From Comaiwiki

Revision as of 08:08, 16 February 2013 by Root (Talk | contribs)

Flowers.jpg

Contents

Research

The Comai Lab is in the Department of Plant Biology and the UC Davis Genome Center. One part of the laboratory studies how chromosome number and type affect gene regulation, development and genome evolution. Our model systems are Arabidopsis thaliana and rice. The other laboratory part is adapting next generation sequencing to a functional discovery tool called TILLING. We are developing methods and services to efficiently find mutations in genes of interest in rice, wheat, tomato, and tetraploid Arabidopsis. Click on the research links below to find out more.

Polyploidy, Heterosis, and TILLING

_______________________________

Publications

Pubmed report

News

Recently published or in press

Tetraploid tilling.png Helen Tsai and colleagues demonstrate that treating Arabidopsis thaliana Col-0 autotetraploid with EMS results in high density mutations. A 500-individual population allows searches of KOs with an efficiency comparable to that of very large tagging populations. The paper can be accessed freely in Plant Physiology.
Rescan adapters.png Jennifer Monson-Miller et al. describe the Comai lab method for reduced complexity sequencing, called RESCAN. In collaboration with the Tai lab they demonstrate its use for mutation discovery in rice (BMC Genomics 2012, 13:72 link to journal). In collaboration with the Maloof and Chan labs the method was used for ultradense mapping of RIL lines made by dihaploid induction Seymour et al., PNAS.
Circos fee.png Why do certain plant varieties hybridize more easily with other species than others? Diana Burkart-Waco, Caroline Josefsson, et al. describe the mapping of quantitative trait loci determining the differential response to interspecific hybridization in Arabidopsis thaliana. The work, revealing a network of interacting loci, can be accessed freely in Plant Physiology.

TILLING workshops

A TILLING training workshop was held Aug 24 and 25 2009, Aug 23 and 24 2010, and August 22 and 23 2011. There is no workshop planned for 2012. We may resume our free workshop program if funding allows. Future workshop might include RESCAN and mutation discovery by exome capture.

Video tutorials on analysis of high throughput sequence data and on multiplexing

The Y adapter for Illumina sequencing We offer instructional video tutorials on manipulating and analyzing datasets from next-generation sequencing, as well as on sample multiplexing. The target audience is biologists who might use these techniques but would like to perform some of the analysis themselves.

Funding sources

Our research is funded by the National Science Foundation Plant Genome grant DBI-0733857 (Functional Genomics of Polyploids), NSF Plant Genome award DBI-0822383, (TRPGR: Efficient identification of induced mutations in crop species by ultra-high-throughput DNA sequencing), and National Institutes of Health R01 GM076103-01A1 (Dosage dependent regulation in hybridization) to LC.

Personal tools