Perspectives for identification of mutations in the zebrafish: making use of next-generation sequencing technologies for forward genetic approaches

Methods. 2013 Aug 15;62(3):185-96. doi: 10.1016/j.ymeth.2013.05.015. Epub 2013 Jun 5.


The ability to identify a phenotype causing mutation is essential for successful use of mutagenesis screens in many model organisms. Mapping mutations was for a long time a bottleneck in zebrafish research, as the standard method for mapping and identification of mutations was time consuming and expensive. The development of new sequencing technologies in the last couple of years has enabled the rapid and cost-effective sequencing of whole genomes. This has led to the establishment of new strategies for mapping and identification of mutations in several model organisms. The application of these techniques to the zebrafish model, with its large genome and the high level of variation in and between strains, was not trivial. Several techniques have been developed recently, taking the specific characteristics of the zebrafish genome into account. Here we give an overview on how to plan a mapping experiment, detail the critical parameters and discuss available tools for mapping and identification of mutations in zebrafish using next-generation sequencing. Using these methods, zebrafish mutants can now be mapped in a couple of weeks for a fraction of the costs. The increased efficiency of identification of mutations in the zebrafish broadens the utility of the model and allows for systematic analysis of gene function in a vertebrate model.

Keywords: Bulked segregant analysis; Homozygosity-by-descent; Mutation mapping; Whole genome sequencing; Zebrafish.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Animals
  • Chromosome Mapping
  • Chromosomes / chemistry*
  • Genetic Linkage
  • Genome*
  • High-Throughput Nucleotide Sequencing / instrumentation
  • High-Throughput Nucleotide Sequencing / methods
  • Homozygote
  • Mutation*
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Software*
  • Zebrafish / genetics*