A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs

Abstract

Induction of a pluripotent cell mass termed callus is the first step in an in vitro plant regeneration system, which is required for subsequent regeneration of new organs or whole plants. However, the early molecular mechanism underlying callus initiation is largely elusive. Here, we analyzed the dynamic transcriptome profiling of callus initiation in Arabidopsis aerial and root explants and identified 1342 differentially expressed genes in both explants after incubation on callus-inducing medium. Detailed categorization revealed that the differentially expressed genes were mainly related to hormone homeostasis and signaling, transcriptional and post transcriptional regulations, protein phosphorelay cascades and DNA- or chromatin-modification. Further characterization showed that overexpression of two transcription factors, HB52 or CRF3, resulted in the callus formation in transgenic plants without exogenous auxin. Therefore, our comprehensive analyses provide some insight into the early molecular regulations during callus initiation and are useful for further identification of the regulators governing callus formation.

A transcriptional view on somatic embryogenesis

“…Direct SE appears to involve less reprogramming than indirect SE and probably occurs in cells where totipotency genes are transcriptionally accessible. The involvement of more extensive chromatin remodeling during indirect SE is suggested by the differential expression of many chromatin modifiers after 2,4‐D‐induced callus formation from protoplasts, leaves, hypocotyls, and roots (Chupeau et al., 2013; Xu et al., 2012). …”

Transcriptome analysis indicates that GmAGAMOUS-Like 15 may enhance somatic embryogenesis by promoting a dedifferentiated state

“…A number of studies have examined transcriptomes in response to dedifferentiation including (but not limited to) those of Xu et al 19 where a timecourse comparing explant tissue to tissue placed for 12, 24, 48 and 96 hours on callus-induction medium that contains 2,4-D (2.2 mM) and kinetin (0.2 mM). The explants were aerial or root fragments from 10 day old seedlings.…”

“…There also does not appear to be much overlap between root markers (according to Brady et al 18 , sum of AGL42, RM1000 and S4 lists) and the list of "dedifferentiation-associated" TFs 13 with only 2 genes on both lists (At1g69490 and At4g34000). For the data sets of Xu et al 19 all of the dedifferentiation TFs that show a significant change in transcript accumulation during callus induction are down regulated when roots are used as explants (23 of the list of 44 TF genes), but 8 are upregulated when the explants are derived from shoots. In general, there does not appear to be much correlation between the TFs associated with dedifferentiation and at least some types of de-or redifferentiation.…”

“…Although amount of time on hormone containing medium could make a difference as found for AGL15, the dataset in ref. 19 included early timepoints (24 and 49 hours).…”

“…This AP2/ERF TF does not cause root meristem marker expression and in fact some markers are downregulated. 22 Of the QC list of Brady et al, 19 4 genes are upregulated by 35Spro:WIND1, and 14 genes are downregulated. Interestingly twelve of the TF genes associated with dedifferentiation are significantly upregulated by 35Spro:WIND1, but none are repressed.…”