Plant Biotechnology 23, 437–450 (2006)

Biotechnology requires robust and predictable expression of transgenes. Most commercial Genetically Modified (GM) crops contain the viral 35S promoter to drive insecticide and herbicide resistance genes. In cotton there have been reductions in efficacy of Bacillus thuringiensis toxin (Bt) expressing plants late in the season that have been attributed to reductions in promoter activity. We have used genomic approaches to identify cotton genes whose expression remains high during the season to find promoters that might better maintain expression of transgenes in the field. A cDNA library from young late season leaves was used to generate about 2000 ESTs. Clustering of ESTs was used to determine relative transcript abundance and identify the most highly-expressed genes. These were primarily photosynthetic and housekeeping genes and some metabolic genes. The ESTs were printed to a small cDNA microarray and probed with both earlyand lateseason leaf mRNAs. Absolute fluorescence levels were used to rank genes and confirm the EST abundance data. Candidate genes, including the small subunit of Rubisco (RbcS) were selected. An RbcS promoter (Genbank Accession DQ648074) was isolated and analysed in both Arabidopsis and cotton linked to a GUS reporter gene. Expression of the reporter gene was consistently high in green tissues throughout the life cycle of cotton in the glasshouse, and in the field. A number of other candidate promoters have been identified that may be useful in a variety of biotechnology applications.