Abstract
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.
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The transcriptome data generated through this research have been submitted to NCBI SRA database with Bio Project ID: PRJNA415556. All supplementary files supporting results of this research work are submitted to the Harvard Dataverse and can be access https://doi.org/10.7910/DVN/DZ9SZP.
Abbreviations
- TDZ:
-
1-Phenyl-3-(1,2,3-thiadiazol-5-yl) urea (thidiazuron)
- 2,4-D:
-
2,4-Dichlorophenoxyacetic acid
- 2-iP:
-
2-Isopentenyladenine
- BP:
-
Biological processes
- C-SD:
-
Castor cultured tissues
- CC:
-
Cellular components
- CC:
-
Control castor
- CPM:
-
Count per million
- DAC:
-
Days after culture
- DEGs:
-
Differentially expressed genes
- FPKM:
-
Fragments per kilobase per million mapped fragments
- GO:
-
Gene ontology
- IAA:
-
Indoleacetic acid
- JC:
-
Jatropha control
- J-SD:
-
Jatropha cultured tissues
- KN:
-
Kinetin
- MF:
-
Molecular function
- MS:
-
Murashige and Skoog
- BA:
-
N6-Benzyladenine
- RIN:
-
RNA integrity number
- SAM:
-
Shoot apical meristem
- SC:
-
Sunflower control
- S-SD:
-
Sunflower cultured tissues
- WAT1:
-
Walls Are Thin1
- NAA:
-
α-Naphthaleneacetic acid
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Acknowledgements
SSP, TM and SM thank the Director, ICAR-IIOR for providing the necessary facilities for carrying out the research work.
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The work was carried out at ICAR-IIOR without any funding support.
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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.
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Puvvala, S.S., Muddanuru, T., Thangella, P.A.V. et al. Deciphering the transcriptomic insight during organogenesis in Castor (Ricinus communis L.), Jatropha (Jatropha curcas L.) and Sunflower (Helianthus annuus L.). 3 Biotech 9, 434 (2019). https://doi.org/10.1007/s13205-019-1960-9
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DOI: https://doi.org/10.1007/s13205-019-1960-9