The present invention provides methods for modulating cellulose, hemicellulose and lignin composition and deposition in secondary cell wall layers of plants to improve plant traits that are commercially desirable (e.g., enhanced digestibility of forage crops by animals, increased post-harvest processing of wood and crops for energy production and pulping, increase mechanical strength of plants, and others). The invention also provides methods for identifying genes encoding transcription factors that regulate the formation of secondary cell walls, polynucleotide sequences that encode key components of secondary cell walls, and transgenic plants comprising these sequences.