Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)
| Autor: | Nicolai, Maryse, Pisani, Cédric, Bouchet, Jean-Paul, Vuylsteke, M. |
|---|---|
| Přispěvatelé: | Palloix, Alain |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Vegetal Biology
marqueur génétique empreinte digitale food and beverages polymorphisme snp légume variation allélique pyroséquençage capsicum annuum Agricultural sciences plante cultivée séquençage du génome cartographie du génome séquençage à haut débit reproduction végétale marqueur ssr High-throughput sequencing Transcriptome Single-nucleotide polymorphism Single-sequence repeats pepper transcriptome Sciences agricoles Biologie végétale séquençage de gènes |
| Zdroj: | Genetics and Molecular Research 3 (11), 2295-2300. (2012) |
| Popis: | 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 Morclos 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. |
| Databáze: | OpenAIRE |
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