ARS | Publication request: Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: May 5, 2007
Publication Date: June 11, 2007
Citation: Pan, Y.-B., Scheffler, B.E., Richard Jr, E.P. 2007. Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program. Journal of the American Society of Sugar Cane Technologists. 27:71.

Technical Abstract: Sugarcane propagates asexually through vegetative cuttings. To validate the genetic identity of sugarcane clones during shipping and handling, we produced molecular fingerprints based on 21 microsatellite (SSR) DNA markers for 116 Louisiana parental clones that were included in the crossing programs at Canal Point, Florida and Houma and St. Gabriel, Louisiana. Of the 116 clones, 48 were planted at more than one location and the identity of these clones was verified across the locations. DNA was extracted from leaf tissue and subjected to PCR amplification and capillary electrophoresis (CE) using a liquid-handling station, 384-well reaction plates, and fluorescence-labeled SSR primers. The genotyping files were recorded automatically during the CE and were then analyzed using GeneMapper™ software. A total of 144 distinctive SSR alleles were designated in a sequential order. The presence (A) or absence (C) of these alleles in designated sequential order constituted a DNA sequence, which represented the molecular characteristic or SSR genotype of that clone. An alignment of all SSR genotypes using the DNAMAN® software produced homology and phylogenetic trees. Analysis among different samples of 39 of the 48 clones planted at multiple locations produced identical SSR genotypes. For the other 9 clones, SSR genotypes from one or more locations did not group together with the original on the phylogenetic trees. These plants/clones were considered to be mis-labeled and were removed from the crossing program. The SSR genotypes produced from this study were stored in a local molecular database for future use in clonal verifications, cross fidelity assessments, and polycross paternity determinations.