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The genetics of black bean pigmentation has been studied by various researchers and summarized by Hosfield (2001). Feenstra (1960) isolated 18 different compounds from 12 experimental lines. These pigment compounds were identified as anthocyanins, flavonol glycosides, and leucoanthocyanidins. The secondary plant metabolites known as flavonoids are water‐soluble phenolic compounds that possess the basic structural C15 skeleton of flavones. Beninger et al. (1998) reported that the pigments responsible for the wide variation in the color of bean seed coats are flavonoids.

Water‐soluble pigments are readily leached from the seed coat during hydration, blanching, and thermal processing. Retention of pigment is generally a desirable characteristic that imparts attractive appearance and appeal. Black beans are particularly susceptible to pigment leaching during soaking and preparation procedures. The use of extended high‐temperature hydration procedures (hot soaking, pipe blanching, or extended blanch conditions) generally renders black beans pale and opaque with a gray or chocolate brown “muddy” appearance. The leaching of pigment during soaking, blanching, and thermal processing is a major quality problem associated with all colored beans, particularly black beans. The primary anthocyanin pigments in black beans include: (1) delpinidin‐O‐gluscoside, (2) petunidin‐O‐glucoside, and (3) malvidin‐O‐glucoside. These phenolic glucosides are highly soluble in water, and excessive leaching may occur, resulting in beans with a flat brownish appearance (Bushey et al. 2000, Bushey and Hosfield 2007). The deposition of pigment in black beans is relatively late in the plant growth cycle and appears to be under genetic and environmental influence (Fletcher et al. 2003). Failure to achieve full maturity of seed may result in reduced or nonuniform pigmentation.