Databasing Molecular Identities of Sugarcane (Saccharum spp.) Clones Constructed with Microsatellite (SSR) DNA Markers

Yong-Bao Pan

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DOI: 10.4236/ajps.2010.12011                

Abstract

This paper reports the development of the first SSR marker-based sugarcane (Saccharum spp.) molecular identity database in the world. Since 2005, 1,025 sugarcane clones were genotyped, including 811 Louisiana, 45 Florida, 39 Texas, 130 foreign, and eight consultant/seed company clones. Genotyping was done on a fluorescence-capillary electrophoresis detection platform involving 21 highly polymorphic SSR markers that could potentially amplify 144 distinctive DNA fragments. Genotyping data were processed with the GeneMapper? software to reveal electrophoregrams that were manually checked against the 144 fragments. The presence (A) or absence (C) of these 144 fragments in any sugarcane clone was recorded in an affixed sequence order as a DNAMAN® file to represent its molecular identity being achieved into a local molecular identity database. The molecular identity database has been updated annually by continued genotyping of newly assigned sugarcane clones. The database provides molecular descriptions for new cultivar registration articles, enables sugarcane breeders to identify mis-labeled sugarcane clones in crossing programs and determine the paternity of cross progeny, and ensures the desired cultivars are grown in farmers’ fields.

