ZFIN ID: ZDB-PUB-120105-50
Efficient Mapping and Cloning of Mutations in Zebrafish by Low-Coverage Whole-Genome Sequencing
Bowen, M.E., Henke, K., Siegfried, K.R., Warman, M.L., and Harris, M.P.
Date: 2012
Source: Genetics   190(3): 1017-1024 (Journal)
Registered Authors: Harris, Matthew, Henke, Katrin, Siegfried, Kellee
Keywords: mapping, mutation detection, whole genome sequencing, zebrafish
MeSH Terms:
  • Animals
  • Chromosome Mapping*
  • Databases, Nucleic Acid
  • Gene Library
  • Genetic Association Studies
  • Genome*
  • High-Throughput Nucleotide Sequencing
  • Homozygote
  • Mutation*
  • Polymorphism, Single Nucleotide
  • Zebrafish/genetics*
PubMed: 22174069 Full text @ Genetics
The generation and analysis of mutants in zebrafish has been instrumental in defining the genetic regulation of vertebrate development, physiology, and disease. However, identifying the genetic changes that underlie mutant phenotypes remains a significant bottleneck in the analysis of mutants. Whole genome sequencing has recently emerged as a fast and efficient approach for identifying mutations in non-vertebrate model organisms. However, this approach has not been applied to zebrafish due to the complicating factors of having a large genome and lack of fully inbred lines. Here we provide a method for efficiently mapping and detecting mutations in zebrafish using these new parallel sequencing technologies. This method utilizes an extensive reference SNP database to define regions of homozygosity-by-descent by low coverage, whole genome sequencing of pooled DNA from only a limited number of mutant F2 fish. With this approach we mapped each of the five different zebrafish mutants we sequenced, identified likely causative nonsense mutations in two, and candidate mutations in the remainder. Furthermore, we provide evidence that one of the identified mutations, a nonsense mutation in bmp1a, underlies the welded mutant phenotype.