ArticleMolecular breeding : new strategies in plant improvement2010
A pipeline for high throughput detection and mapping of SNPs from EST databases.
Article in Molecular breeding : new strategies in plant improvement, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- Article
- Genetical genomics of quality related traits in potato tubers using proteomics.BMC plant biology · 2018Article
- QTL mapping in diploid potato by using selfed progenies of the crossEuphytica: Netherlands journal of plant breeding · 2018Article
- A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
- Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies.PloS one · 2016Article
- Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.BMC genomics · 2015Article
- High quality SNPs/Indels mining and characterization in ginger from ESTs data base.Bioinformation · 2015Article
- A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.Functional & integrative genomics · 2014Article
- Comprehensive analysis of expressed sequence tags from cultivated and wild radish (Raphanus spp.).BMC genomics · 2013Article
- Novel applications of motif-directed profiling to identify disease resistance genes in plants.Plant methods · 2013Article
- QualitySNPng: a user-friendly SNP detection and visualization tool.Nucleic acids research · 2013Article
- Tomato breeding in the genomics era: insights from a SNP array.BMC genomics · 2013Article
- A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato.PloS one · 2013Article
- Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data.BMC genomics · 2012Article
- Genetic dissection of drought tolerance and recovery potential by quantitative trait locus mapping of a diploid potato population.Molecular breeding : new strategies in plant improvement · 2012Article
- An EST-derived SNP and SSR genetic linkage map of cassava (Manihot esculenta Crantz).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- A transcriptome map of perennial ryegrass (Lolium perenne L.).BMC genomics · 2012Article
- Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.