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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #315993

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research

Title: Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

item Pan, Yong-Bao
item Scheffler, Brian
item Dufrene, Edwis
item WAGUESPACK, HERMAN - American Sugar Cane League
item Grisham, Michael

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2015
Publication Date: 6/1/2015
Citation: Pan, Y., Scheffler, B.E., Dufrene Jr, E.O., Waguespack, H., Grisham, M.P. 2015. Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry. Journal of the American Society of Sugar Cane Technologists. 35:51.

Interpretive Summary:

Technical Abstract: A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current Louisiana cultivars and newly assigned breeding lines with a panel of 21 SSR primer pairs. The fluorescent SSR fragments are separated according to their sizes through CE on a DNA Sequencer. A panel of 16 ROX fluorescence-labeled DNA size markers is mixed with every sugarcane genotyping sample for accurate fragment size determination. The fluorescence- and CE-based SSR fingerprints are visualized with sizes indicated using genotyping software. One hundred forty-four distinctive DNA fingerprints from the 21 SSR primer pairs are targeted through manual checking. The molecular identity of any Louisiana sugarcane clone is represented by how many of 144 fingerprints are detected and the order of their appearance. Since 2005, approximately 2,000 molecular identities have been constructed and are available from the database. The molecular identity database has been utilized to: 1) provide molecular descriptor information for newly released cultivars’ registration articles; 2) identify in a timely fashion any mislabeled or unidentifiable clones from cross parents and evaluation field plots; 3) provide clone-specific fingerprint information for assessing cross quality and paternity of polycross; 4) provide information for molecular marker inheritance studies. The integration of fluorescence- and CE-based SSR genotyping and the molecular identity database into the Louisiana sugarcane breeding program improves the overall efficacy of cultivar development and commercialization in Louisiana.