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(Research)
(Funding sources)
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===Funding sources===
 
===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.
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Our research is funded by the Department of Energy grant 201118510 (Creation of High-Precision Characterization of Novel Poplar Biomass Germplasm) and by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation through Grant GBMF3068 (Chan research). Recent previous support was from 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.

Revision as of 13:42, 6 April 2013

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Contents

Research

The Comai Lab is in the Department of Plant Biology and the UC Davis Genome Center. We study how chromosome number, type, and hybridization affect gene regulation, development and genome evolution. Our model systems are Arabidopsis thaliana, rice, poplar and tomato. With collaborators, we are continuing the work of our colleague Simon Chan investigating the role of Centromeric Histone 3 in centromere function. We are developing improved methods for TILLING to efficiently discover mutations in plant genes. Click on the research links below to find out more.

Polyploidy, Heterosis, Centromeres, and TILLING

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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. A copy of CAMBa2.0 can be downloaded here.
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 2013. 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 Department of Energy grant 201118510 (Creation of High-Precision Characterization of Novel Poplar Biomass Germplasm) and by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation through Grant GBMF3068 (Chan research). Recent previous support was from 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.

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