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This is just a simplistic, hypothetical explanation of colours in Ipomoea (Not set in stone, plust there are many modifier, mutable, etc. genes that must be considered).
Source: Morita, Yasumasa (2005) et. al. Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-Oglucosyltransferase, due to 4-bp insertions in the gene. The Plant Journal, 42: pp. 353-363.
"The Japanese morning glory (Ipomoea nil) displays bright blue flowers (Figure 1b) that contain the peonidin (3¢-methylcyanidin) 3-O-sophoroside derivative named Heavenly Blue Anthocyanin (HBA) (Figure 1f; Kondo et al., 1987; Lu et al., 1992), and a number of spontaneous mutants exhibiting various flower colors have been isolated since the 17thcentury (Iida et al., 1999, 2004; Imai, 1927). Genetic studies on the color of I. nil have shown that blue flower coloration was mainly controlled by two genetic loci, Magenta and Purple (Hagiwara, 1931; Imai, 1931). Recessive magenta and purple mutants bloom magenta and purple flowers, respectively, and double mutants carrying both magenta and purple alleles display red flowers (Figure 1d)... Among the various colors of I. nil flowers, the most favorite hue for Japanese floriculturists has been reddish-brown or purplishgray petals (Figure 1c,e) since the early 19th century, and the flower coloration is caused by recessive dusky mutations (Hagiwara, 1956; Imai, 1931)...Although their flower coloration may subtly vary due to various genetic backgrounds, the dusky mutants carrying the wild-type Magenta allele generally exhibit bluish or purplish-gray flowers that contain cyanidin derivatives, whereas those with the magenta mutation tend to display reddish-brown flowers that contain pelargonidin derivatives, as represented in Figure 1(c,e). Among them, Magenta plants with the wild-type Purple or Purple-revertant allele show a tendency to produce more bluish-gray flowers than those with the purple mutation. Similarly, magenta mutants with the Purple or Purple-revertant allele generally exhibit darker reddish-brown flowers than those with the purple mutation."
Taken from Morita (2005) pg. 355
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