Flavonoid pigments as tools in molecular genetics

In the plant kingdom, the flavonoid biosynthetic pathway is ubiquitous and produces a variety of pigmented as well as nonpigmented compounds. Flavonoid compounds have been implicated in several biological processes and some of their functions include the attraction of pollinating agents via pigmentation of floral organs (Huits et al., 1994), pollen tube germination (Mo et al., 1992), protection from UV exposure (Bieza and Lois, 2001), and defense against insects by acting as insecticides (Wiseman et al., 1996) and fungal pathogens by acting as phytoalexins (Nicholson and Hammerschmidt, 1992; Dixon and Steele, 1999). Flavonoid pigments have been used as a convenient visible marker in molecular genetic experiments and to study regulation of gene expression (Styles and Ceska, 1977, 1981, 1989; Dooner et al., 1991; Koes et al., 2005). Flavonoid biosynthesis takes place through the phenylpropanoid pathway, and depending on the genetic constitution of the plant naringenin can have several different fates leading to the formation of flavonoid metabolites that include anthocyanins, flavones, and anthocyanidins (Figure 6.1) (Styles and Ceska, 1989; Dooner et al., 1991; Winkel-Shirley, 2001a, 2001b; Schijlen et al., 2004). Since the isolation of chalcone synthase (CHS), which catalyzes the first committed step of this pathway (Kreuzaler et al., 1983), efforts have been focused on the isolation of mutants and the cloning of structural genes that are required for the different biosynthetic steps (Harborne and Williams, 2000; Winkel-Shirley, 2001a). Progress in our understanding of gene expression and regulation has been enhanced by targeting structural as well as regulatory genes that are required for the biosynthesis of these pigmented flavonoids. Since various aspects of the gene structure and regulation, genetics, epigenetics, biochemistry, and regulation of flavonoid biosynthesis have been reviewed recently (Springob et al., 2003; Schwinn and Davies, 2004; Tanner, 2004; Koes et al., 2005; Tanaka et al., 2005) and also discussed in other chapters of this book, we will focus on the biosynthesis and accumulation of 3-deoxyflavonoid (phlobaphene) pigments in maize (Zea mays) and sorghum (Sorghum bicolor) (Figure 6.2), proanthocyanidins (condensed tannins) in Arabidopsis (Arabidopsis thaliana), and anthocyanins in snapdragon (Antirrhinum majus), petunia (Petunia hybrida), and three Ipomoea species: the Japanese morning glory (Ipomoea nil), the common morning glory (Ipomoea purpurea), and Ipomoea tricolor (Figure 6.3). We will also discuss molecular genetic aspects by emphasizing phenotypes of mutant alleles characterized at the sequence level and describe briefly epigenetic aspects of regulation in the genes for phlobaphenes, proanthocyanidins, and anthocyanins.