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Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.)

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Abstract

Background

Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs.

Method

The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed.

Results

In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively.

Conclusions

The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.

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Data availability

The datasets supporting the conclusions of this article are included in this.

Abbreviations

P:

Phosphate

Pi:

Inorganic phosphate

mRNA:

Messenger RNA

miRNA:

MicroRNA

C:

Complete fertiliser (dozage based on standard procedure)

P0:

SOP fertiliser without phosphate

F0:

No fertilizers

RT-qPCR:

Reverse transcription-quantitative polymerase chain reaction

DxP:

Oil palm progeny that from Dura and Pisifera crossing called Tenera

Ho_P0:

Hoagland solution medium with 0% phosphorus

Ho_P65:

Hoagland solution medium with 65% phosphorus

ABMix:

Standard commercial nutrient solution

cDNA:

Complementary DNA

LncRNA:

Long non-coding RNA

sRNA:

Small RNA

rRNA:

Ribosome RNA

GO:

Gene ontology

BLAST:

Basic local alignment search tool

RP:

Reverse primer

FP:

Forward primers

Ct:

Cycle thresholds

MFE:

Minimum free energy

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Acknowledgements

We thank Ogi Ajitio Ramadhan and Redy Wahyu Permana for their technical support. We thank Reno Tryono, Redi Aditama, and Chris Darmawan, who read and improved the manuscript.

Funding

This work was funded by PT SMART Tbk under a research project code 3.1.1.057.

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Authors and Affiliations

  1. Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia

    Tengku Imam Saputra,  Roberdi & Sigit Dwi Maryanto

  2. Bioinformatics Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia

    Zulfikar Achmad Tanjung

  3. Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia

    Condro Utomo

  4. Division of Plant Production and Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia

    Tony Liwang

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Contributions

TIS, RBD, and SDM: conceived and designed the experiments. TIS and SDM: performed the experiments. TIS and ZAT: analyzed the data. TIS and RBD: wrote the paper. CU and TL: funding acquisition, review and supervision. All authors have read and approved the final manuscript.

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Correspondence to Tengku Imam Saputra.

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Saputra, T.I., Roberdi, Maryanto, S.D. et al. Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.). Mol Biol Rep 50, 5609–5620 (2023). https://doi.org/10.1007/s11033-023-08484-4

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