ArticlePlant methods2008
Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice.
Article in Plant methods, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 40 citations in OpenAlex.
- Inferring the evolutionary mechanism of the chloroplast genome size by comparing whole-chloroplast genome sequences in seed plants.Scientific reports · 2017Article
- Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome.BMC plant biology · 2015Article
- A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.International journal of molecular sciences · 2013Review
- An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.G3 (Bethesda, Md.) · 2013Article
- Dissecting quantitative resistance against blast disease using heterogeneous inbred family lines in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Mutagenesis as a tool in plant genetics, functional genomics, and breeding.International journal of plant genomics · 2011Article
- High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.PloS one · 2010Article
- High-throughput marker discovery in melon using a self-designed oligo microarray.BMC genomics · 2010Article
- High-throughput genotyping by whole-genome resequencing.Genome research · 2009Article
- Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array.BMC plant biology · 2009Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.
resultsWe have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP) elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype.
conclusionWe anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.
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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.