ArticlePloS one2007
Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed, 228 citations in OpenAlex.
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- A New Assessment of Robust Capuchin Monkey (Genes · 2023Article
- Genetic resources and breeding of maize forFrontiers in plant science · 2023Review
- Genetic approaches to exploit landraces for improvement ofFrontiers in plant science · 2023Review
- Strategies for sample labelling and library preparation in DNA metabarcoding studies.Molecular ecology resources · 2022Review
- The First Genetic Map for a Psoraleoid Legume (Plants (Basel, Switzerland) · 2020Article
- Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.G3 (Bethesda, Md.) · 2020Article
- Legume genomics and transcriptomics: From classic breeding to modern technologies.Saudi journal of biological sciences · 2020Review
- Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize.Annals of botany · 2019Article
- Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.).BMC plant biology · 2018Article
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- tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci.Nucleic acids research · 2017Article
- Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application.Plant biotechnology journal · 2017Review
- A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis.Scientific reports · 2017Article
- Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data.BMC bioinformatics · 2017Article
- The First Genetic Map in Sweet Osmanthus (Frontiers in plant science · 2017Article
- Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.
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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.