The basic cellular machinery that generates the genetic diversity central to evolution does not operate quite the way scientists have thought, says a team of Iowa State University plant scientists.
Their 10-year investigation of recombination events on a section of a maize chromosome showed that not all recombination occurs in genes and not all genes are active sites for recombination. Their research was published this week by the Proceedings of the National Academy of Sciences (PNAS).
By advancing the understanding of recombination in plants, the Iowa State research could lead to more precise control of gene integration in both traditional and biotechnological methods of plant breeding.
“Our research certainly changes the way we look at how recombination occurs in complex genomes like those of crop plants,” said Patrick Schnable, a professor of agronomy and of zoology and genetics, who led the research team. “Recombination is the grease that keeps the evolutionary machinery running. Without it, evolution slows down.”
Recombination is a fundamental process of sexual reproduction. In maize, as in humans, chromosomes are shuffled or recombined during sexual reproduction. The process, called crossing over, results in offspring with genes arranged in combinations that differ from those in either parent. It is an important means of producing genetic variation, which is the key to evolution.
For many years, scientists thought that most recombination occurs within genes and that the non-genic regions of complex genomes are recombinationally inert.
The research, “Molecular Characterization of Meiotic Recombination Across the 140-kb Multigenic a1-sh1 Interval of Maize,” was published in the April 16 online edition of PNAS.
“When transgenes are inserted into random places on chromosomes, they may not function properly. It would be much more desirable to be able to surgically insert a piece of DNA into precise chromosomal positions. These fundamental studies on recombination may teach us how to accomplish that,” Schnable said.
Schnable’s research team became interested in recombination in 1989, while studying the region in the maize genome from the a1 gene (anthocyaninless1) to the sh2 gene (shrunken2).
The a1 gene is involved in coding an enzyme that gives color to ornamental corn. The Sh2 gene codes an enzyme that is involved in starch metabolism. A kernel of corn with a mutation of sh2 will shrink, or collapse on itself, because it doesn’t contain normal amounts of starch.
Mutations in these two genes are visible in the kernels, allowing the traits to be traced through research experiments involving generations of crossbreeding. Eventually, after screening through hundreds of thousands of individual kernels, the researchers identified and collected about 100 kernels that carried the desired recombinant chromosomes, Schnable said.
Rather than isolate the genes between the a1 and sh2 genes and test to see if they were recombinant hotspots, the researchers identified all of the recombinant hotspots between the a1 and sh2 genes and then asked if these hotspots were genes. A hotspot has a high frequency of recombination events.
“We isolated genetic markers between the a1 and sh2 genes and used them to ask–for each recombinant–where did the crossover happen? Did it occur on this side or that side of a particular marker? Eventually, we could physically map where each recombination event happened along the chromosome,” Schnable explained.
The map showed that not all recombination was occurring in genes and not all genes were hotspots for recombination.
“Our finding changes our thinking about how the cellular machinery decides where crossovers occur,” Schnable said. “The real burning question now is: what controls where recombination events are occurring?”
Schnable and his colleagues are investigating that question now.
“We’re taking two approaches. One is to make mutations in maize genes that are similar to yeast genes and are known to be involved in recombination and see what effect that has in selection of recombination sites,” Schnable said. “The other is to shuffle the DNA on maize chromosomes to see if we can change the patterns of recombination.”