Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 391012
Title A pipeline for high throughput detection and mapping of SNPs from EST databases
Author(s) Anithakumari, A.M.; Tang, Jifeng; Eck, H.J. van; Visser, R.G.F.; Leunissen, J.A.M.; Vosman, B.; Linden, C.G. van der
Source Molecular Breeding 26 (2010)1. - ISSN 1380-3743 - p. 65 - 75.
DOI https://doi.org/10.1007/s11032-009-9377-5
Department(s) Plant Breeding
Bioinformatics
PRI Biodiversity and Breeding
EPS-3
Publication type Refereed Article in a scientific journal
Publication year 2010
Keyword(s) single-nucleotide polymorphisms - map-based cloning - linkage maps - genome - markers - potato - discovery - construction - varieties - haplotype
Abstract Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation. Electronic supplementary material The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users
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