The composition of secondary cell wall determines the industrially relevant wood properties in tree species. Hence, its biogenesis is one of the most extensively studied developmental processes during wood formation. Presently, systems genetics approach is being applied to understand the biological networks and their interactions operational during secondary development. Genome-scale analyses of secondary cell wall formation were documented and gene regulatory networks were reported in Arabidopsis, poplar, pine, spruce, rice and sugarcane. In the present study, the expression patterns of 2651 transcripts representing different pathways governing secondary development was documented across four genotypes of E. tereticornis. A co-expression network was constructed with 330 nodes and 4512 edges and the degree ranged from 11 to 53. The network documented 75 (22 %) transcription factors with high degree of interaction. Secondary wall associated NAC domain transcription factor (SND2) was identified as the top hub transcript with 53 interactions. The present study revealed that functional homologs regulating secondary cell wall formation are conserved among angiosperms and gymnosperms.