Research Activities


Research in our lab is centered around the natural haploid induction system in potato and the centromere-mediated genome elimination system in the plant model, Arabidopsis thaliana. The natural haploid induction system in potato is still poorly characterized and we hope to learn more about potato haploid induction using genomic techniques that we have developed for the centromere-mediate genome elimination system in Arabidopsis. We are interested to understand how these two phenomena are connected as well as the evolutionary consequences of such drastic changes to the genome.

Potato Research


Cultivated potato (Solanum tuberosum Group Tuberosum) is tetraploid, which means that it contains four copies of each chromosome, with a total of 48 chromosomes (2n = 4x = 48). Therefore, potato breeding tends to be complex and takes a long time. In order assist in potato improvement efforts, we plan to utilize the natural haploid induction cross in potato, coupled with genomic analyses to test methods that may lead to new varieties in a shorter period of time.

As a proof of concept, we are developing and characterizing dihaploid potato populations generated via haploid induction crosses to test our hypothesis. This research is part of a collaboration between the Comai Lab at the University of California, Davis and the International Potato Center in Lima, Peru.

Arabidopsis Research


The model system for plants is an unassuming, small plant in the mustard family known as Arabidopsis thaliana. Despite its "weedy" appearance, it is a highly sophisticated, advanced genetic tool that is indispensable for basic and applied genetics research. A. thaliana is typically diploid, with ten chromosomes (2n = 2x = 10) and has a monoploid genome size of about 125 million base-pairs (125 Mb).

Unlike potato, Arabidopsis does not have a natural genome elimination system. Therefore, a pivotal advance was made when Ravi & Chan (Nature 2010) discovered that we can artificially induce genome elimination by making changes to the centromere-specific histone, CENH3. This technique allows for the creation of haploid inducers in any plant species by making modifications to the CENH3 gene. We plan to leverage the many tools available in Arabidopsis to help test hypotheses that will not only help with efforts to improve important food crops, but will also provide molecular insight on chromosome evolution.

Chromothripsis


An unexpected outcome from genome elimination crosses in Arabidopsis is the creation of highly rearranged chromosomes that have undergone chromothripsis, or chromosome shattering. Because chromothripsis was first described in cancer and has been implicated in the progression of cancer, the occurence of chromothripsis during genome elimination provides a unique opportunity to gain more insight in this phenomenon.


Chromothripsis (chromosome shattering), observed here as rapidly oscillating copy number changes, can occur on all five chromosomes in Arabidopsis

We are currently pursuing a whole genome sequencing, RNA-seq and proteomics approach to characterize chromothripsis during genome elimination. We are also interested in the evolutionary consequences of chromosomes that have undergone chromothripsis because we have shown that these chromosomes can be transmitted to the next generation.

If you have any questions on genome elimination in potato or Arabidopsis, please send me an email.