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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND BIOINFORMATICS RESEARCH IN AGRICULTURALLY IMPORTANT ORGANISMS Title: Optimized Construction of SSR-enriched Libraries

Authors
item Techen, Natascha - UNIV. OF MISSISSIPPI
item Arias De Ares, Renee
item Glynn, Neil
item Pan, Zhiqiang
item Khan, Ikhlas - UNIV. OF MISSISSIPPI
item Scheffler, Brian

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 23, 2009
Publication Date: May 15, 2010
Citation: Techen, N., Arias De Ares, R.S., Glynn, N.C., Pan, Z., Khan, I.A., Scheffler, B.E. 2010. Optimized Construction of SSR-enriched Libraries. Molecular Ecology Resources. 10(3)508-515

Interpretive Summary: Certain regions of the DNA in organisms are variable between individuals and these regions can be used as DNA markers to characterize variability within species or closely related species. There are techniques to extract and identify those regions, though these methods are not very effective and are difficult to use. We have designed a highly effective method to pull those variable regions of DNA for analysis, and we tested it on various types of DNA from different organisms, and showed its effectiveness on DNA samples of animals, plants and fungi.

Technical Abstract: We have developed a more efficient method to construct simple sequence repeat (SSR) libraries. We have designed and tested several new adapter. We changed the typical blunt-end ligation of adapters for the more effective sticky-end ligation. We optimized temperature, enzymes and length of each step, and tested the system for making libraries of a nematode, a tree, a crop and a fungus to show that the system is effective using DNA of various origins. We provide an easy to follow protocol for the users, and emphasize critical point to be successful in the constructions. The result was libraries containing SSRs on 74% or higher percentage of the contigs assembled.

Last Modified: 10/25/2014