Keywords

Sugarcane (Saccharum spp.), Breeding, SSR Marker, Molecular Identity Database

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	D. J. Heinz, “Sugarcane Improvement through Breeding,” Elsevier, Amsterdam.
[2]	L. Grivet and P. Arruda, “Sugarcane Genomics: Depicting the Complex Genome of an Important Tropical Crop,” Current Opinion in Plant Biology, Vol. 5, No. 2, 2002, pp. 122-127.
[3]	K. P. Bischoff and K. A Gravois, “The Development of New Sugarcane Varieties at the LSU Ag Center,” Journal of American Society Sugar Cane Technologists, Vol. 24, 2004, pp. 142-164.
[4]	J. C. Skinner, “Description of Sugarcane Clones. III. Botanical Description,” Proceedings International Society Sugar Cane Technologists, Vol. 14, 1972, pp. 124-127.
[5]	C. LaBorde, B. Legendre, K. Bischoff, K. Gravois and T. Robert, “Sugarcane Variety Identification Guide 2008,” Louisiana State University AgCenter Publication, 2008.
[6]	Y.-B. Pan, G. M. Cordeiro, E. P. Richard Jr. and R. J. Henry, “Molecular Genotyping of Sugarcane Clones with Microsatellite DNA Markers,” Maydica, Vol. 48, No. 4, 2003, pp. 319-329.
[7]	Y.-B. Pan, J. D. Miller, R. J. Schnell, E. P. Richard Jr. and Q. Wei, “Application of Microsatellite and RAPD Fingerprints in the Florida Sugarcane Variety Program,” Sugar Cane International, March-April 2003, pp. 19-28.
[8]	Y.-B. Pan, B. S. Scheffler and E. P. Richard Jr., “High Throughput Genotyping of Commercial Sugarcane Clones with Microsatellite (SSR) DNA Markers,” Sugar Tech, Vol. 9, No. 2, 2007, pp. 176-181.
[9]	A. Edwards, A. Civitello, H. A. Hammond and C. T. Caskey, “DNA Typing and Genetic Mapping with Trimeric and Tetrameric Tandem Repeats,” American Journal Human Genetics, Vol. 49, No. 4, 1991, pp. 746-756.
[10]	M. H. Polymeropoulos, H. Xiao, D. S. Rath and C. R. Merril, “Tetranucleotide Repeat Polymorphism at the Human Tyrosine Hydroxylase Gene,” Nucleic Acids Research, Vol. 19, No. 13, 1991, pp. 3753.
[11]	G. M. Cordeiro, G. O. Taylor and R. J. Henry, “Characterisation of Microsatellite Markers from Sugarcane (Saccharum sp.), a Highly Polyploid Species,” Plant Science, Vol. 155, No. 2, 2000, pp. 161-168.
[12]	G. M. Cordeiro, R. Casu, C. L. McIntyre, J. M. Manners and R. J. Henry, “Microsatellite Markers from Sugarcane (Saccharum sp.) ESTs Transferable to Erianthus and Sorghum,” Plant Science, Vol. 160, No. 6, 2001, pp. 1115-1123.
[13]	Y.-B. Pan, “Highly Polymorphic Microsatellite DNA Markers for Sugarcane Germplasm Evaluation and Variety Identity Testing,” Sugar Tech, Vol. 8, No. 4, 2006, pp. 246-256.
[14]	T. L. Tew and Y.-B. Pan, “Microsatellite (Simple Sequence Repeat) Marker–Based Paternity Analysis of a Seven-Parent Sugarcane Polycross,” Crop Science, Vol. 50, No. 4, 2010, pp. 1401-1408.
[15]	Y.-B. Pan, D. M. Burner and B. L. Legendre, “An Assessment of the Phylogenetic Relationship among Sugarcane and Related Taxa Based on the Nucleotide Sequence of 5s Rrna Intergenic Spacers,” Genetica, Vol. 108, No. 3, 2000, pp. 285-295.
[16]	Z. Xin, J. P. Velten, M. J. Oliver and J. J. Burke, “High-Throughput DNA Extraction Method Suitable for PCR,” BioTechniques, Vol. 34, No. 4, 2003, pp. 820-826.
[17]	T. H. Jukes and C. R. Cantor, “Evolution of Protein Molecules,” In: H. N. Munro, Ed., Mammalian Protein Metabolism, Academic Press, New York, 1969, pp. 21-132.
[18]	T. L. Tew, D. M. Burner, B. L. Legendre, W. H. White, M. P. Grisham, E. O. Dufrene Jr., D. D. Garrison, J. C. Veremis, Y.-B. Pan and E. P. Richard Jr., “Registration of ‘Ho 95-988’ Sugarcane,” Crop Science, Vol. 45, No. 4, 2005, pp. 1660-1661.
[19]	T. L. Tew, W. H. White, B. L. Legendre, M. P. Grisham, E. O. Dufrene Jr., D. D. Garrison, J. C. Veremis, Y.-B. Pan, E. P. Richard Jr. and J. D. Miller, “Registration of ‘HoCP 96-540’ Sugarcane,” Crop Science, Vol. 45, No. 2, 2005, pp. 785-786.
[20]	T. L. Tew, W. H. White, M. P. Grisham, E. O. Dufrene, D. D. Garrison, Y.-B. Pan, E. P. Richard Jr., B. L. Legendre, and J. D. Miller, “Registration of ‘HoCP 00-950’ sugarcane,” Journal Plant Registrations, Vol. 3, No. 1, 2009, pp. 42-50.
[21]	T. L. Tew, E. O. Dufrene, W. H. White, R. M. Cobill, B. L. Legendre, M. P. Grisham, D. D. Garrison, Y.-B. Pan, E. P. Richard Jr., and J. D. Miller, “Registration of ‘HoCP 91-552’ high-fiber sugarcane,” Journal Plant Registrations, in press.
[22]	W. H. White, R. M. Cobill, T. L. Tew, D. M. Burner, M. P. Grisham, E. O. Dufrene, Y.-B. Pan, E. P. Richard Jr. and B. L. Legendre, “Registration of ‘Ho 00-961’ sugarcane,” Journal Plant Registrations, in press.
[23]	S. B. Milligan, R. W. Davidson, S. J. Edmé, J. C. Comstock, C. J. Hu, D. G. Holder, B. Glaz, N. C. Glynn and R. A. Gilbert, “Registration of ‘CPCL 97-2730’ Sugarcane,” Journal Plant Registrations, Vol. 3, No. 2, 2009, pp. 158-164.
[24]	R. A. Gilbert, J. C. Comstock, B. Glaz, S. J. Edmé, R. W. Davidson, N. C. Glynn, J. D. Miller and P. Y. P. Tai, “Registration of ‘CP 00-1101’ Sugarcane,” Journal Plant Registrations, Vol. 2, No. 2, 2008, pp. 95-101.
[25]	Juárez, J. L., J. D. Miller, H. Orozco, E. Solares, P. Y. P. Tai, J. C. Comstock, B. Glaz, J. L. Quemé de León, W. Ovalle, S. J. Edmé, N. C. Glynn, and C. W. Deren, “Registration of ‘CP 88-1165’ Sugarcane,” Journal Plant Registrations, Vol. 2, No. 2, 2008, pp. 102-109.
[26]	J. C. Comstock, B. Glaz, S. J. Edmé, R. W. Davidson, R. A. Gilbert, N. C. Glynn, J. D. Miller, and P. Y. P. Tai, “Registration of ‘CP 00-1446’ Sugarcane,” Journal Plant Registrations, Vol. 3, No. 1, 2009, pp. 28-34.
[27]	B. Glaz, S. J. Edmé, R. W. Davidson, R. A. Gilbert, J. C. Comstock, N. C. Glynn, J. D. Miller and P. Y.P. Tai, “Registration of ‘CP 00-2180’ Sugarcane,” Journal Plant Registrations, Vol. 3, No. 1, 2009, pp. 35-41.
[28]	P. Y. P. Tai, J. D. Miller and B. L. Legendre, “Preservation of Saccharum spontaneum Germplasm through Storage of True Seeds,” Sugar Cane, Vol. 6, 1994, pp. 3-8.
[29]	Y.-B. Pan, D. M. Burner, Q. Wei, G. M. Cordeiro, B. L. Legendre and R. J. Henry, “New Saccharum Hybrids in S. spontaneum Cytoplasm Developed through a Combination of Conventional and Molecular Breeding Approaches,” Plant Genetic Resources, Vol. 2, No. 2, 2004, pp. 131-139.