Molecular characterization of the SCAR markers tightly linked to the Tm-2 locus of the genus Lycopersicon

Abstract 

The Tm-2 gene and its alleles conferring tomato mosaic virus resistance in tomato originate from Lycopersicon peruvianum, a wild relative of tomato. DNA fragments of several RAPD markers tightly linked with the Tm-2 locus in tomato were successfully cloned and sequenced. Subsequently, the 24-mer oligonucleotide primer pairs of the SCAR markers corresponding to the RAPD markers were designed based on the 5’-endmost sequences. A fragment of the same size as that of a SCAR marker was amplified in the ToMV-susceptible tomato line with no Tm-2, but the digests of the PCR fragments by AccI exhibited polymorphism in fragment length between the two lines. We chose three SCAR markers and three RAPD markers tightly linked with the Tm-2 locus, and examined whether the same-sized fragments corresponding to these markers were also present in three other lines carrying Tm-2a or one of the other Tm-2 alleles. The fragments corresponding to the three SCAR markers were present in all of the three lines, but the other markers (three RAPDs ) were absent in one or two lines, suggesting that the three SCAR markers are closer to Tm-2 than the other markers. Comparison of the nucleotide sequences of these fragments revealed that they are all homologous to the corresponding SCAR markers.