Location: Sugarcane ResearchTitle: Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing Author
Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/9/2011
Publication Date: 6/22/2011
Publication URL: http://handle.nal.usda.gov/10113/58477
Citation: Liu, P., Que, Y., Pan, Y.-B. 2011. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech. 13(2):129-136. Interpretive Summary: The initial stage of identifying useful SSR markers, also called simple sequence repeats (SSRs) that are widely distributed in the genetic makeup of sugarcane, is a tedious and costly process; as such the utilization of these markers is somehow limited in sugarcane. Since sugarcane varieties grown in the world today share over 70% similarity in their chromosome make ups, it is more efficient and economical to evaluate SSR markers whose information is available in the public domain. In this study, 152 SSR markers that were developed from an Indian variety Co7201 by the Indian Agricultural Research Institute were extensively evaluated using the genomic DNA of a Louisiana cultivar LCP 85-384. One hundred and ten of these SSR markers were able to work on LCP 85-384. The remaining 42 SSR markers were not, hence an indication of difference in chromosome make up in these two varieties. Twenty-three of the 110 SSR markers were further evaluated on 10 wild clones representing five related ancestral species by fluorescence, capillary electrophoresis-based fingerprinting technique. A total of 200 SSR-PCR DNA fingerprints were amplified, of which 199 fingerprints showed variability among the 10 wild clones. It is anticipated that many of the SSR markers evaluated in this study can be used by the Louisiana sugarcane breeders to differentiate varieties and their cross progeny as well as to develop DNA maps for traits (characteristics) of interest in the hopes of developing trait-specific markers.
Technical Abstract: The objective of this study was to evaluate 152 sugarcane microsatellite (SSR) markers originally developed in India for their transferability to germplasm being used by sugarcane breeders in the U.S. The commercial sugarcane cultivar, LCP 85-384, was used for the initial screening of the SSR markers because it is a parent in many of the most recently released cultivars. Ten wild clones representing five related Saccharum species were also used in a follow-up screen, namely, S. officinarum, S. spontaneum, S. robustum, S. sinense, and S. barberi. Of 152 SSR markers tested, 110 primed the amplification of PCR products from the genomic DNA of LCP 85-384, of which 39 were derived from genomic sequences and 71 were derived from expressed sequence tags (ESTs). Twenty-three SSR markers that amplified relatively higher yields of PCR products migrating as a single intensely stained band were chosen for further evaluation on the 10 wild clones using a capillary electrophoresis-based genotyping platform and fluorescently-labeled primers. Sizes of amplified DNA fragments were accurately computed against GS500 DNA size standards. A total of 200 DNA fragments (alleles) were scored, of which 199 fragments were polymorphic, averaging 8.7 polymorphic alleles per marker, with sizes ranging from 100 to 505 bp. The polymorphism information content (PIC) values of these 23 SSR markers varied from 0.42 to 0.90. It is anticipated that many of the SSR markers evaluated in this study can be used by the Louisiana sugarcane breeders to differentiate varieties and their cross progeny as well as to develop DNA maps for traits (characteristics) of interest in the hopes of developing trait-specific markers.