Jumping genes make fall come alive

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.

1354 crop


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.

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12 Responses to Jumping genes make fall come alive

  1. Craig Maxey says:

    Good work and very interesting.
    How about jelly belly or jelly bean as a name?

  2. Cathy Moran says:

    Interesting…nay fascinating. Satisfying to the inner 2-5 year old who wants to know “Why”. Gorgeous photography. Thanks to the blessing within a curse of insomnia, here are a couple ideas for the new color name. Thought about “canfetti” or “cornfetti”…maybe “candy cornfetti”. Regardless, just a beautiful ear. Hmmm…”eye candy corn”?

  3. Gea says:

    Good morning!
    I am an Italian biologist and I am about to start a blog about biology in real life, nothing complicated, I would just pass on my passion for this topic. One of my first posts will be on Glass Gem Corn and, as I was looking for some more explanation about this argument, I “stumbled” upon your post.
    I found it very interesting and it helped me a lot on concentrating on the causes of this “phenomenon”. I was starting to lose myself in the labirynth of scientific notions and your words kept me focused instead! Thank you!

    Good job!

    • Kirk Maxey says:

      I’m happy to learn that people in Italy are interested in Native American corn! Glass Gem is a variety that was developed by Carl Barnes, who like me traces his heritage through the Cherokee tribe. Glass Gem is a popcorn with very thick, rounded aleurones that give it the appearance of a glass bead. I can send you the seeds if you would like to grow some yourself.

      • Gea says:

        Good morning!
        First I wanted to apologize for my belated reply: I didn’t receive any notification of your reply to my post and I found it by chance while completing my little article about Glass Gem Corn.
        Anyway, it would be an interesting experience for me to grow some of the plants; I would like to send you my address in a private message, but I couldn’t find a contact address on the website. Can you help me?
        Thank you again!

  4. kirkmike157 says:

    I’m sure I would enjoy reading your article on Glass Gem corn. Just send a direct message to me on Twitter – I’m @KirkMMaxey. I’ll get a package of seeds off to you in time for spring. 🙂

  5. Hi Kirk, I would love to have a packet of Glass Gem seeds and thanks for offering to send them. My address should be available through my website.

    • kirkmike157 says:

      Great! I usually send out packets of seeds around February. If they go out now, they tend to get lost in the Christmas madhouse.

  6. Michael P says:

    Hello, I’m really glad you are interested in genetics and corn anthocyanins! This is my grad school research. I just wanted to inform you that a lot of your information is incorrect though. Pericarp is the outermost layer and is the layer pigmented by phlobaphenes. Aleurone is inside and is part of the endosperm. Endosperm causes the glass gem appearance. Also, corn can segregate for genes that make yellow vs white, it is mostly not due to transposons. Sorry to be picky, I liked this article though!

    • kirkmike157 says:

      Thanks for your helpful comments Michael. I’m making some revisions to the post to insure that it’s accurate. I’m continually finding out that things I believed about Indian corn are not always true. In the 2016 crop, I found a strain of pink seeds that segregates as a trait, and does not seem to be variable any longer

  7. Pingback: DNA mobile e mais arlecchino | Biologica Blog

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