Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L.

Porceddu, Andrea; Albertini, Emidio; Barcaccia, Gianni; Marconi, G.; Bertoli, F. B.; Veronesi, F.

doi:10.1007/s00438-002-0643-z

Cited by 71 publications

(41 citation statements)

References 28 publications

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“…In the SSAP procedure, it is important to maximize the sequence complexity of the template for the specifi c primer amplifi cation, so a single enzyme digestion is used [ 25 ]. As with the method described for BARE1 [ 18 ], the adapter primer is selective.…”

Section: Introductionmentioning

confidence: 99%

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Kalendar

Schulman

2013

Methods in Molecular Biology

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Retrotransposons are a major component of virtually all eukaryotic genomes, which makes them useful as molecular markers. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplifi cation between the retrotransposon termini and some component of fl anking genomic DNA. The main methods of IRAP, REMAP, RBIP, and SSAP all detect the polymorphic sites at which the retrotransposon DNA is integrated into the genome. Marker systems exploiting these methods can be easily developed and are inexpensively deployed in the absence of extensive genome sequence data. Here, we describe protocols for the IRAP, REMAP, and iPBS techniques, including methods for PCR amplifi cation with a single primer or with two primers, and agarose gel electrophoresis of the product using optimal electrophoresis buffers; we also describe iPBS techniques for the rapid isolation of retrotransposon termini and full-length elements.

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Section: Introductionmentioning

confidence: 99%

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Kalendar

Schulman

2013

Methods in Molecular Biology

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“…A variety of PCR-based systems have been developed to detect insertional polymorphism of retrotransposons in plants (Waugh et al 1997;Ellis et al 1998;Flavell et al 1998;Kalendar et al 1999;Provan et al 1999;Yu and Wise 2000;Porceddu et al 2002). Most of these are multiplex approaches, which display the regions flanking individual retrotransposon insertions as bands on gels.…”

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confidence: 99%

Insertional Polymorphism and Antiquity ofPDR1Retrotransposon Insertions in Pisum Species

et al. 2005

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Sequences flanking 73 insertions of the retrotransposon PDR1 have been characterized, together with an additional 270 flanking regions from one side alone, from a diverse collection of Pisum germ plasm. Most of the identified flanking sequences are repetitious DNAs but more than expected (7%) lie within nuclear gene protein-coding regions. The approximate age of 52 of the PDR1 insertions has been determined by measuring sequence divergence among LTR pairs. These data show that PDR1 transpositions occurred within the last 5 MY, with a peak at 1-2.5 MYA. The insertional polymorphism of 68 insertions has been assessed across 47 selected Pisum accessions, representing the diversity of the genus. None of the insertions are fixed, showing that PDR1 insertions can persist in a polymorphic state for millions of years in Pisum. The insertional polymorphism data have been compared with the age estimations to ask what rules control the proliferation of PDR1 insertions in Pisum. Relatively recent insertions (, 1.5MYA) tend to be found in small subsets of the Pisum accessions set, ''middle-aged'' insertions (between 1.5 and 2.5 MYA) vary greatly in their occurrence, and older insertions (. 2.5 MYA) are mostly found in small subsets of Pisum. Finally, the average age estimate for PDR1 insertions, together with an existing data set for PDR1 retrotransposon SSAP markers, has been used to derive an estimate of the effective population size for Pisum of 7.5 3 10 5 .

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“…The inclusion of SSAP markers in our map further provides efficient, stable and extensive coverage of the lettuce genome, because inserted copies of retrotransposons do not excise from their sites, unlike DNA transposons ). The usefulness of SSAP for studying genetic diversity, mapping populations and species relationships has been reported for barley (Waugh et al 1997;Leigh et al 2003;Schulman et al 2004), pea Pearce et al 2000), wheat (Gribbon et al 1999;Queen et al 2004), oat (Yu and Wise 2000) and alfalfa (Porceddu et al 2002). This property of genomic stability will give the map shown here an added value.…”

Section: Discussionmentioning

confidence: 79%

“…SSAP has been applied to barley, pea, wheat and alfalfa. In these studies SSAP markers revealed twofold to threefold higher polymorphism rates per primer combination than AFLP markers (Waugh et al 1997;Ellis et al 1998;Flavell et al 1998;Gribbon et al 1999;Porceddu et al 2002;Queen et al 2004). The transposon display approach, which uses another transposon type called miniature inverted repeat transposable elements (MITEs) is virtually identical to SSAP and has been deployed in Maize (Casa et al 2000).…”

Section: Introductionmentioning

confidence: 95%

A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

et al. 2005

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Molecular markers based upon a novel lettuce LTR retrotransposon and the nucleotide binding site-leucine-rich repeat (NBS-LRR) family of disease resistance-associated genes have been combined with AFLP markers to generate a 458 locus genetic linkage map for lettuce. A total of 187 retrotransposon-specific SSAP markers, 29 NBS-LRR markers and 242 AFLP markers were mapped in an F 2 population, derived from an interspecific cross between a Lactuca sativa cultivar commonly used in Europe and a wild

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Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L.

Cited by 71 publications

References 28 publications

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Transposon-Based Tagging: IRAP, REMAP, and iPBS

Insertional Polymorphism and Antiquity ofPDR1Retrotransposon Insertions in Pisum Species

A detailed linkage map of lettuce based on SSAP, AFLP and NBS markers

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