An Integrated Transcriptome and Proteome Analysis Reveals Putative Regulators of Adventitious Root Formation in Taxodium 'Zhongshanshan'

Adventitious root (AR) formation from cuttings is the primary manner for the commercial vegetative propagation of trees. Cuttings is also the main method for the vegetative reproduction of Taxodium ‘Zhongshanshan’, while knowledge of the molecular mechanisms regulating the processes is limited. Here, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative proteomic (iTRAQ) analysis to measure changes in gene and protein expression levels during AR formation in Taxodium ‘Zhongshanshan’. Three comparison groups were established to represent the three developmental stages in the AR formation process. At the transcript level, 4743 genes showed an expression difference in the comparison groups as detected by RNA sequencing. At the protein level, 4005 proteins differed in their relative abundance levels, as indicated by the quantitative proteomic analysis. A comparison of the transcriptome and proteome data revealed regulatory aspects of metabolism during AR formation and development. In summary, hormonal signal transduction is different at different developmental stages during AR formation. Other factors related to carbohydrate and energy metabolism and protein degradation and some transcription factor activity levels, were also correlated with AR formation. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling AR formation.

Rooting of eucalypt cuttings as a problem-solving oriented model in plant biology

Species of Eucalyptus are some of the most planted trees in the world, providing fiber, cellulose, energy, and wood for construction and furniture in renewable fashion, with the added advantage of fixing large amounts of atmospheric carbon. The efficiency of eucalypts in forestry relies mostly on the clonal propagation of selected genotypes both as pure species and interspecific hybrids. The formation of new roots from cambium tissues at the base of cuttings, referred to as adventitious rooting (AR), is essential for accomplishing clonal propagation successfully. AR is a highly complex, multi-level regulated developmental process, affected by a number of endogenous and environmental factors. In several cases, highly desirable genotypes from an industrial point of view carry along the undesirable trait of difficulty-to-root (recalcitrance). Understanding the bases of this phenotype is needed to identify ways to overcome recalcitrance and allow efficient clonal propagation. Herein, an overview of the state-of-the-art on the basis of AR recalcitrance in eucalypts addressed at various levels of regulation (transcript, protein, metabolite and phenotype), and OMICs techniques is presented. In addition, a focus is also provided on the gaps that need to be filled in order to advance in this strategic biological problem for global forestry industry relying on eucalypts.