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United States Department of Agriculture

Agricultural Research Service

Research Project: GENOMICS AND BIOINFORMATICS RESEARCH IN AGRICULTURALLY IMPORTANT ORGANISMS

Location: Genomics and Bioinformatics Research Unit

Title: Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing

Authors
item Arias De Ares, Renee
item Irish, Brian
item Ballard, Linda
item Duke, Mary
item Liu, Xiaofen
item Simpson, Sheron
item Scheffler, Brian

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: November 10, 2010
Publication Date: January 11, 2010
Citation: Arias De Ares, R.S., Irish, B.M., Ballard, L.L., Duke, M.V., Liu, X.F., Simpson, S.A., Scheffler, B.E. 2010. Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing. Plant and Animal Genome. Abstract P089.

Technical Abstract: Microsatellites were developed for ten tropical species using a method recently developed in our laboratory that involves a combination of two adapters at the SSR-enrichment stage and allows for cost saving and simultaneous loading of samples. The species for which microsatellites were isolated are: Nephelium lappaceum (Rambutan), Manilkara zapota (sapodilla), Pouteria sapota (sapote), Litchi chinensis (lychee), Melicoccus bijugatus (Spanish lime), Annona squamosa (Custard apple, sugar apple), Dimorcarpus longan (longan), Averrhoa carambola (star fruit), Garcinia mangostana (mangosteen) and Bambusa vulgaris var. vittata (bamboo). A total of 2,510,291 reads assembled into 224,815 contigs where a total of 49,898 repeats were detected for the ten species combined. For testing, 384 primer sets were selected under high stringency conditions (high melting temperature and GC clamp). The 384 primer sets of each species were tested on a subset of DNA samples to select the best subsets of markers for their use in variety/cultivar identification and plant breeding.

Last Modified: 7/23/2014