Protocol

Plant Functional Genomics

Volume 1284 of the series Methods in Molecular Biology pp 381-395

Date:

SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens

  • Hequan SunAffiliated withDepartment of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research
  • , Korbinian SchneebergerAffiliated withDepartment of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research Email author 

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Abstract

Whole-genome resequencing of pools of recombinant mutant genomes allows direct linking of phenotypic traits to causal mutations. Such analysis, called mapping-by-sequencing, combines classical genetic mapping and next-generation sequencing by relying on selection-induced patterns within genome-wide allele frequency (AF) in pooled genomes. Mapping-by-sequencing can be performed with computational tools such as SHOREmap. Previous versions of SHOREmap, however, did not implement standardized analyses, but were specifically designed for particular experimental settings. Here, we introduce the usage of a novel and advanced implementation of SHOREmap (version 3.0), including several new features like file readers for commonly used file formats, SNP marker selection, and a stable calculation of mapping intervals. SHOREmap can be downloaded at shoremap.org.

Key words

Forward genetics Bulk segregant analysis Next-generation sequencing Mapping-by-sequencing SNP marker Allele frequency analysis