July 6, 2010

For the better part of eight years, University of Kentucky College of Agriculture researcher Seth DeBolt has wanted to focus study efforts toward how much duplications and deletions in the plant genome influence natural variation. His recent discoveries on this subject suggest the answer is ‘a lot' and could have broad implications on crop science, evolutionary biology and genome evolution.

"A. thaliana is the model plant, and plant biologists worldwide grow it to better understand plant growth and development at a molecular level," said DeBolt, assistant professor in the Department of Horticulture. "With this experiment, I was trying to understand what influences natural variation. I've always been curious about the genomic differences between the plants I may be studying in my lab due to my particular experimental conditions and the force and selection that I impose, and what I found was surprising."

DeBolt said A. thaliana is an annual plant that grows and regenerates very quickly, in about six weeks. It is a weed that's often found growing between cracks in pavement during spring, and it produces an enormous amount of seed.

"The seeds disperse around this, quite often, unpleasant environment, and so small changes in the genome structure may allow natural variations that can give the plant an adaptive advantage," he said.

DeBolt started growing A. thaliana plants at three different temperatures and sprayed an alterative lineage with salicylic acid-a hormone plants use for defense- while imposing a reference temperature and spray regime for each treatment.

"Every generation, from a tray of plants, I'd select the one with the most seed and regrow that plant," he explained. "I essentially applied force and selection for five generations derived from a single parent seed."

For each of the five lineages, DeBolt used three completely random sibling plants and compared them to siblings from the reference genome lineage.

"I wanted to know if there were subtle differences because of copy number variation that were stably incorporated into a lineage, and what I found was that there is an incredible amount of change," he said. "In one instance, more than 400 genes were different and, to me that suggests that plants are probably prolific gene duplicators and deleters. So, they can manage copy number variation in a population."

Gene copy number variation refers to the number of copies of a specific gene or genetic segment in the genetic code that vary between two individuals in a population. 

"So overall, does copy number variation influence growth potential, flowering potential, disease resistance and so on?" DeBolt said. "We don't know that yet, but this study lays the groundwork for further research that could answer those questions. We want to see if this variation phenomenon is linked to adaptation."

He added that although the experiment was very simple, it shows that stable incorporation of gene copy number variation is happening a lot faster than originally thought.

"It's the way robustness is built into a population, that it has enough variation to adapt to change," he said. "We have to be cautious in that this is only one step showing adaption, but I think it shows a surprising result."

Debolt's lab is funded by the National Science Foundation and a paper explaining his recent work will appear in the Journal of Genome Biology and Evolution. It's titled Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales.