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

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...

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Bibliographic Details
Published in:Molecular genetics and genomics : MGG 2002-03, Vol.267 (1), p.107-114
Main Authors: Porceddu, A, Albertini, E, Barcaccia, G, Marconi, G, Bertoli, F B, Veronesi, F
Format: Article
Language:English
Subjects:
DNA, Complementary
Exons
Genes
Genetic Markers
Genomes
Genomics
Medicago coerulea
Medicago falcata
Medicago sativa
Medicago sativa - genetics
Polymorphism
Polymorphism, Genetic
Repetitive Sequences, Nucleic Acid
transposon Yms1
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Summary: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 16 x 10(3) 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 F(1) 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.
ISSN:1617-4615
1617-4623
DOI:10.1007/s00438-002-0643-z