Development of SCAR and CAPS markers linked to the Beta gene in tomato

Two previously identified random amplified polymorphic DNA (RAPD) markers, OPAR18(1100) and UBC792(830), linked to the Beta (B) locus in tomato (Lycopersicon esculentum Mill.) were cloned and sequenced. Their end sequences were used to design allele specific sequence characterized amplified region (SCAR) primer pairs, SCAR18Df/r and SCBC792f/r. Each of these primer pairs amplified a single product of the same size as their respective progenitor RAPID markers, but did not differentiate the two parental genotypes under a variety of polymerase chain reaction (PCR) conditions. Sequence analysis of cloned RAPD and SCAR products revealed an RsaI site mutation in the allele of the high beta-carotene parent in the SCAR18f/r amplified DNA product which was used to develop the codominant SCAR18(1067), cleaved amplified polymorphic sequence (CAPS) marker. Similarly, a Hinf1 site mutation in the allele of the high beta-carotene parent in SCBC792f/r amplified DNA product was used to develop the codominant SCBC792(779) CAPS marker. Sequences from SCBC792f/r amplified DNA products revealed additional single nucleotide polymorphisms between the two parental genotypes. Three such polymorphisms were used to design the nested primer SCBC792f1 located 97 bp internal to the SCBC792f sequence. The SCBC792f1/r primer pair amplified the dominant SCB792(682) SCAR marker present only in the high beta-carotene parent. Linkage of the CAPS and SCAR markers to B was confirmed by means of a population of 144 F-2 individuals segregating for B. Using introgression line analysis, we mapped the two CAPS and the SCAR markers to the long arm of chromosome 6, consistent with the location of B on the classical linkage map of tomato.