**4.4. GeneChip (Affymetrix, USA)**

The GeneChip assays are based on allelic discrimination by the direct hybridization of genomic DNA to arrays containing locus- and allele-specific oligonucleotides (25 mers). Genomic DNA is digested with a restriction endonuclease and ligated to adaptors, which are then amplified by PCR using a single universal primer thereby creating a reduced representation of the genome [168]. These PCR amplicons are fragmented, end-labeled, and hybridized. The fluorescence signal is recorded by the GeneChip 3000 scanner (Affymetrix). The hybridization scanning is evaluated as positive and negative signals. Hill et al. [42] developed a GeneChip® array for analysis of polymorphism and expression in Capsicum. The array was designed from 30,815 unigenes, and hybridization was performed using genomic DNA of 40 diverse lines of *C. annum*. They detected 33,401 single-position polymorphisms within 13,323 unigenes. A total of 251 highly informative markers across these *C. annuum* lines were found. Also, a region of 8.7 cM was detected around Pun1 locus in nonpungent line that showed no polymorphism.

In tomato, an oligonucleotide array was developed with 22,821 probe sets, which correspond to 22,714 unigenes [169]. Genomic DNA isolated from three *S. lycopersicum* varieties, i.e., FL7600 (fresh-market), OH9242 (processing), and PI114490 (var. cerasiformae), were used to hybridize with that array. They identified 189 putative single feature polymorphisms, and a subset of these was utilized for validation which resulted in the identification of 279 SNPs and 27 InDels in 111 loci. Moreover, a subset of validated SNPs was used for analysis of genetic diversity in 92 tomato varieties and accessions.
