Deciphering the transcriptomic insight during organogenesis in Castor (Ricinus communis L.), Jatropha (Jatropha curcas L.) and Sunflower (Helianthus annuus L.)
Cultivation of the castor crop is hindered by various factors and one of the approaches for genetic improvement of the crop is through exploitation of biotechnological tools. Response of castor tissues to in vitro culture is poor which necessitated this study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis and by comparing with jatropha and sunflower having good regeneration ability. Transcriptome profiling analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Differentially expressed genes 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, vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were up-regulated accounting for regeneration recalcitrance. Validation of 62 DEGs through qRT-PCR showed a consensus of 77.4% of the genes expressed. Overall study provides 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.
KeywordsAuxins Castor Callus DEGs RNA-seq Organogenesis
1-Phenyl-3-(1,2,3-thiadiazol-5-yl) urea (thidiazuron)
Castor cultured tissues
Count per million
Days after culture
Differentially expressed genes
Fragments per kilobase per million mapped fragments
Jatropha cultured tissues
Murashige and Skoog
RNA integrity number
Shoot apical meristem
Sunflower cultured tissues
Walls Are Thin1
SSP, TM and SM thank the Director, ICAR-IIOR for providing the necessary facilities for carrying out the research work.
SM conceived the idea, work plan, interpretation, data analysis and guided the work. SSP was involved in tissue culture work, RNA isolation and manuscript preparation; TM in tissue culture experiments, data recording, RNA isolation, qRT-PCR experiments; PAVT & AKO in wet lab data interpretation and analysis. Sequencing, transcriptome analysis, bioinformatic analysis, data interpretation done by: NC, SG, VKV, AVSKMK, SPL, BK, and VBRL. Manuscript preparation and critical comments performed by PAVT, AKO, SSP, SM SG and VBLR.
The work was carried out at ICAR-IIOR without any funding support.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
This research does not perform any experiment on human and animals. Hence all the authors declare that there is no non-compliance with ethical standards.
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