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3 Biotech

, 9:434 | Cite as

Deciphering the transcriptomic insight during organogenesis in Castor (Ricinus communis L.), Jatropha (Jatropha curcas L.) and Sunflower (Helianthus annuus L.)

  • Sai Sudha Puvvala
  • Tarakeswari Muddanuru
  • Padmavathi A. V. Thangella
  • O. Aniel Kumar
  • Navajeet Chakravartty
  • Vineeth Kodengil Vettath
  • A. V. S. K. Mohan Katta
  • Sivarama Prasad Lekkala
  • Boney Kuriakose
  • Saurabh GuptaEmail author
  • Sujatha MulpuriEmail author
  • Vijaya Bhaskar Reddy Lachagari
Original Article

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.

Keywords

Auxins Castor Callus DEGs RNA-seq Organogenesis 

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

Notes

Acknowledgements

SSP, TM and SM thank the Director, ICAR-IIOR for providing the necessary facilities for carrying out the research work.

Author contributions

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.

Funding

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.

Ethical standards

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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Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  • Sai Sudha Puvvala
    • 1
    • 2
  • Tarakeswari Muddanuru
    • 2
  • Padmavathi A. V. Thangella
    • 3
  • O. Aniel Kumar
    • 1
  • Navajeet Chakravartty
    • 4
  • Vineeth Kodengil Vettath
    • 5
  • A. V. S. K. Mohan Katta
    • 4
  • Sivarama Prasad Lekkala
    • 4
  • Boney Kuriakose
    • 5
  • Saurabh Gupta
    • 4
    Email author
  • Sujatha Mulpuri
    • 2
    Email author
  • Vijaya Bhaskar Reddy Lachagari
    • 4
  1. 1.Andhra UniversityVisakhapatnamIndia
  2. 2.ICAR-Indian Institute of Oilseeds Research (Formerly DOR)HyderabadIndia
  3. 3.Osmania UniversityHyderabadIndia
  4. 4.AgriGenome Labs Pvt. Ltd, BTIC, MN iHubGenome ValleyHyderabadIndia
  5. 5.AgriGenome Labs Pvt. LtdSmartCity KochiKakkanadIndia

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