Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence

Ghanasyam Rallapalli, Pilar Corredor-Moreno, Edward Chalstrey, Martin Page, Daniel Maclean

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Abstract

Background
Traditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. High throughput sequencing based Mapping-by-sequencing approach requires an ordered genome assembly and cannot be used with fragmented, un-scaffolded draft genomes, limiting its application to model species and precluding many important organisms.

Results
We addressed this gap in resource and presented a computational method and software implementations called CHERIPIC (Computing Homozygosity Enriched Regions In genomes to Prioritise Identification of Candidate variants). We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively.

Conclusions
CHERIPIC allows users to rapidly analyse bulk segregant sequence data and we have made it available as a pre-packaged binary with all dependencies for Linux and MacOS and as Galaxy tool.
Original languageEnglish
Article number9
JournalBMC Bioinformatics
Volume20
DOIs
Publication statusPublished - 7 Jan 2019

Keywords

  • Bulk segregant analysis
  • Mapping by sequencing
  • Next generation mapping

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