Oligonucleotide Array Comparative Genomic Hybridization (oaCGH) based characterization of genetic deficiencies as an aid to gene mapping in Caenorhabditis elegans

Martin R Jones,Stephane Flibotte,Jason S Maydan,David L Baillie,Donald G Moerman

doi:10.1186/1471-2164-8-402

Abstract

Background:A collection of genetic deficiencies covering over 70% of the Caenorhabditis elegans genome exists, however the application of these valuable biological tools has been limited due to the incomplete correlation between their genetic and physical characterization.Results:We have applied oligonucleotide array Comparative Genomic Hybridization (oaCGH) to the high resolution, molecular characterization of several genetic deficiency and duplication strains in a 5 Mb region of Chromosome III. We incorporate this data into a physical deficiency map which is subsequently used to direct the positional cloning of essential genes within the region. From this analysis we are able to quickly determine the molecular identity of several previously unidentified mutations.Conclusion:We have applied accurate, high resolution molecular analysis to the characterization of genetic mapping tools in Caenorhabditis elegans. Consequently we have generated a valuable physical mapping resource, which we have demonstrated can aid in the rapid molecular identification of mutations of interest.

Highlights

In this study we demonstrate the successful application of oligonucleotide array Comparative Genomic Hybridization (oaCGH) to the physical characterization of deficiency strains in C. elegans
Results and Discussion oaCGH mapped deletions and duplications physically define 17 zones around the dpy-17 region of Chromosome III; sDp3 (III) 7 deficiencies and 2 duplications lying in the region of dpy-17 on chromosome III were chosen for oaCGH analysis (Nimblegen) as they have been previously characterized by both genetic linkage and PCR analysis, and used to roughly position a large number of unidentified EMS generated lethal mutants [7]
After oaCGH mapping had precisely defined the gene complement for each of these deficiencies a refined candidate gene approach was implemented to rapidly identify mutations in essential genes which map to this region

Summary

Introduction

A collection of genetic deficiencies covering over 70% of the Caenorhabditis elegans genome exists, the application of these valuable biological tools has been limited due to the incomplete correlation between their genetic and physical characterization. A large resource of deletion strains ( known as genetic deficiencies) accounting for over 70% of the Caenorhabditis elegans genome has been generated by various research groups over the past three decades [1]. These genetic deficiencies have proven advantageous for a variety of purposes including; characterization of mutant alleles [2], identification of specific loci affecting developmental processes [3], investigation of genome replication and stability [4,5] and, most significantly, as tools for positional cloning of unmapped mutations to discrete regions of the genome [1,6,7,8]. Characterization of genetic deficiencies has been performed by fairly low resolution or labor intensive techniques such as genetic linkage mapping, PCR analysis [7] and, more recently, by the application of snip-SNP [9,10] and as a consequence many available deficiency strains remain poorly characterized

Methods

Results

Conclusion