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Title: Application of microsatellite and RAPD fingerprints in the Florida sugarcane variety program

Author
item Pan, Yong-Bao
item Miller, Jimmy
item Schnell Ii, Raymond
item Richard Jr, Edward
item Wei, Qijian - Mei Mei

Submitted to: Sugar Cane International
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2003
Publication Date: 3/20/2003
Citation: Pan, Y.-B., Miller, J.D., Schnell, R.J., Richard Jr, E.P., Wei, Q. 2003. Application of microsatellite and RAPD fingerprints in the Florida sugarcane variety program. Sugar Cane International. March/April 2003:19-28.

Interpretive Summary: Varietal identity is one of the fundamental issues sugarcane breeders now deal with. To help address this issue, 25 Florida sugarcane varieties were molecularly characterized using three DNA markers called microsatellites. A total of 18 variable size DNA products were found. Presence or absence of these DNA products constituted the fingerprint for that variety. In 2002, one of the nine field trial plots of variety CP 96-1602 in southern Florida showed severe smut disease. Sugarcane breeders were deeply concerned and wanted to know if the plantings in this plot were of the same variety as the plantings in the other eight plots. Fingerprints of the three microsatellites and four other markers called RAPDs were produced from the DNA of the leaf samples taken from the field trial plots. The fingerprints from the smut plot were the same as those of CP 96-1602, whereas the fingerprints of the smut-free plot were different from any of the 25 varieties. It was concluded that variety CP 96-1602 should no longer be used as a parent in the breeding program and that the plantings from the smut-free plots should be advanced for further testing as a potential new variety. The availability of these DNA fingerprints allows sugarcane breeders to identify mis-labeled plantings in their field trials, evaluate the efficiency of the current conventional breeding methods, and improve pollination control during the crossing season.

Technical Abstract: Twenty-five Florida sugarcane varieties were fingerprinted with three microsatellites, namely, SMC334BS, SMC336BS, and MCSA068G08, using a capillary electrophoresis system. Multiple alleles were detected from each microsatellite that exhibited a high level of polymorphism. There were six alleles for SMC334BS, five for SMC336BS, and seven for MCSA068G08 for a total of 18 alleles. A putative genotype is assigned to each variety by an arbitrary nucleotide sequence of A (if a particular allele is present) or C (if the same allele is absent). The genetic similarity among these varieties was assessed with a DNA sequence analysis software, DNAMAN to produce a pairwise homology matrix and a homology tree. Only two pairs of varieties, CP 70-1133/CP 92-1213 and CP 81-1384/CP 98-1462, shared an identical genotype. The 25 varieties were clustered into three groups, with genetic similarities greater than 70% within each group. Group I included CP 98-1462, CP 81-1384, CP 92-1666, CP 98-1119, CP 92-1641, CP 72-2086, CP 89-2143, CP 96-1602, CP 81-1254, and CP 94-1340. Group II included CP 92-1213, CP 70-1133, CP 73-1547, CP 93-1309, CP 86-1633, CP 82-1592, CP 72-1210, CP 94-1100, CP 98-1840, CP 95-1039, CP 88-1762, CP 80-1743, and CP 94-1591. Group III included CP 85-1308 and CP 84-1198. The availability of these microsatellite fingerprints allowed the sugarcane breeders to identify mis-labeled plantings in their field trials, evaluate the efficiency of the current conventional breeding methods, and improve the pollination control during the crossing season.