27. Pan, Y. B., Burner, D. M. andLegendre, B. L. (2000). An assessment of the phylogenetic relationship among sugarcane and related taxa based on the nucleotide sequence of 5S rRNA intergenic spacers.Genetica,108: 285–295.CrossRefGoogle Scholar
  28. Pan, Y. B., Burner, D.M. andWei, Q. (2001). Developing species-specific DNA markers to assist in sugarcane breeding.Proc. Intl. Sugar Cane Technol.,24(II): 337–342.Google Scholar
  29. Pan, Y. B., Burner, D. M., Ehrlich, K. C., Grisham, M. P. andWei, Q. (1997). Analysis of primer-derived, non-specific amplification products in RAPD-PCR.Bio Techniques,22(6): 1072–1074.Google Scholar
  30. Pan, Y. B., Miller, J. D., Schnell, R. J., Richard Jr., R.P. and Wei, Q. (2003a). Application of microsatellite and RAPD fingerprints in the Florida sugarcane variety program.Sugar Cane International, 19–28.Google Scholar
  31. Pan, Y. B., Cordeiro, G.M., Richard Jr.,E.P. andHenry, R.J. (2003b). Molecular genotyping of sugarcane clones with microsatellite DNA markers.Maydica,48: 319–329.Google Scholar
  32. Pan, Y. B., Burner, D.M., Legendre, B.L., Grisham, M.P. andWhite, W.H. (2004). An assessment of the genetic diversity within a collection ofSaccharum spontaneum with RAPD-PCR.Genet. Res. Crop Evol.,51: 895–903.CrossRefGoogle Scholar
  33. Pinto, L.R., Oliveira, K.M., Ulian, E.C., Garcia, A.A.F. andde Souza, A.P. (2004). Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats.Genome,47: 795–804.CrossRefGoogle Scholar
  34. Piperidis, G., Christopher, M.J., Carroll, M.J., Berding, N. andD’Hont, A. (2000). Molecular contribution to selection of intergeneric hybrids beween sugarcane and the wild speciesErianthus arundinaceus. Genome,43:1033–1037.PubMedGoogle Scholar
  35. Schlotterer, C. andTautz, D. (1992). Slippage synthesis of simple sequence DNA.Nuc. Acids Res.,20: 211–215.CrossRefGoogle Scholar
  36. Tai, P. Y. P. (1989). Progress and problems of intergeneric hybridization in sugarcane breeding.Proc. Inter-Am Sugar Cane Sem.,Vol. I: 391–395.Google Scholar
  37. Tew, T.L. (2003). World sugarcane variety census — 2000.Sugar Cane Intl.: 12–18.Google Scholar
  38. Tew, T.L., White, W.H., Grisham, M.P., Dufrene Jr.,E.O., Garrison, D.D. Veremis, J.C., Pan, Y. B., Richard Jr.,E.P., Legendre, B.L. andMiller, J.D. (2003). Registration of ‘HoCP 96-540’Sugarcane.Crop Sci. 45: 785–786.Google Scholar
  39. Tew, T.L. andPan, Y. B. (2005). Molecular assessment of the fidelity of sugarcane crosses with high-throughput microsatellite genotyping.J. Amer. Soc. Sugar Cane Technol.,25: 119.Google Scholar
  40. Weber, J.L. andMay, P.E. (1989). Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction.Am. J. Hum. Genet. 44: 388–396.PubMedPubMedCentralGoogle Scholar

Copyright information

© Society for Sugar Research & Promotion 1999

Authors and Affiliations

  1. 1.USDA-ARS, Southern Regional Research CenterSugarcane Research UnitHoumaUSA

Personalised recommendations