title: Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks.
abstract: 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.
authors: Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, Max Planck Society, 50829 Cologne, Germany.
authors: Benjamin
authors: B
authors: Hartwig
authors: Geo Velikkakam
authors: GV
authors: James
authors: Kathryn
authors: K
authors: Konrad
authors: Korbinian
authors: K
authors: Schneeberger
authors: Franziska
authors: F
authors: Turck
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping / Q000379:methods*; D003433:Crosses, Genetic; D004251:DNA Transposable Elements; D005020:Ethyl Methanesulfonate; D035264:Flowers / Q000235:genetics / Q000502:physiology; D005787:Gene Frequency; D017343:Genes, Plant; D005816:Genetic Complementation Test; D026161:MADS Domain Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009154:Mutation; D010641:Phenotype; D063150:Polycomb Repressive Complex 1 / Q000235:genetics / Q000378:metabolism; D013997:Time Factors
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004251:DNA Transposable Elements; C418902:At5g10140 protein, Arabidopsis; D026161:MADS Domain Proteins; C443901:like heterochromatin protein 1; D005020:Ethyl Methanesulfonate; D063150:Polycomb Repressive Complex 1