RAD marker microarrays enable rapid mapping of zebrafish mutations

Michael R Miller,B Frank Eames,Eric A Johnson,Yi-Lin Yan,Tressa S Atwood,John H Postlethwait,Johann K Eberhart

doi:10.1186/gb-2007-8-6-r105

Abstract

A RAD marker microarray was constructed to facilitate rapid genetic mapping of zebrafish mutations and used to localize previously unmapped mutations to genomic regions just a few centiMorgans in length.

Highlights

Zebrafish (Danio rerio) has become an important model system for the study of vertebrate development and human disease, for the assignment of function to genes otherwise known only by sequence, and for the identification of novel functions for genes with previously described functions [1,2,3,4,5]
Production of the zebrafish restriction site associated DNA (RAD) marker microarray One powerful aspect of the RAD approach is that RAD markers can be genotyped on low-cost microarrays that are made from the DNA of two polymorphic RAD tag samples [15]
In this report we describe the production of a zebrafish RAD marker microarray and show that this microarray can facilitate rapid and inexpensive genetic mapping of zebrafish mutations

Summary

Introduction

Zebrafish (Danio rerio) has become an important model system for the study of vertebrate development and human disease, for the assignment of function to genes otherwise known only by sequence, and for the identification of novel functions for genes with previously described functions [1,2,3,4,5]. The first eight zebrafish mutations were mapped using a bulk segregant approach with a map constructed from anonymous random amplified polymorphic DNA markers [8]. The same basic approach is commonly used today with microsatellite markers [13,14]. These approaches have been effective, they are expensive, labor intensive, and time consuming. We have previously shown that restriction site associated DNA (RAD) marker genotyping is a microarray-based method that allows thousands of polymorphic markers to be screened in parallel [15]. RAD tags are a genome-wide representation of a particular restriction enzyme's recognition sequence by short DNA tags, and DNA sequence polymorphisms that disrupt restriction sites allow RAD tags to serve as high-density genetic markers. The RAD approach has been used to map natural variation in stickleback [15], but it has not yet been applied to map induced mutations in any species

Methods

Results

Conclusion