2006 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Virginia Polytechnic Institute and State University. Additional details of the research can be found in the report for the parent project 1275-21000-172-00D “Genetic enhancement of quality constituents and disease resistance in Solanaceous vegetables.” Color attributed to anthocyanins contributes to product sensory quality attributes, potential nutritive value, and plant stress response. A Capsicum (pepper) line we have developed, 02C27, accumulates anthocyanin in various tissues and accumulation is markedly sensitive to environmental stress. Real-time PCR analysis of tissues that varied in anthocyanin pigmentation intensity in response to environmental conditions and virus infection revealed functional but differentially expressed structural genes in the anthocyanin biosynthetic pathway. Likewise, analysis of three transcription factor encoding genes demonstrated differential expression of these regulatory elements, coincident with anthocyanin accumulation. These results enable us to now investigate transcription factor protein interactions in order to characterize mechanisms of gene regulation. The results are important for identification of key regulatory elements that influence anthocyanin accumulation and will result in new knowledge to facilitate enhancement of anthocyanin content in pepper and related crops. The research combines the complementary expertise at ARS and Virginia Tech and is cooperative with the ARS Floral and Nursery Products Research Unit in Beltsville.