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
Conventional 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 part of the Potato 2.0 community, a collaborative effort between public potato breeding programs in the United States that is funded by USDA-NIFA SCRI, we have begun the development of pre-breeding material that can be used towards diploid potato breeding. We take some of the best conventional potato clones from the Eastern potato breeding region and are actively performing haploid induction crosses to generate a pool of primary dihaploids. This effort also provides an opportunity for the lab to study disease resistance traits in some of these primary dihaploids for genetic mapping experiments. This complements conventional potato breeding programs as genetic markers developed by this method can be utilized by both diploid and conventional potato breeding.
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. Instead, 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.
If you have any questions on genome elimination in potato or Arabidopsis, please send me an email.