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

Persistent Link:
http://hdl.handle.net/10150/610235
Title:
Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice
Author:
Edwards, Jeremy; Janda, Jaroslav; Sweeney, Megan; Gaikwad, Ambika; Liu, Bin; Leung, Hei; Galbraith, David
Affiliation:
University of Florida, Gulf Coast Research & Education Center, Wimauma FL, 33598, USA; University of Arizona, Department of Plant Sciences and Bio5 Institute for Collaborative Bioresearch, Tucson AZ, 85721, USA; National Research Centre on DNA Fingerprinting, National Bureau of Plant Genetic Resources, New Delhi, India; Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, Pr China; International Rice Research Institute (IRRI), Los Banos, The Philippines
Issue Date:
2008
Publisher:
BioMed Central
Citation:
This article is available from: http://www.plantmethods.com/content/4/1/13
Journal:
Plant Methods
Rights:
© 2008 Edwards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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.
EISSN:
1746-4811
DOI:
10.1186/1746-4811-4-13
Version:
Final published version
Additional Links:
http://www.plantmethods.com/content/4/1/13

Full metadata record

DC FieldValue Language
dc.contributor.authorEdwards, Jeremyen
dc.contributor.authorJanda, Jaroslaven
dc.contributor.authorSweeney, Meganen
dc.contributor.authorGaikwad, Ambikaen
dc.contributor.authorLiu, Binen
dc.contributor.authorLeung, Heien
dc.contributor.authorGalbraith, Daviden
dc.date.accessioned2016-05-20T09:01:49Z-
dc.date.available2016-05-20T09:01:49Z-
dc.date.issued2008en
dc.identifier.citationThis article is available from: http://www.plantmethods.com/content/4/1/13en
dc.identifier.doi10.1186/1746-4811-4-13en
dc.identifier.urihttp://hdl.handle.net/10150/610235-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.plantmethods.com/content/4/1/13en
dc.rights© 2008 Edwards et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleDevelopment and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in riceen
dc.typeArticleen
dc.identifier.eissn1746-4811en
dc.contributor.departmentUniversity of Florida, Gulf Coast Research & Education Center, Wimauma FL, 33598, USAen
dc.contributor.departmentUniversity of Arizona, Department of Plant Sciences and Bio5 Institute for Collaborative Bioresearch, Tucson AZ, 85721, USAen
dc.contributor.departmentNational Research Centre on DNA Fingerprinting, National Bureau of Plant Genetic Resources, New Delhi, Indiaen
dc.contributor.departmentGuangdong Academy of Agricultural Sciences (GDAAS), Guangdong, Pr Chinaen
dc.contributor.departmentInternational Rice Research Institute (IRRI), Los Banos, The Philippinesen
dc.identifier.journalPlant Methodsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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