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United States Department of Agriculture

Agricultural Research Service

Research Project: CONSERVATION, CHARACTERIZATION, AND EVALUATION OF CROP GENETIC RESOURCES AND ASSOCIATED INFORMATION

Location: Plant Genetic Resources Conservation Unit

Title: Microsatellite markers in plants and insects part II: Databases and in silico tools for microsatellite mining and analyzing population genetic stratification

Authors
item Jenkins, Tracie -
item Wang, Ming
item Barkley, Noelle

Submitted to: Genes, Genomes, and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 4, 2011
Publication Date: January 20, 2012
Citation: Jenkins, T.M., Wang, M.L., Barkley, N.L. 2012. Microsatellite markers in plants and insects part II: Databases and in silico tools for microsatellite mining and analyzing population genetic stratification. Genes, Genomes, and Genomics. 6(1):60-75.

Interpretive Summary: Microsatellites or simple sequence repeat (SSR) markers have popularly been used for genetic studies in various living organisms (including plants and insects). The purpose of this review is to provide targeted information aimed at helping the insect and plant biologist effectively utilize in silico resources to find, navigate and analyze empirically derived data from sequence databases. The objectives are threefold. First, since the basic characteristics of microsatellites make them the markers of choice for studies of genetic structure that underlie adaptation and evolution, these will be delineated. Second, because sequence databases are increasingly mined for microsatellites, the major databases are discussed, as well as, available programs for in silico mining of sequence databases to retrieve microsatellites for a species of interest. Lastly, a general review is given of population genetics software for in silico genetic analyses of microsatellite data to determine population genetic structure, phylogenetic relationships, and genetic diversity in a species of interest.

Technical Abstract: Nucleotide sequence information available in searchable sequence databases and the free in silico software with which to extract and analyze microsatellite data continues to grow at a rapid rate across eukaryote taxa. The sheer amount of information available means that a comprehensive or exhaustive review of databases and free bioinformatic tools lies beyond the purview of any journal review. The purpose of this review is therefore to provide targeted information aimed at helping the insect and plant biologist effectively utilize in silico resources to find, navigate and analyze empirically derived data from sequence databases. The objectives are threefold. First, since the basic characteristics of microsatellites make them the markers of choice for studies of genetic structure that underlie adaptation and evolution, these will be delineated. Second, because sequence databases are increasingly mined for microsatellites, the major databases are discussed, as well as, available programs for in silico mining of sequence databases to retrieve microsatellites for a species of interest. Lastly, a general review is given of population genetics software for in silico genetic analyses of microsatellite data to determine population genetic structure, phylogenetic relationships, and genetic diversity in a species of interest.

Last Modified: 8/22/2014
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