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identifier PRJDB2751
type bioproject
sra-study  DRP000347
organism Arabidopsis thaliana
title Identification of EMS-induced Causal Mutations in A Nonreference Arabidopsis thaliana Accession by Whole Genome Sequencing
description The most usual method to identify mutations induced by a commonly used mutagen, EMS (ethyl methane sulphonate), in Arabidopsis thaliana has been the map-based cloning. The first step of this method is crossing a mutant with another accession plant as it requires polymorphisms between accessions for linkage analysis. Therefore, to routinely perform the method, it is highly preferred to use accession combinations between which enough polymorphisms are already known. Further, it requires laborious examination of a large number of F2 recombinants using plenty of markers to detect each polymorphism. After linkage analysis narrows down the chromosomal region containing the causal mutation, sequencing candidate genes one by one within the region is necessary until the mutation is finally identified. Overall, this method is generally time/labor-consuming and it becomes harder when multiple loci are involved in phenotypes. A few recent reports showed that causal mutations induced by EMS could be identified by deep-sequencing technologies with less labor compared with the conventional method when mutants were generated in the Arabidopsis reference Columbia background, whose genome information has been organized well. Here we report that we succeeded in quick identification of EMS-induced causal mutations in a nonreference accession background, whose whole genome sequence is not publicly available, using one round of whole genome sequencing. Moreover, in our case, we could monitor the causal locus and the transgenic reporter locus simultaneously, implying that this methodology could be theoretically applicable to analyzing even complex traits. We describe the pipeline of this methodology and discuss its characteristics. none provided
data type DDBJ SRA Study
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