Tracking Down Transposable Elements in Maize: New Map Will Aid Research and Breeding Efforts

Overview: A new map of transposons in maize will help identify the role of transposable elements, and help with the breeding of maize, a major global crop.

Transposable elements (also called transposons or “jumping genes”) have been an elusive DNA component for decades, primarily because they’ve been so difficult to sequence and assemble, until now. Michelle Stitzer, a Ph.D. student in population biology, and maize geneticist Jeff Ross-Ibarra, a plant sciences professor at UC Davis, worked with colleagues at Cold Spring Harbor Lab and several universities and genome technology companies, to create a new maize reference genome, which now includes the many complex repeat regions. The new sequencing technology they used is described in a recent Nature publication.

Michelle Stitzer records the GPS coordinates of an individual Zea mays plant in a field in eastern Jalisco, Mexico, to investigate hybridization between maize and its wild relative teosinte. (photo: Jeffrey Ross-Ibarra/UC Davis)

Transposable elements (TEs) are DNA sequences that can move locations within a genome. Discovered in corn by Nobel-winning geneticist Barbara McClintock in the 1940s, transposable elements were long considered by many scientists to have little role in genetics. Others, however, including McClintock, thought that TEs within a genome may regulate gene expression and have other important roles in cells. More recently, it has been discovered that transposable elements are found in most organisms, making up more than 80 percent of the maize genome and nearly 50 percent of the human genome.

Identifying and classifying transposable elements in maize

“Earlier maize reference genomes did not identify all of the repetitive regions,” said Stitzer. “Until now, we knew relative positions of sequence segments, but not all of the messy parts in between. This new technology has allowed us to sequence all of the repetitive regions.” Stitzer has developed methods to identify the positions of transposons in maize even when they jump into each other.

“The Nature publication focused on the technology, which gave a valuable, high-quality genome sequence,” said Ross-Ibarra, “but Michelle then created computational algorithms to identify individual transposable elements across the whole genome, which had never been done before.”

“Her work is revealing an entire ecology of transposons, complete with complex relationships of competition and cooperation. This is enabling us to begin to understand the rich biodiversity of the genome as an ecosystem.”

Nathan Springer, a professor at the University of Minnesota and co-author on the Nature paper, noted, “Michelle’s new approaches to identifying and classifying the full complement of transposable elements in maize should lead to new fundamental biological discoveries.”

Transposons are mobile pieces of DNA that influence other genes. In this photo, each spot on a corn kernel is caused by a transposon.

New windows in transposon research

“When transposons land somewhere in the genome, they can regulate and change the expression of nearby genes,” said Stitzer. “That’s very important to know, but was difficult to identify when we couldn’t figure out where they were in the genome sequence.”

Transposon insertions, and their impact on gene expression, are known to impact the way in which the maize plant interacts with its environment. Different transposon insertions confer drought tolerance, altered flowering time, ability to grow in toxic aluminum-rich soils, and have allowed maize to spread to temperate latitudes by breaking sensitivity to the long days of the tropics. And broadly, transposable element insertions have been shown to alter gene expression in stressful conditions. But these insertions with characterized functional consequences only represent a handful of the hundreds of thousands of transposable elements in the maize genome.

Damon Lisch, a professor at Purdue University, who studies the regulation and evolution of plant transposable elements, said, “We simply cannot understand the complexity of plant genomes unless we can identify transposable elements. Michelle’s work provides an invaluable road map that allows us to begin to untangle the diversity of all of the genetic elements that make up the maize genome.”

Ross-Ibarra says that now that the maize genome is fully sequenced and transposon locations have been determined, it is opening a new realm of research beyond the role of individual genes in maize – determining the role of individual transposons.

In a world in which maize is the major crop, the population is growing, and climate change will impact maize adaptation, identifying and understanding the role of transposons will likely benefit maize breeding, production, and global food supplies.

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