Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Workshop: Abiotic Stress
            

LINKING PROTEOMIC AND GENOMIC ANALYSES OF ABIOTIC STRESS RESPONSES IN RICE AND OTHER CEREALS

¹ International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

Proteomic analysis is used at IRRI to examine the responses of different rice cultivars to drought and salt stresses at the vegetative and reproductive stages. Analysis is currently applied to “total” proteins extracted from roots, stems, leaves, panicles and selected constituent tissues rather than sub-cellular fractions. Out of more than 3000 proteins detectable on any given gel by silver stain, at least 1000 proteins may be reproducibly quantified by sampling in triplicate. In the case of leaf proteins from drought experiments, about 42 proteins are drought-responsive in terms of changes in abundance (at least 50% change in either direction) or position on 2D gels (reflecting post-translational modifications or differential splicing). The identity of the more abundant proteins may be examined by mass spectrometry (MS) – either MALDI-TOF MS for tryptic fingerprinting or ESI-Q-TOF MS/MS for partial internal sequencing. Post-translational modifications may frequently be identified and located by the same techniques. Bioinformatic linkage to protein and genomic databases is the key to the identification of proteins from MS data. Other links to genomics are provided by (a) the use of partial sequence data to design redundant primers for isolation of the corresponding cDNA and gene, (b) comparisons of 2D gel and microarray analyses, (c) analysis of gene expression across mapping populations and in transformants and mutants. The application of proteomics to cereal breeding programs is greatly assisted by these links.