RFLPs were used to generate the first high-density linkage maps in tomato (Bernatzky and Tanksley 1986; Tanksley etal. 1992) (see Sect. 1.5) but are not amenable to high-throughput and automated genotyping analyses. AFLP markers alleviated the throughput limitations of RFLPs, but are largely anonymous, population-specific, and dominant
(Haanstra etal. 1999). Sequence-dependent PCR based markers are preferred over RFLP and AFLP, and are now exploited in many plant species. These markers display important characteristics including codominance of alleles and robustness of the assay, features that are particularly attractive for high throughput MAS as well as high-resolution fine-mapping. SSRs, insertion and deletion polymorphisms (indels), and nucleotide substitutions provide the basis for sequence-dependent PCR-based markers. SSRs consist of two, three or four base-pair units that are repeated in a sequence of interest. A polymorphism arises when a difference in the number of repeats is found between alleles. Insertion or deletions that are not SSR are designated indel. Single base changes or single base indels define the single nucleotide polymorphisms (SNPs) class. These are valuable DNA markers because of their high frequency, widespread distribution in the genome, and their suitability for high-throughput, automated genotyping (Shi 2001). Furthermore, SNPs located in coding and regulatory regions may be the direct cause of phenotypic variation. Therefore, SNP markers are very promising in association mapping studies which aim to link phenotype to genotype without the development of structured mapping populations.
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