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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #240021

Title: Databasing Molecular Identities of Louisiana, Florida, and Texas Sugarcane Clones

item Pan, Yong-Bao

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 4/30/2009
Publication Date: 6/17/2009
Citation: Pan, Y.-B. Databasing Molecular Identities of Louisiana, Florida, and Texas Sugarcane Clones. J. Am. Soc. Sugar Cane Technol. 29:87.

Interpretive Summary:

Technical Abstract: Sugarcane (Saccharum spp. hybrids) clones (cultivars and superior breeding lines) are routinely exchanged across geographic locations for field-testing or crossing. It is crucial to maintain the genetic identity of these clones during field collection, shipping, and quarantine. Traditionally, sugarcane researchers identify clones using gross morphological traits. Although this may work well for the breeders who developed the clones, others may not be able to identify mislabeled clones because morphological traits are known to change across years and locations. Since the early 2000s, a sugarcane molecular genotyping technology was developed which uses the leaf tissue DNA and fluorescence-based capillary electrophoresis for definitive identification of sugarcane clones. Using this technology, 21 polymorphic microsatellite (SSR) markers generated 144 distinctive DNA fingerprints from the U.S. sugarcane clones. The 144 DNA fingerprints are arranged in an affixed linear order and the presence (denoted by A) or absence (C) of each fingerprint in a clone being genotyped is recorded into an Excel spreadsheet to generate a unique sequence of As or Cs. This unique sequence was converted into a DNAMAN® file to define the molecular identity of that clone. All the resulting DNAMAN® files were stored in a molecular identity database at the USDA-ARS, SRL in Houma, LA, which may be retrieved for clone identity verification using the DNAMAN® multiple sequence alignment program. Since 2005, a total of 689 leaf tissue samples from Florida, Texas, and Louisiana have been genotyped (222 in 2005; 183 in 2006; 249 in 2007; and 35 in 2008). A few important Louisiana clones have been sampled multiple times across years and locations to confirm the genetic identity. If any sample were mislabeled, then it would produce a different molecular identity than the rest of the samples of that same clone. The database and the DNAMAN® program were then used to correctly identify the sample of the mislabeled clone. The molecular identity database of newly designated clones is updated yearly, providing molecular descriptions for cultivar registrations, tools for enhancing breeding efficiency by maintaining the right clones in the crossing programs to ensure the desired crosses, identifying male parent in polycross, and verifying that growers have the correct cultivars.