An increasingly common method of refining the identification of QTL is the production of near isogenic lines (NILs) and positional cloning. Technical limitations, such as the lack of contiguous coverage and the large amounts of repetitive DNA in the genomes of many plant species, prevent the successful implementation of positional cloning by means of chromosome walking. Aside from these techni- cal issues, positional cloning may not be efficient at identifying genes responsible for complex traits. This is due in part both to the difficulty of developing NILs for loci that explain less than 20% of the variance and to constraints created by only using two alleles. The majority of genes cloned via positional cloning explain large portions of the phenotypic variation, e.g., “fruit weight2.2” in tomato, “teosinte branched1 (tb1)” in maize, “heading date1” in rice, and FRIGIDA and CRYPTO- CHROME2 in Arabidopsis (6, 8, 13, 25, 59). The productin of NILs is also time consuming, especially for long-generation species. However, when nothing is known about the genes in a particular pathway, positional cloning may be the best option.