Mapping Mutations in C. elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 4

homozygotes, as well as mutations that can only be scored in specialized genetic
backgrounds, for example, suppressor, enhancer, and modifier mutations.
I. Introduction
In 1974, Sydney Brenner outlined the essential methods for genetic mapping in
C. elegans and described the relative positions of nearly 100 different loci distributed
across the six linkage groups ( Brenner, 1974 ). This provided the fundamental
framework upon which the current genetic map has been built. Brenner used a
combination of two- and three-factor mapping methods to determine the relative
positions of loci along each chromosome. Subsequent workers have described
methods for using deficiencies (i.e., deletions) ( Rogalski et al., 1982; Sigurdson
et al., 1984 ), free duplications ( Bullerjahn and Riddle, 1988; McKim and Rose,
1990 ), and translocations ( Albertson, 1984; McKim et al., 1988; Rosenbluth and
Baillie, 1981; Sigurdson et al., 1986 ) to determine gene locations. See Fay (2006) for
an extensive discussion of gene mapping methods in C. elegans. Since the three-
point cross is arguably the single most useful standard mapping cross, its use is
described in Sections VIB and VII.
With the advent of gene cloning technology, a progressively sophisticated series of
methods have been enlisted to establish direct correlations between genetically
defined loci and the DNA sequence of the genome. These began with Southern
blot-based methods such as RFLP (restriction fragment length polymorphism) map-
ping ( Ruvkun et al., 1989 ) and transposon tagging ( Collins et al., 1987; Moerman
et al., 1986 ), and evolved into higher-resolution, high-throughput techniques for
detecting polymorphisms ( Davis et al., 2005; Flibotte et al., 2009; Fuhrman et al.,
2008; Jakubowski and Kornfeld, 1999; Shelton, 2006; Swan et al., 2002; Wicks et al.,
2001; Williams, 1995 ). Drastic reductions in the cost of whole genome sequencing
(WGS; also termed resequencing), have now made it feasible to ''map'' mutations
simply by sequencing the entire genome of a strain that carries the newly isolated
allele ( Hobert, 2010 ). Since the standard conditions that are used for mutagenesis
generate hundreds of mutations within the genome ( Flibotte et al., 2010; Sarin et al.,
2010 ), combining WGS and mapping can greatly reduce the number of candidate loci
that need to be considered ( Doitsidou et al., 2010 ). The purpose of this chapter is to
describe the fundamental principles and practices involved in establishing the basic
genetic properties of a newly isolated mutation and also to discuss the use of methods
for determining the correspondence between a newly isolated genetic mutation and
the causative sequence alteration(s) within the genome.
II. Mutant Origination
Mutations typically are identified via forward genetic screens, since these pro-
vide a powerful method for identifying both loss-of-function and alteration-of-
function alleles of any given gene of interest. Hundreds of different single-mutant