Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

Handle URI:
http://hdl.handle.net/10754/334634
Title:
Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
Authors:
Belfield, E.J.; Gan, X.; Mithani, A.; Brown, C.; Jiang, C.; Franklin, K.; Alvey, E.; Wibowo, A.; Jung, M.; Bailey, K.; Kalwani, S.; Ragoussis, J.; Mott, R.; Harberd, N.P.
Abstract:
Ionizing radiation has long been known to induce heritable mutagenic change in DNA sequence. However, the genome-wide effect of radiation is not well understood. Here we report the molecular properties and frequency of mutations in phenotypically selected mutant lines isolated following exposure of the genetic model flowering plant Arabidopsis thaliana to fast neutrons (FNs). Previous studies suggested that FNs predominantly induce deletions longer than a kilobase in A. thaliana. However, we found a higher frequency of single base substitution than deletion mutations. While the overall frequency and molecular spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of "background" mutations arising spontaneously in laboratory-grown plants, G:C>A:T transitions were favored in both. We found that FN-induced G:C>A:T transitions were concentrated at pyrimidine dinucleotide sites, suggesting that FNs promote the formation of mutational covalent linkages between adjacent pyrimidine residues. In addition, we found that FNs induced more single base than large deletions, and that these single base deletions were possibly caused by replication slippage. Our observations provide an initial picture of the genome-wide molecular profile of mutations induced in A. thaliana by FN irradiation and are particularly informative of the nature and extent of genome-wide mutation in lines selected on the basis of mutant phenotypes from FN-mutagenized A. thaliana populations.
KAUST Department:
Plant Stress Genomics Research Lab; Information Technology Department
Citation:
Belfield EJ, Gan X, Mithani A, Brown C, Jiang C, et al. (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Research 22: 1306-1315. doi:10.1101/gr.131474.111.
Publisher:
Cold Spring Harbor Laboratory Press
Journal:
Genome Research
Issue Date:
12-Apr-2012
DOI:
10.1101/gr.131474.111
PubMed ID:
22499668
PubMed Central ID:
PMC3396371
Type:
Article
ISSN:
10889051
Appears in Collections:
Articles; Information Technology Department

Full metadata record

DC FieldValue Language
dc.contributor.authorBelfield, E.J.en
dc.contributor.authorGan, X.en
dc.contributor.authorMithani, A.en
dc.contributor.authorBrown, C.en
dc.contributor.authorJiang, C.en
dc.contributor.authorFranklin, K.en
dc.contributor.authorAlvey, E.en
dc.contributor.authorWibowo, A.en
dc.contributor.authorJung, M.en
dc.contributor.authorBailey, K.en
dc.contributor.authorKalwani, S.en
dc.contributor.authorRagoussis, J.en
dc.contributor.authorMott, R.en
dc.contributor.authorHarberd, N.P.en
dc.date.accessioned2014-11-11T14:32:58Z-
dc.date.available2014-11-11T14:32:58Z-
dc.date.issued2012-4-12en
dc.identifier.citationBelfield EJ, Gan X, Mithani A, Brown C, Jiang C, et al. (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Research 22: 1306-1315. doi:10.1101/gr.131474.111.en
dc.identifier.issn10889051en
dc.identifier.pmid22499668en
dc.identifier.doi10.1101/gr.131474.111en
dc.identifier.urihttp://hdl.handle.net/10754/334634en
dc.description.abstractIonizing radiation has long been known to induce heritable mutagenic change in DNA sequence. However, the genome-wide effect of radiation is not well understood. Here we report the molecular properties and frequency of mutations in phenotypically selected mutant lines isolated following exposure of the genetic model flowering plant Arabidopsis thaliana to fast neutrons (FNs). Previous studies suggested that FNs predominantly induce deletions longer than a kilobase in A. thaliana. However, we found a higher frequency of single base substitution than deletion mutations. While the overall frequency and molecular spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of "background" mutations arising spontaneously in laboratory-grown plants, G:C>A:T transitions were favored in both. We found that FN-induced G:C>A:T transitions were concentrated at pyrimidine dinucleotide sites, suggesting that FNs promote the formation of mutational covalent linkages between adjacent pyrimidine residues. In addition, we found that FNs induced more single base than large deletions, and that these single base deletions were possibly caused by replication slippage. Our observations provide an initial picture of the genome-wide molecular profile of mutations induced in A. thaliana by FN irradiation and are particularly informative of the nature and extent of genome-wide mutation in lines selected on the basis of mutant phenotypes from FN-mutagenized A. thaliana populations.en
dc.language.isoenen
dc.publisherCold Spring Harbor Laboratory Pressen
dc.rightsThis article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.en
dc.rightsArchived with thanks to Genome Researchen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/en
dc.subjectpyrimidineen
dc.subjectArabidopsisen
dc.subjectfast neutron therapyen
dc.subjectgene deletionen
dc.subjectgene frequencyen
dc.subjectgenetic associationen
dc.subjectgenetic modelen
dc.subjectindel mutationen
dc.subjectphenotypeen
dc.subjectplant genomeen
dc.subjectradiation mutagenesisen
dc.subjectChromosome Aberrationsen
dc.subjectChromosomes, Planten
dc.subjectDNA Mutational Analysisen
dc.subjectDNA Replicationen
dc.subjectDNA, Planten
dc.subjectFast Neutronsen
dc.subjectGenome, Planten
dc.subjectINDEL Mutationen
dc.subjectPhenotypeen
dc.subjectPoint Mutationen
dc.subjectPyrimidine Nucleotidesen
dc.subjectSequence Deletionen
dc.subjectArabidopsis thalianaen
dc.subjectMagnoliophytaen
dc.titleGenome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thalianaen
dc.typeArticleen
dc.contributor.departmentPlant Stress Genomics Research Laben
dc.contributor.departmentInformation Technology Departmenten
dc.identifier.journalGenome Researchen
dc.identifier.pmcidPMC3396371en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdomen
dc.contributor.institutionWellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdomen
dc.contributor.institutionSchool of Biological Sciences, University of Bristol, Bristol BS8 1UG, United Kingdomen
dc.contributor.institutionDepartment of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdomen
dc.contributor.institutionOxford e-Research Centre, University of Oxford, Oxford OX1 3QG, United Kingdomen
dc.contributor.institutionDepartment of Biology, LUMS School of Science and Engineering, Sector U-DHA, Lahore 54792, Pakistanen
dc.contributor.institutionDepartment of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdomen
dc.contributor.institution1142 Terra Ct., Rochester, MI 48306, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorWibowo, Anjar Trien
kaust.authorKalwani, Sharanen

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