ArticleGenome research2009
High-throughput genotyping by whole-genome resequencing.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 433 papers.
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Who cites it
433 citing papers in PubMed, 959 citations in OpenAlex.
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- Skim-sequencing for genomic selection in wheat: a comparison of marker platforms.The plant genome · 2026Article
- Genome-Assisted Breeding of an Elite Sterile Line From Restorer Line for Hybrid Rice.Plant biotechnology journal · 2026Article
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- Genomic Variation and GWAS Analysis for Salt Tolerance Discovered in Egyptian Rice Germplasm.Plants (Basel, Switzerland) · 2026Article
- Identification of major loci governing 13 agronomic traits and the fine-mapping of CaSUN29 regulating fruit length in pepper.Molecular horticulture · 2025Article
- Genetic Mapping and Transcriptomic Analysis of Sepal-Derived Seed Shape in Spinach.International journal of molecular sciences · 2025Article
- Analysis of genetic differences underlying chilling stress tolerance using whole genome Re-Sequencing in walnut (Juglans regia L.).BMC genomics · 2025Article
- Combining QTL mapping and RNA-Seq reveals candidate genes controlling flag leaf width in foxtail millet.BMC plant biology · 2025Article
- Integrative linkage mapping, GWAS, and RNA-Seq analysis unravel the genetic architecture and candidate genes for drought tolerance inHorticulture research · 2025Article
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
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- Regulation of heterosis-associated gene expression complementation in maize hybrids.Genome biology · 2025Article
- Resequencing and phenotyping of the first highly inbred eggplant multiparent population revealHorticulture research · 2025Article
- Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.BMC plant biology · 2025Article
373 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
13 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
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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.