• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Jun 2003; 164(2): 731–740.
PMCID: PMC1462604

Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis.

Abstract

Chemical mutagenesis has been the workhorse of traditional genetics, but it has not been possible to determine underlying rates or distributions of mutations from phenotypic screens. However, reverse-genetic screens can be used to provide an unbiased ascertainment of mutation statistics. Here we report a comprehensive analysis of approximately 1900 ethyl methanesulfonate (EMS)-induced mutations in 192 Arabidopsis thaliana target genes from a large-scale TILLING reverse-genetic project, about two orders of magnitude larger than previous such efforts. From this large data set, we are able to draw strong inferences about the occurrence and randomness of chemically induced mutations. We provide evidence that we have detected the large majority of mutations in the regions screened and confirm the robustness of the high-throughput TILLING method; therefore, any deviations from randomness can be attributed to selectional or mutational biases. Overall, we detect twice as many heterozygotes as homozygotes, as expected; however, for mutations that are predicted to truncate an encoded protein, we detect a ratio of 3.6:1, indicating selection against homozygous deleterious mutations. As expected for alkylation of guanine by EMS, >99% of mutations are G/C-to-A/T transitions. A nearest-neighbor bias around the mutated base pair suggests that mismatch repair counteracts alkylation damage.

Full Text

The Full Text of this article is available as a PDF (158K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bentley A, MacLennan B, Calvo J, Dearolf CR. Targeted recovery of mutations in Drosophila. Genetics. 2000 Nov;156(3):1169–1173. [PMC free article] [PubMed]
  • Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S. High-throughput screening for induced point mutations. Plant Physiol. 2001 Jun;126(2):480–484. [PMC free article] [PubMed]
  • Culligan KM, Hays JB. Arabidopsis MutS homologs-AtMSH2, AtMSH3, AtMSH6, and a novel AtMSH7-form three distinct protein heterodimers with different specificities for mismatched DNA. Plant Cell. 2000 Jun;12(6):991–1002. [PMC free article] [PubMed]
  • Nickerson DA, Kolker N, Taylor SL, Rieder MJ. Sequence-based detection of single nucleotide polymorphisms. Methods Mol Biol. 2001;175:29–35. [PubMed]
  • Dany AL, Tissier A. A functional OGG1 homologue from Arabidopsis thaliana. Mol Genet Genomics. 2001 Apr;265(2):293–301. [PubMed]
  • García-Ortiz MV, Ariza RR, Roldán-Arjona T. An OGG1 orthologue encoding a functional 8-oxoguanine DNA glycosylase/lyase in Arabidopsis thaliana. Plant Mol Biol. 2001 Dec;47(6):795–804. [PubMed]
  • Oleykowski CA, Bronson Mullins CR, Godwin AK, Yeung AT. Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 1998 Oct 15;26(20):4597–4602. [PMC free article] [PubMed]
  • Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000;132:365–386. [PubMed]
  • Shi H, Ishitani M, Kim C, Zhu JK. The Arabidopsis thaliana salt tolerance gene SOS1 encodes a putative Na+/H+ antiporter. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6896–6901. [PMC free article] [PubMed]
  • Henikoff Steven, Comai Luca. Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol. 2003;54:375–401. [PubMed]
  • Spiegelman JI, Mindrinos MN, Oefner PJ. High-accuracy DNA sequence variation screening by DHPLC. Biotechniques. 2000 Nov;29(5):1084–1092. [PubMed]
  • Jander Georg, Baerson Scott R, Hudak Jebecka A, Gonzalez Kathleen A, Gruys Kenneth J, Last Robert L. Ethylmethanesulfonate saturation mutagenesis in Arabidopsis to determine frequency of herbicide resistance. Plant Physiol. 2003 Jan;131(1):139–146. [PMC free article] [PubMed]
  • Till Bradley J, Reynolds Steven H, Greene Elizabeth A, Codomo Christine A, Enns Linda C, Johnson Jessica E, Burtner Chris, Odden Anthony R, Young Kim, Taylor Nicholas E, et al. Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 2003 Mar;13(3):524–530. [PMC free article] [PubMed]
  • Kovalchuk I, Kovalchuk O, Hohn B. Genome-wide variation of the somatic mutation frequency in transgenic plants. EMBO J. 2000 Sep 1;19(17):4431–4438. [PMC free article] [PubMed]
  • Tuteja N, Singh MB, Misra MK, Bhalla PL, Tuteja R. Molecular mechanisms of DNA damage and repair: progress in plants. Crit Rev Biochem Mol Biol. 2001;36(4):337–397. [PubMed]
  • Kwok PY. Methods for genotyping single nucleotide polymorphisms. Annu Rev Genomics Hum Genet. 2001;2:235–258. [PubMed]
  • Vidal A, Abril N, Pueyo C. DNA repair by Ogt alkyltransferase influences EMS mutational specificity. Carcinogenesis. 1995 Apr;16(4):817–821. [PubMed]
  • Li Qingbo, Liu Zhaowei, Monroe Heidi, Culiat Cymbeline T. Integrated platform for detection of DNA sequence variants using capillary array electrophoresis. Electrophoresis. 2002 May;23(10):1499–1511. [PubMed]
  • Weigel D, Alvarez J, Smyth DR, Yanofsky MF, Meyerowitz EM. LEAFY controls floral meristem identity in Arabidopsis. Cell. 1992 May 29;69(5):843–859. [PubMed]
  • Wienholds Erno, Schulte-Merker Stefan, Walderich Brigitte, Plasterk Ronald H A. Target-selected inactivation of the zebrafish rag1 gene. Science. 2002 Jul 5;297(5578):99–102. [PubMed]
  • McCallum CM, Comai L, Greene EA, Henikoff S. Targeted screening for induced mutations. Nat Biotechnol. 2000 Apr;18(4):455–457. [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...