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Genetic markers based on single nucleotide  polymorphisms (SNPs) are in increasing demand for genome mapping and  fingerprinting of breeding populations in crop plants. Recent advances in  high-throughput sequencing provide the opportunity for whole-genome  resequencing and identification of allelic variants by mapping the reads to a  reference genome. However, for many species, such as pepper (Capsicum annuum),  a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing  and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of  10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv.  "Criollo de Morelos 334" to the "Yolo Wonder" transcriptome allowed for SNP  identification. By setting a threshold value that allows selecting reliable  SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919  isotigs were identified. In addition, 853 single sequence repeats were  obtained. This information has been made available online.

Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)