SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis

PeerJ
Wei LuoZongjun Du

Abstract

Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher (P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub (https://github.com/byemaxx/SSREnricher).

References

Feb 18, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·T ThielA Graner
May 21, 2003·Molecular Ecology·J SquirrellW Powell
May 22, 2004·Nature Reviews. Genetics·Hans Ellegren
Oct 6, 2005·Nature Reviews. Genetics·Christopher E PearsonJohn D Cleary
Oct 24, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Swarup K ParidaTrilochan Mohapatra
Sep 3, 2010·The Journal of Heredity·Jen C Perry, Locke Rowe
Oct 5, 2010·Journal of Forensic Sciences·Mitchell M Holland, Walther Parson
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jan 10, 2013·MBio·M E PalmerC D Bayliss

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Datasets Mentioned

BETA
SRR2048540
SRR1618542

Methods Mentioned

BETA
genotyping
PCR
electrophoresis

Software Mentioned

SSREnricher
EST
macOS
Linux
HIT
GeneMarker
Primer premier
MISA
CD

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