Literature DB >> 17406531

Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions.

Naeem H Syed1, Andrew J Flavell.   

Abstract

Multiple copies of transposable elements, inserted at random around the host genome, can be used as molecular markers. Sequence-specific amplification polymorphisms (SSAPs) amplify the region between a PCR primer site near the end of an element and an adjacent restriction site in the flanking genomic DNA. Each amplified insertion is revealed as a band on a sequencing gel or capillary electrophoresis, and a genomic DNA sample produces a characteristic fingerprint of bands. Here, we explain the SSAP marker development method, which can be performed for any species, with recommendations for experimental parameters in several plant species. It takes about 1-2 weeks to complete the whole SSAP marker procedure.

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Year:  2006        PMID： 17406531     DOI： 10.1038/nprot.2006.407

Source DB:  PubMed          Journal:  Nat Protoc        ISSN： 1750-2799            Impact factor:   13.491


  17 in total

Review 1.  Analysis of plant diversity with retrotransposon-based molecular markers.

Authors:  R Kalendar; A J Flavell; T H N Ellis; T Sjakste; C Moisy; A H Schulman
Journal:  Heredity (Edinb)       Date:  2010-08-04       Impact factor: 3.821

2.  iPBS: a universal method for DNA fingerprinting and retrotransposon isolation.

Authors:  Ruslan Kalendar; Kristiina Antonius; Petr Smýkal; Alan H Schulman
Journal:  Theor Appl Genet       Date:  2010-07-10       Impact factor: 5.699

3.  Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome.

Authors:  Maura Lyons; Linda Cardle; Nils Rostoks; Robbie Waugh; Andrew J Flavell
Journal:  Mol Genet Genomics       Date:  2008-07-09       Impact factor: 3.291

4.  Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker.

Authors:  Pasqualina Woodrow; Giovanni Pontecorvo; Loredana F Ciarmiello
Journal:  Mol Biol Rep       Date:  2011-07-02       Impact factor: 2.316

5.  LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species.

Authors:  Sung-Il Lee; Jong-Hwa Kim; Kyong-Cheul Park; Nam-Soo Kim
Journal:  Genetica       Date:  2015-03-19       Impact factor: 1.082

6.  Agrobacterium-mediated Tnt1 mutagenesis of moss protonemal filaments and generation of stable mutants with impaired gametophyte.

Authors:  Boominathan Mohanasundaram; Vyankatesh B Rajmane; Sukanya V Jogdand; Amey J Bhide; Anjan K Banerjee
Journal:  Mol Genet Genomics       Date:  2019-01-28       Impact factor: 3.291

7.  Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays.

Authors:  Neha Samir Roy; Kyong-Cheul Park; Sung-Il Lee; Min-Ji Im; Rahul Vasudeo Ramekar; Nam-Soo Kim
Journal:  Genetica       Date:  2017-09-15       Impact factor: 1.082

8.  Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes.

Authors:  Wee Tek Tay; Gajanan T Behere; Philip Batterham; David G Heckel
Journal:  BMC Evol Biol       Date:  2010-05-17       Impact factor: 3.260

9.  Isolation, characterization, and marker utility of KCRE1, a transcriptionally active Ty1/copia retrotransposon from Kandelia candel.

Authors:  Wenwen Liu; Yushuai Wang; Xu Shen; Tian Tang
Journal:  Mol Genet Genomics       Date:  2016-08-04       Impact factor: 3.291

10.  Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis.

Authors:  Sung-Il Lee; Jeong-An Gim; Min-Ji Lim; Heui-Soo Kim; Bo-Hye Nam; Nam-Soo Kim
Journal:  Genes Genomics       Date:  2017-10-13       Impact factor: 1.839
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