Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks

Plant Physiol. 2012 Oct;160(2):591-600. doi: 10.1104/pp.112.200311. Epub 2012 Jul 26.


Mapping-by-sequencing (or SHOREmapping) has revitalized the powerful concept of forward genetic screens in plants. However, as in conventional genetic mapping approaches, mapping-by-sequencing requires phenotyping of mapping populations established from crosses between two diverged accessions. In addition to the segregation of the focal phenotype, this introduces natural phenotypic variation, which can interfere with the recognition of quantitative phenotypes. Here, we demonstrate how mapping-by-sequencing and candidate gene identification can be performed within the same genetic background using only mutagen-induced changes as segregating markers. Using a previously unknown suppressor of mutants of like heterochromatin protein1 (lhp1), which in its functional form is involved in chromatin-mediated gene repression, we identified three closely linked ethyl methanesulfonate-induced changes as putative candidates. In order to assess allele frequency differences between such closely linked mutations, we introduced deep candidate resequencing using the new Ion Torrent Personal Genome Machine sequencing platform to our mutant identification pipeline and thereby reduced the number of causal candidate mutations to only one. Genetic analysis of two independent additional alleles confirmed that this mutation was causal for the suppression of lhp1.

MeSH terms

  • Alleles
  • Amino Acid Sequence
  • Arabidopsis / genetics*
  • Arabidopsis / physiology
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosomal Proteins, Non-Histone / genetics
  • Chromosomal Proteins, Non-Histone / metabolism
  • Chromosome Mapping / methods*
  • Crosses, Genetic
  • DNA Transposable Elements
  • Ethyl Methanesulfonate
  • Flowers / genetics
  • Flowers / physiology
  • Gene Frequency
  • Genes, Plant*
  • Genetic Complementation Test
  • MADS Domain Proteins / genetics
  • MADS Domain Proteins / metabolism
  • Molecular Sequence Data
  • Mutagenesis*
  • Mutation
  • Phenotype
  • Polycomb Repressive Complex 1 / genetics
  • Polycomb Repressive Complex 1 / metabolism
  • Time Factors


  • Arabidopsis Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • DNA Transposable Elements
  • FLF protein, Arabidopsis
  • MADS Domain Proteins
  • like heterochromatin protein 1
  • Ethyl Methanesulfonate
  • Polycomb Repressive Complex 1