Sequence-indexed mutations in maize using the UniformMu transposon-tagging population

Persistent Link:
http://hdl.handle.net/10150/610402
Title:
Sequence-indexed mutations in maize using the UniformMu transposon-tagging population
Author:
Settles, A. M.; Holding, David; Tan, Bao; Latshaw, Susan; Liu, Juan; Suzuki, Masaharu; Li, Li; O'Brien, Brent; Fajardo, Diego; Wroclawska, Ewa; Tseung, Chi-Wah; Lai, Jinsheng; Hunter, Charles; Avigne, Wayne; Baier, John; Messing, Joachim; Hannah, L. C.; Koch, Karen; Becraft, Philip; Larkins, Brian; McCarty, Donald
Affiliation:
Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA; Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
Issue Date:
2007
Publisher:
BioMed Central
Citation:
BMC Genomics 2007, 8:116 doi:10.1186/1471-2164-8-116
Journal:
BMC Genomics
Rights:
© 2007 Settles 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:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations.RESULTS:Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill.CONCLUSION:We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-8-116
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/8/116

Full metadata record

DC FieldValue Language
dc.contributor.authorSettles, A. M.en
dc.contributor.authorHolding, Daviden
dc.contributor.authorTan, Baoen
dc.contributor.authorLatshaw, Susanen
dc.contributor.authorLiu, Juanen
dc.contributor.authorSuzuki, Masaharuen
dc.contributor.authorLi, Lien
dc.contributor.authorO'Brien, Brenten
dc.contributor.authorFajardo, Diegoen
dc.contributor.authorWroclawska, Ewaen
dc.contributor.authorTseung, Chi-Wahen
dc.contributor.authorLai, Jinshengen
dc.contributor.authorHunter, Charlesen
dc.contributor.authorAvigne, Wayneen
dc.contributor.authorBaier, Johnen
dc.contributor.authorMessing, Joachimen
dc.contributor.authorHannah, L. C.en
dc.contributor.authorKoch, Karenen
dc.contributor.authorBecraft, Philipen
dc.contributor.authorLarkins, Brianen
dc.contributor.authorMcCarty, Donalden
dc.date.accessioned2016-05-20T09:06:02Z-
dc.date.available2016-05-20T09:06:02Z-
dc.date.issued2007en
dc.identifier.citationBMC Genomics 2007, 8:116 doi:10.1186/1471-2164-8-116en
dc.identifier.doi10.1186/1471-2164-8-116en
dc.identifier.urihttp://hdl.handle.net/10150/610402-
dc.description.abstractBACKGROUND:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations.RESULTS:Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill.CONCLUSION:We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/8/116en
dc.rights© 2007 Settles 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.titleSequence-indexed mutations in maize using the UniformMu transposon-tagging populationen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentHorticultural Sciences Department, University of Florida, Gainesville, FL 32611, USAen
dc.contributor.departmentDepartment of Plant Sciences, University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentDepartment of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USAen
dc.contributor.departmentWaksman Institute, Rutgers University, Piscataway, NJ 08854, USAen
dc.identifier.journalBMC Genomicsen
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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