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United States Department of Agriculture

Agricultural Research Service

Title: Highly Polymorphic Microsatellite DNA Markers for U.S. Sugarcane Germplasm Evaluation and Variety Fingerprinting

Authors
item Pan, Yong-Bao
item Comstock, Jack
item Scheffler, Brian

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: September 30, 2004
Publication Date: January 15, 2005
Citation: Pan, Y.B., Comstock, J.C., Scheffler, B.E. 2005. Highly Polymorphic Microsatellite DNA Markers for U.S. Sugarcane Germplasm Evaluation and Variety Fingerprinting [abstract]. Guide of Plant and Animal Genome XIII. p. 36.

Technical Abstract: Sugarcane breeding programs can be enhanced by the utilization of a diverse group of DNA markers to genetically characterize parental lines and the progeny that are produced. To meet the need for additional markers to characterize the U.S. sugarcane germplasm, we evaluated 221 sugarcane microsatellite (SSR) markers from the existing database. These included 77 SSR markers developed from the Réunion variety R570 at the Centre de Coopération International en Recherché Agronomique Pour le Development (CIRAD) and 144 SSR markers from the Australian variety Q124 under the Sugarcane Microsatellite Consortium (SMC). Five U.S. sugarcane clones were tested, including LCP 85-384 and HoCP 96-540 from Louisiana, CP 72-1210 and CP 85-1308 from Florida, and Green German, which has been an active sugarcane genetic stock in both states. All forward primers were labeled with the FAM fluorescence dye. Fragment analyses of PCR-amplified DNA fragments were done on an ABI PRIZM3730 Genetic Analyzer, and data were analyzed using the GeneMapper software. Evaluation criteria included PCR robustness, mis-priming, stutter, and polymorphism information content (PIC) value. Fifty-seven (26%) of the SSR markers (11 from CIRAD and 46 from SMC) were highly polymorphic with PIC values ranging from 53% to 78%. Thirty-six (63%) markers contained dinucleotide repeats, 11 (19%) markers contained trinucleotide repeats, and 10 (18%) markers contained composite repeats. A total of 375 polymorphic DNA bands were identified, averaging seven bands per marker, with sizes ranging from 90 to 450 bp. Currently, we are investigating the distribution of 20 of the most highly polymorphic SSR markers among the U.S. sugarcane germplasm. These same markers will be used to produce more comprehensive molecular genotypes for the U.S. sugarcane varieties and breeding lines.

Last Modified: 4/20/2014
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