I’m only two pages into the latest children’s book on learning one’s colors, and my 3-year old hits a snag. “Corn is NOT yellow!” he shouts indignantly. For several weeks now, he’s been going with me to the garden and bringing back armfuls of native corn, then sitting and husking them one leaf at a time until the kernels come into sight. Then, with “Oooohs!” and “Aaaahs!” worthy of a fireworks display, everyone admires the deep reds, purples, pinks, and greens that make up the true colors of maize.

Enough people have asked me about this recently that I thought I would take a stab at a topic so complicated that it won Barbara McClintock a Nobel prize. Maize is the ultimate transgenic exhibitionist, flagrantly moving bits of its genes around with each generation. This is not recombination – it is unguided transposition engineered by ancient parasitic bits of DNA that stick themselves in and out of the maize pigmentation genes at random. It made me smile when golden rice became all the buzz recently, as I’ve watched many generations of maize revert back and forth from white to golden without Greenpeace getting lathered up about it.

That’s as good a place to start as any, because the carotenoids are expressed mainly in the endosperm, forming the base color of the kernel. See the illustration for the names and locations of the various seed layers. The endosperm forms the substance of the corn kernel, and it is the canvas, while the thinner pericarp and aleurone layers are like paint layered over this base color. Corn has a robust production of deep yellow carotenoids including zeaxanthin (Fig1), and these genes are either disabled by the insertion of transposons, giving a white background, or intact, giving yellow.

Figure 1: Zeaxanthin

There are two additional primary pigments in maize – anthocyanins (Fig2) and phlobaphenes (Fig3). Anthocyanins come in a number of shades, their colors are pH-dependent, but tend to be pinks, purples, and reds. Phlobaphenes are deep magenta. While most native maize cultivars have one or more copies of each gene needed to form all of these pigments, some or all of them will not be expressed in each generation because a transposable genetic element has spliced itself into either the structural gene or its promoter, disabling it. Each time you plant a seed of native corn, these mobile pieces of DNA hop back and forth between the 10 available chromosomes. Most stop after formation of the gametes, but some keep jumping in and out even as the newly fertilized seed is growing. That leads to kernels with spots and stripes, as we’ll see later on.

Figure 3: Phlobaphene

Figure 2: Anthocyanidin

For now, let’s just keep things simple. Let’s make M Go-Blue corn. A deep red phlobaphene expressed in the paricarp layered over a yellow endosperm base gives you the dark blue. Add enough transposition events to knock out the DFR gene in about 1/2 of the embryos, and those seeds will lose the ability to polymerize flavones to phlobaphenes, reverting them to yellow. See an example below.

Chromatin modifying enzymes are at the heart of the epigenetic battle in maize to silence the transposable elements that come to life with each meiosis. While mammals methylate cytosine mainly in CG dinucleotides, plants use a more sophisticated RNA-directed DNA methylation system with unique plant RNA polymerases Pol IV and Pol V to obtain the specificity to methylate cytosine in any sequence context. Many aspects of epigenetic gene modification that impact human cancers have an equivalent that can be observed visually in maize.

The infinite complexity of the biochemistry of kernel pigmentation can be seen in the activity of the Bronze2 (Bz2) gene. Bz2 is a glutathione S-transferase that tags finished cyanidin-3-glucosides with GSH, permitting the tonoplast GS-X pump to move them into the vacuole. This is directly analogous to the complex process of melanin packaging and transfer from melanocyte to keratinocyte in humans, with important implications for cosmetics and protection from UV exposure. The picture below shows the “tanning effect” of the Bz2 gene on an ear of “Kansas Jayhawk” corn.

Bz2(-)    Bz2(+)

If you think about paint mixing, it’s now clear why you can’t really make green and white Michigan State corn. The carotenoid pathway has to be shut down to provide the white canvas you want to start with.  But green takes yellow plus blue. All kinds of Kansas Jayhawk and Northwestern corn is possible (have a look) but no green and white – sorry Sparty.

If you go overboard with phlobaphene genes, adding copy numbers and expressing them in both aleurone and pericarp layers, you first get Cranberry corn, and then finally Kwanza corn – absolutely black.

Catseye is a pattern that develops when any red or purple pigment gene that was silenced in the fertilized embryo gets re-activated while the kernel is growing. That leads to a clone of pigment expressing cells growing in a stripe over the underlying background, which can be white, yellow or purple. Very late transposition events are rare, but when they happen the kernel will develop a small (usually purple) spot like an ink splatter. Instability in the genome this late in development often means short, stunted plants and ears with few viable seeds (below, right).

Crossing corn is endless fun. The result of crossing Glass Gem, a mainly carotenoid( +), phlobaphene(-) anthocyanidin (+) popcorn [Oh yeah – aleurone thickness determines if your corn is hard and shiny like a button and will pop, or soft and dented and makes tortilla flour – whole ‘nother story] with Cranberry, a pholbaphene (+) eastern meal corn gave this bright progeny in 2013.

Leave a comment below and suggest a name for this new corn.