Many traits of agronomic interest are controlled by genes whose products, function, sequence and position in the genome are unknown. To isolate these genes it is necessary to use methods, which do not require prior knowledge of the gene product(s). One such method is map-based cloning (MBC), also referred to as positional cloning. MBC is a forward genetics approach, which aims to identify the nucleotide sequence(s) that underlie a specifi c trait, which may be the product of either induced or naturally occurring variation. Quantitative trait loci (QTL), the basis of many important agronomic traits, are defi ned by position and, unless a corresponding mutant can be identifi ed, MBC or association mapping are the only ways to obtain the sequence of genes underlying a quantitative trait. MBC is also essential for understanding the genetic basis underlying phenotypes amongst ecotypes of model species such as Arabidopsis (Jander et al. 2002).