Deciphering the transcriptomic insight during organogenesis in castor (Ricinus communis L.), jatropha (Jatropha curcas L.) and sunflower (Helianthus annuus L.)

Background Castor is a non-edible oilseed crop with a multitude of pharmaceutical and industrial uses. Profitable cultivation of the crop is hindered by various factors and one of the approaches for genetic improvement of the crop belonging to a monotypic genus is to exploit biotechnological tools. The major limitation for successful exploitation of biotechnological tools is the in vitro recalcitrance of castor tissues. Response of castor tissues to in vitro culture is poor which necessitated study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis, by comparing with two other crops (jatropha and sunflower) with good regeneration ability. Results RNA-seq analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Genes that showed strong differential expression analysis during dedifferentiation and organogenic differentiation stages of callus included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis and homeostasis like WAT1 (Wall associated thinness), vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were upregulated accounting for regeneration recalcitrance. Validation of 62 differentially expressed genes through qRT-PCR showed a consensus of 77.4% with the RNA-Seq analysis. Conclusion This study provides information on the set of genes involved in the process of organogenesis in three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and genetic transformation in castor. * BA : N6–Benzyladenine BP : Biological processes CC : Cellular components CPM : Counts per million 2,4-D : 2,4-dichlorophenoxyacetic acid DEG : Differentially expressed genes/transcripts FPKM : Fragments per kilobase per million mapped fragments GO : Gene ontology IAA : Indoleacetic acid 2-iP : 2-isopentenyladenine KN : kinetin MF : Molecular function MS : Murashige and Skoog NAA : α-Naphthaleneacetic acid TDZ : 1-Phenyl-3-(1,2,3-thiadiazol-5-yl) urea (thidiazuron)