SAGE profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda)

Abstract

Wood formation has been studied extensively at the cellular and biochemical levels, but remains poorly understood with respect to gene expression and regulation. As a first step toward identifying genes specifically involved in wood formation and characterizing their roles in determining wood quality, serial analysis of gene expression (SAGE) was used to quantify gene expression in lignifying xylem from a single, 10-year-old loblolly pine (Pinus taeda L.). Two SAGE libraries were generated based on lignifying xylem isolated from either the upper (crown) or lower (base) portions of the trunk. Over 85,000 tags representing a maximum of 27,398 expressed genes were analyzed from the crown wood library, and more than 65,000 tags, representing a maximum of 25,983 expressed genes, were analyzed in the base wood library. Combining these data sets to reflect the sum of genes expressed in lignifying xylem, 150,855 tags were cataloged, representing a maximum of 42,641 different genes. Currently, this study represents the most extensive analysis of its kind in a higher plant and provides a quantitative description of the transcriptome representing the lignifying xylem of a 10-year-old loblolly pine.