Phenotypic, genotypic, and transcript level (microarray) data from an interspecific backcross population of Eucalyptus grandis and Eucalyptus globulus were integrated to dissect the genetic and metabolic network underlying growth variation. Transcript abundance, measured for 2,608 genes in the differentiating xylem of a 91 (E. grandis 3 E. globulus) 3 E. grandis backcross progeny was correlated with diameter variation, revealing coordinated down-regulation of genes encoding enzymes of the lignin biosynthesis and associated methylation pathways in fast growing individuals. Lignin analysis of wood samples confirmed the content and quality predicted by the transcript levels measured on the microarrays. Quantitative trait locus (QTL) analysis of transcript levels of lignin-related genes showed that their mRNA abundance is regulated by two genetic loci, demonstrating coordinated genetic control over lignin biosynthesis. These two loci colocalize with QTLs for growth, suggesting that the same genomic regions are regulating growth, and lignin content and composition in the progeny. Genetic mapping of the lignin genes revealed that most of the key biosynthetic genes do not colocalize with growth and transcript level QTLs, with the exception of the locus encoding the enzyme S-adenosylmethionine synthase. This study illustrates the power of integrating quantitative analysis of gene expression data and genetic map information to discover genetic and metabolic networks regulating complex biological traits.Wood is composed of secondary xylem, a highly specialized conductive and structural support tissue produced by lateral growth and differentiation of the meristematic vascular cambium (Fukuda, 1996). Genes expressed during the developmentally regulated process of xylogenesis determine the physical and chemical properties of wood. The product of xylogenesis represents one of the world's most important natural resources, yet relatively little is known about the genetic regulation of this process. Wood serves as a renewable source of energy, and it is a sink for atmospheric carbon. Wood is also the raw material for the global pulp and paper, and timber industries. The growth and development of trees and other woody plants are fundamental determinants of the dynamics and composition of forest ecosystems.At the plant cell level, growth is determined by cell division and expansion. Expansion is driven primarily by internal osmotic pressure generated by water uptake. Expansion is constrained by the cell wall and depends on cell wall composition and the degree of association between its different components (Buchanan et al., 2000). Growth of secondary xylem results from a sequential developmental process that begins with cambial cell division, followed by cell expansion, secondary wall formation, lignification, and programmed cell death (Fukuda, 1996). Wood growth has been associated with the number and rate of cell divisions at the meristematic cambium (Gregory and Wilson, 1968;Wilson and Howard, 1968;Zobel and van Buijtenen, 1989...