What Happens to Genes Without a Role? Identifying the Lost Genes That Once Controlled the Production of Red Pigments in Amaranth

Abstract

Although they may not seem to move or change, plants are alive. Like other living beings, they have to react to their environment in order to survive. For example, many plants turn darker colors when sunlight threatens to damage their leaves. These colors are pigments, a type of chemical that can absorb specific colors of light, and these pigments can also absorb harmful UV light before it reaches the inside of a plant and damages the DNA.

 Evolution constantly changes both wild and domesticated plants. The red color of many plant and crop species is controlled by pigments called anthocyanins. Anthocyanins have an ancient evolutionary history and are common across many diverse types of plants, including the most well-studied model plant Arabidopsis thaliana. However, some plants including amaranth, make a completely different type of red pigment called betalains. Betalains are much rarer, and the ancestors of amaranth likely made anthocyanins instead. It is unclear why a plant would evolve a new type of red pigment when it already produces an ancient, time-tested, and clearly useful type of red pigment.

To understand the evolution of the two different red pigments, we will reconstruct the regulatory network of anthocyanins in maize, Arabidopsis thaliana, and a plant closely related to amaranth, called Silene conica, that still produces anthocyanins. Using what we learn from the anthocyanin regulatory network, we will be able to identify ex-anthocyanin genes in amarnath. Finally, we will see whether these ex-anthocyanin amaranth genes now have new functions. If the old anthocyanin genes have new roles making betalains, this could tell us that plants had to lose anthocyanins to make betalains.
 

Dr. Elli Cryan

Dr. Elli Cryan is a plant evolutionary geneticist who studies traits controlled by networks of interacting loci and alleles. Currently, she is postdoctoral researcher at the University of California, Irvine where she studies how related genes have evolved to silence each other across the maize genome. She earned her doctoral degree in Plant Biology from the University of California, Davis in December 2025 for her thesis on “Molecular evolution of complex plant traits.” In addition to her research, she has taught university courses on evolution, genetics, and plant developmental anatomy.<