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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



Pubmed report


Little tribe of tomato people discovered in a Davis field

Tomato man.png September 19 2011. We have made contact with a tribe of small tomato people. The little fellas are very boisterous and delighted to speak to humans. The one in this picture is a live wire and told us his name is "Luigi Pomodoro". He claims to be a prophet among the tomato people. Luigi Pomodoro is scheduled to appear on the major late evening TV shows. Stay tuned: he is guarnteed to sauce them up.

Recently published or in press

Samba.png Victor Missirian et al. describe a efficient computational method, called CAMBa, to identify mutants from pooled resequencing data. The paper explains the bioinformatics component of our TILLING-by-sequencing method and appeared in BMC Bioinformatics. More on the TILLING_by_Sequencing page.
3d.png In a paper in Plant Physiology, Helen Tsai et al. describe the use of Illumina sequencing for TILLING populations of rice and wheat. The image above illustrates a tri-dimensional pooling strategy to identify mutant individuals for genes of interest in large populations. Methods and data from this work are available on the TILLING_by_Sequencing page.
Chr4 ih.png Isabelle Henry et al. characterize the aneuploids of Arabidopsis. They conclude that multiple developmental phenotypes can be explained simply by the dosage of one or two chromosomes and are insensitive to the imbalance of others. They demonstrate that karyotyping can be easily accomplished by low-density sequencing with Illumina. Unexpectedly, the diploid progeny of trisomics are not fully wild-type but exhibit distinct alterations in development. The paper, entitled "Phenotypic consequences of aneuploidy in Arabidopsis thaliana", was published in the journal Genetics. The image above demonstrates that effect of a terminal translocation of chr 4 onto one copy of a trisomic chromosome.

TILLING workshops

A TILLING training workshop was held Aug 24 and 25 2009, and Aug 23 and 24 2010 in Davis. An additional one is planned for August 2011.

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.

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