alleles arose subsequent to the down-regulation of AN2 expression. In Mimulus aurantiacus, segregation analysis of an F2 population for both color and sequence variants of the core ABP genes, along with analysis of their expression and functional capabilities, indicated that a locus acting in trans accounts for 45% of color variation (Streisfeld and Rausher, 2009). These 2 studies provide the strongest evidence that changes in trans-regulators are responsible for shifts involving changes in the production of anthocyanins as a whole. Shifts from blue to red flowers have been studied in Ipomoea (Zufall and Rausher, 2004). Two mutations, 1 causing a loss of F3′H expression and 1 causing a change in the specificity of DFR for the substrate produced by F3′H rather than that produced by F3′H, are sufficient for this color transition. However, which of these mutations occurred first and thus produced the initial color shift is unclear. In these examples, the primary focus has been on the core ABP genes and their regulators. We know of no study that also has considered how changes in flux from side branches of the core ABP may have affected anthocyanin production in natural systems.
Aquilegia has been used for nearly 50 years to study the evolution and genetics of flower color. Prazmo (1961, 1965) made extensive crossing studies among purple-, white-, red-, and yellow-flowered species of Aquilegia and followed segregation ratios in F2, F3, and backcross populations. She found that flower color variation could largely be ascribed to 4 independently assorting factors (Prazmo, 1965): Y, which regulates the existence of yellow chromoplasts; C and R, which are needed for the formation of anthocyanins; and F, which modifies red anthocyanins into bluish-violet pigments. In crosses between either Aquilegia chrysantha or Aquilegia longissima (both of which lack floral anthocyanins) and species with floral anthocyanins, Prazmo (1961, 1965) found that a single gene (R) could account for anthocyanin production. Whittall et al. (2006b) found that multiple genes late in the core anthocyanin pathway, especially DFR and ANS, were down-regulated in A. chrysantha, A. longissima, and Aquilegia pinetorum, which together form a clade of taxa lacking floral anthocyanins (Fig. 2.2). These results suggest that Prazmo’s factor R is a transregulator of genes late in the ABP. In crosses with the white form of Aquilegia flabellata, Prazmo also found that a second gene (C) could account for anthocyanin production. Whittall et al. (2006b) found that only CHS was down-regulated in white A. flabellata. Thus, Prazmo’s factor C is likely a mutation in either a transregulator or the cis-regulatory region of CHS. Significantly, F1 progeny from crosses between white A. flabellata and