is the ability to cross virtually any 2 species (Prazmo, 1965; Taylor, 1967). Segregating populations allows for quantitative trait loci (QTL) analysis and the subsequent ability to identify whether genes in the ABP cosegregate with QTL. In an initial analysis of flower color in A. formosa and A. pubescens a single QTL was identified (Hodges et al., 2002) and it should now be possible to determine which, if any, of the genes in the flavonoid pathway cosegregate with flower color. The ability to cross species also allows introgression and the creation of near-isogenic lines as described above. Second is the high degree of sequence similarity among species of Aquilegia (Whittall et al., 2006a), which makes molecular resources developed in 1 species very likely to be transferable to others. For example, a reverse genetic approach, virus-induced gene silencing (VIGS), was developed in A. vulgaris, a European species, but using sequence information of ANS from North American species (A. formosa and A. pubescens) (Gould and Kramer, 2007). Silencing the ANS gene in A. vulgaris converted the normally deep-purple flowers to white (Gould and Kramer, 2007), confirming that a single copy of ANS is expressed in floral tissue. Furthermore, the VIGS technique itself is applicable across species of Aquilegia (Gould and Kramer, 2007).
Natural populations of Aquilegia that vary in flower color also will offer distinct advantages for uncovering the genetic basis of flower color. The production of controlled crosses in the laboratory can be labor intensive and does not necessarily break up genes linked even at relatively great physical distances. Thus, a single QTL may harbor many genes that could potentially affect the trait of interest. For instance, we have identified 34 genes that may play a role in the core ABP and its side-branch pathways (Table 2.1), thus implicating an average of nearly 5 such genes per chromosome (there are 7 pairs of chromosomes in Aquilegia). Of course, there may be even more genes involved in the flavonoid pathway as the Aquilegia gene index likely does not contain all paralogs of the ABP genes and additional side-branch enzymes are possible (Yonekura-Sakakibara et al., 2008). Thus, it is likely that any 1 QTL region may harbor multiple genes in the ABP. However, natural populations polymorphic for flower color are likely to have had long histories of recombination and low linkage disequilibria. In such populations, it should be possible to follow sequence variation at all of the genes in the ABP and identify specific genes that correlate with (and actually influence) flower color.
Aquilegia offers many examples of pronounced variation in flower color. For example, populations of A. coerulea (Miller, 1978, 1981) and Aquilegia scopulorum are often polymorphic for this trait (Fig. 2.1B). In addition, many natural hybrids exist between several Aquilegia species. Hybrid populations of A. formosa (red; Fig. 2.1G) and A. pubescens (primarily white; Fig. 2.1F) have been studied for many years and produce a broad range of