Chloroplast phenomics: systematic phenotypic screening of chloroplast protein mutants in Arabidopsis

As part of a project to analyze chloroplast functional networks systematically, we have subjected mutants in >3,200 nuclear genes predicted to encode chloroplast-targeted proteins in Arabidopsis thaliana (http://www.plastid.msu.edu) to parallel phenotypic assays. Detailed methods are presented for the various assays being used in this project to study chloroplast biology. These include morphological analysis of plants, chloroplasts, and seeds using controlled vocabulary. Metabolites synthesized in the chloroplast such as starch, amino acids, and fatty acids are analyzed in groups according to their chemical properties. As an indicator for the relative composition of seed storage oil and proteins, the carbon and nitrogen contents are determined by an elemental analyzer. The methods in this chapter describe how the assays are configured to run in relatively high throughput, maximizing data quality.