Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

Jeremy D. Edwards, Jaroslav Janda, Megan T. Sweeney, Ambika B. Gaikwad, Bin Liu, Hei Leung, David W Galbraith

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Background. We 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. Results. We 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. Conclusion. We 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.

Original languageEnglish (US)
Article number13
JournalPlant Methods
Volume4
Issue number1
DOIs
StatePublished - 2008

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oligonucleotides
Oligonucleotide Array Sequence Analysis
genotyping
Costs and Cost Analysis
rice
blast disease
chromosome mapping
cultivars
Magnaporthe
genetic polymorphism
Genome
genomics
Magnaporthe grisea
genome
Chromosome Mapping
inbred lines
hybridization
Oryza
Phenotype
phenotype

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Plant Science

Cite this

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. / Edwards, Jeremy D.; Janda, Jaroslav; Sweeney, Megan T.; Gaikwad, Ambika B.; Liu, Bin; Leung, Hei; Galbraith, David W.

In: Plant Methods, Vol. 4, No. 1, 13, 2008.

Research output: Contribution to journalArticle

Edwards, Jeremy D. ; Janda, Jaroslav ; Sweeney, Megan T. ; Gaikwad, Ambika B. ; Liu, Bin ; Leung, Hei ; Galbraith, David W. / Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice. In: Plant Methods. 2008 ; Vol. 4, No. 1.
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