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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #253192
Title: Development of a genetic linkage map for Louisiana sugarcane: New microsatellite (SSR) DNA markers identified for LCP 85-384

Author
item Pan, Yong-Bao
item LIU, PINGWU - Collaborator

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 6/2/2010
Publication Date: 6/16/2010
Citation: Pan, Y.-B., Liu, P. 2010. Development of a genetic linkage map for Louisiana sugarcane: New microsatellite (SSR) DNA markers identified for LCP 85-384 [abstract]. Journal of the American Society of Sugar Cane Technologists. 30:137.

Interpretive Summary:

Technical Abstract: Application of the recently developed genetic linkage map of sugarcane (Saccharum spp.) cultivar LCP 85-384 has been limited due to the small number of DNA markers, in particular microsatellite (SSR) DNA markers, on the map. Adding DNA markers to the map improves its usefulness in identifying associations between important agronomic traits and DNA markers through quantitative trait linkage (QTL) analysis. The objectives of this study were to search the public database for new SSR markers and evaluate their transferability to the U.S. sugarcane germplasm. A total of 376 SSR markers were found, of which 305 markers were reportedly derived from expressed sequence tags (ESTs) and 71 were designed based on genomic DNA sequences. Although EST sequences are highly conserved, more genetic variability can be found in non-expressed regions of genomic DNA sequences. Conventional oligo-nucleotide primers of 81 EST and 71 genomic SSR markers were synthesized commercially and evaluated by polymerase chain reaction (PCR) using the genomic DNA of LCP 85-384 as the template. The PCR-amplified DNA products along with DNA size markers were separated in 1.5% agarose gels, visualized under UV lights by ethidium bromide staining, and photographically documented. The results indicated that 71 (88%) EST and 39 (55%) genomic SSR markers were capable of producing DNA fragment(s) from the genomic DNA of LCP 85-384. These transferable SSR markers will be labeled with fluorescent phosphoramidite dyes and then be used on a capillary electrophoresis-based high throughput genotyping platform to fingerprint the LCP 85-384 mapping population to produce more robust SSR DNA data to be added to the linkage map. The potential utility of these newly transferred SSR markers in enhancing U.S. sugarcane germplasm evaluation and varietal genotyping will also be investigated.