Nicolaï M, Pisani C, Bouchet J-P, Vuylsteke M, Palloix A
INRA, PACA, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, Montfavet Cedex, France.
Genet Mol Res. 2012 Aug 13;11(3):2295-300. doi: 10.4238/2012.August.13.3.
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.
基于单核苷酸多态性（SNP）的遗传标记在作物育种群体的基因组作图和指纹识别中的需求日益增加。高通量测序的最新进展为全基因组重测序以及通过将 reads 比对到参考基因组来鉴定等位基因变异提供了机会。然而，对于许多物种，如辣椒（Capsicum annuum），尚未有参考基因组序列。为此，我们使用罗氏 454 焦磷酸测序技术对辣椒品种“Yolo Wonder”的转录组进行了测序，并从头组装了 23,748 个 isotig 和 60,370 个单拷贝序列。通过将辣椒品种“Criollo de Morelos 334”的 Illumina GA II 测序获得的 10,886,425 条 reads 比对到“Yolo Wonder”转录组实现了 SNP 鉴定。通过设定一个阈值，允许在信息损失最小的情况下选择可靠的 SNP，共鉴定出分布在 5919 个 isotig 上的 11,849 个可靠 SNP。此外，还获得了 853 个单序列重复。这些信息已在网上公布。
