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

Porceddu, Andrea and Albertini, Emidio and Barcaccia, Gianni and Marconi, Gianpiero and Bertoli, F. B. and Veronesi, Fabio (2002) Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Molecular Genetics and Genomics, Vol. 267 (1), p. 107-114. eISSN 1617-4623. Article.

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DOI: 10.1007/s00438-002-0643-z

Abstract

The Sequence-Specific Amplification Polymorphism (S-SAP) method, recently derived from the Amplified Fragment Length Polymorphism (AFLP) technique, produces amplified fragments containing a retrotransposon LTR sequence at one end and a host restriction site at the other. We report the application of this procedure to the LTR of the Tms1 element from Medicago sativa L. Genomic dot-blot analysis indicated that Tms1 LTRs represent about 0.056% of the M. sativa genome, corresponding to 16x103 copies per haploid genome. An average of 66 markers were amplified for each primer combination. Overall 49 polymorphic fragments were reliably scored and mapped in a F1 population obtained by crossing diploid M. falcata with M. coerulea. The utility of the LTR S-SAP markers was higher than that of AFLP or SAMPL (Selective Amplification of Microsatellite Polymorphic Loci) markers. The efficiency index of the LTR S-SAP assay was 28.3, whereas the corresponding values for AFLP and SAMPL markers were 21.1 and 16.7, respectively. The marker index for S-SAP was 13.1, compared to 8.8 for AFLP and 9.5 for SAMPL. Application of the Tms1 LTR-based S-SAP to double-stranded cDNA resulted in a complex banding pattern, demonstrating the presence of Tms1 LTRs within exons. As the technique was successfully applied to other species of the genus Medicago, it should prove suitable for studying genetic diversity within, and relatedness between, alfalfa species.

Item Type:Article
ID Code:3991
Status:Published
Refereed:Yes
Uncontrolled Keywords:Medicago, Long Terminal Repeat (LTR), retrotransposons, Sequence-Specific Amplification Polymorphism (S-SAP)
Subjects:Area 07 - Scienze agrarie e veterinarie > AGR/07 Genetica agraria
Divisions:001 Università di Sassari > 01 Dipartimenti > Scienze agronomiche e genetica vegetale agraria
Publisher:Springer Berlin / Heidelberg
eISSN:1617-4623
Deposited On:28 May 2010 19:18

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