Kevin Schneider and Thomas Wolfgruber

Longstanding genetic question solved by studying corn

A question that has long puzzled geneticists now has a solution: researcher Gernot Presting and three postdoctoral scholars in his lab, all members of the Department of Molecular Biosciences and Bioengineering in the College of Tropical Agriculture and Human Resources, have explained why the DNA at the centromeres evolves so quickly.

The Centromere Paradox

On the X-shaped chromosome, the centromere is at the “cross” point of the two arms. Like the rest of the chromosome, centromeres are composed of double-stranded DNA and protein. Centromeres play an essential role in cell division by ensuring that each new cell obtains a complete set of chromosomes.

Because the centromeres of all organisms play the same role, it seems logical that an optimal  DNA sequence might have evolved to perform this function and that all centromeres would have the same sequence. However, centromere DNA is highly variable. This phenomenon has been called the centromere paradox, and scientists have been trying to figure out what causes it. A previously proposed solution, the centromere drive hypothesis, suggests that an “arms race” between centromeric  DNA and its binding proteins necessitates their rapid evolution, has yet to be proven conclusively.

Genetic diversity in corn

Now, Presting, along with Kevin SchneiderZidian Xie and Thomas Wolfgruber, has resolved the centromere paradox by following the turnover of DNA in centromeres of corn. The team determined which DNA sequences serve as the centromere in different corn varieties using chromatin immunoprecipitation to isolate the DNA that interacts with centromere proteins, followed by large-scale DNA sequencing. They used corn because of the tremendous genetic diversity captured in 10,000 years of breeding, and its importance as a U.S. crop.

In a detailed study of dozens of pure-breeding strains of corn, they concluded that intense selection for centromere-linked genes encoding key traits related to the domestication and agronomic improvement of corn was responsible for the frequent turnover of repeats at the centromeres of corn but not its wild, inedible ancestor teosinte. They discovered that loss of the ancestral centromeric repeat causes the centromere to move to a new location, followed by colonization of these neocentromeres by a specific class of retrotransposons, or jumping genes. The role of these retrotransposons in chromosome integrity remains to be elucidated.

Major advance

This alternative explanation for the centromere paradox represents a major advance in the understanding of centromere evolution and explains not only the frequently observed turnover of centromere repeats in domesticated crop plants, but also similar processes that take place during speciation under natural selection.

The work, published in the prestigious journal Proceedings of the National Academy of Sciences, USA, was funded by the National Science Foundation, the USDA and the University of Hawaiʻi.