Transcriptomic analysis identifies differentially expressed genes(DEGs) associated with bolting and flowering in Saposhnikovia divaricata

Saposhnikovia divaricata is a valuable Chinese medicinal herb; the transformation from vegetative growth to reproductive growth may lead to the decrease of its pharmacological activities. Therefore, the study of bolting and flowering for Saposhnikovia divaricata is warranted. The present study aimed to reveal differentially expressed genes(DEGs) and regularity of expression during the bolting and flowering process, and the results of this study might provide a theoretical foundation for the suppression of early bolting for future research and practical application. Three sample groups, early flowering, flower bud differentiation, and late flowering(groups A, B, and C, respectively) were selected. Transcriptomic analysis identified 67, 010 annotated unigenes, among which 50, 165 were differentially expressed including 16, 108 in A vs B, and 17, 459 in B vs C, respectively. Gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway functional classification analysis were performed on these differentially expressed genes, and five important pathways were significantly impacted(P ≤ 0.01): plant circadian rhythm, other glycan degradation, oxidative phosphorylation, plant hormone signal transduction, and starch and sucrose metabolism. Plant hormone signal transduction might play an important role in the bolting and flowering process. The differentially expressed indole-3-acetic acid(IAA) gene showed significant down-regulation during bolting and flowering, while the transport inhibitor response 1(TIR1) gene showed no significant change during the bolting process. The expression of flowering related genes FLC, LYF, and AP1 also showed a greater difference at different development stages. In conclusion, we speculate that the decrease in auxin concentration is not caused by the degrading effect of TIR1 but by an alternative mechanism.

Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution

in this report, we compared transcriptomic differ- ences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids （SDR-H） and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expres- sion between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes （DEGs） between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigorallotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.