Chloroplast Phenotypic Analysis Overview


The Chloroplast Phenomics Project is running a variety of phenotypic assays nuclear-encoded chloroplast-targeted genes and genes with potential roles in photosynthesis and amino acid metabolism. The phenotypic data and sample tracking information are stored in a relational database and can be queried using a set of tools that can be accessed through this website. You can use these software tools by clicking here; these tools allow the user to see whether there are data for mutants of a gene (use AGI query), or search for mutants with a specific allele designation [use Search by Query Term(s)]. Alternatively, it is possible to do an in silico mutant screen [use Search by Assay Results]. User beware: queries return all genes that have a mutant with one or more individuals exhibiting the queried characteristic. These are first-pass-mutant-screening data and you should scrutinize the data carefully to evaluate the consistency of the results.

Simple Boolean logic is supported for phenotypic queries. Note that we only include data for insertion alleles if a homozygous mutant is found; those mutants with no homozygous mutants should not be returned in searches. It is also possible to link to external sites for more information about the gene or allele of interest (currently TAIR at Carnegie Institution and BAR at University of Toronto).

The software is designed to work with Explorer 7.0 and higher and Mozilla Firefox 2.0 and higher. If you use other browsers and discover unexpected behavior, please let Ashley Shillinger ( know. Beginning users are encouraged to access the help document from each page of the database tools.

Questions about the project or suggestions about new search tools should be directed to Rob Last (

If you publish results that are enabled by the data from this project, please site Ajjawi et al (2010) Plant Physiology 152:529-540. If you use protocols or approaches from this project, please cite Lu et al (2008) Plant Physiology 146:1482-1500. The database and query tools accessible from this site are described in Lu et al (2011) Plant Physiol. 155: 1589-1900. The work is supported by NSF grants MCB-0519740, MCB-1119778 and MCB-1244008.