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Detection of somaclonal variations in tissue cultured date palm (Phoenix dactylifera L.) using transposable element-based markers

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Abstract

In vitro regeneration of date palm (Phoenix dactylifera L.) plants through somatic embryogenesis leads to the generation of somaclonal variants. The transposition of retrotransposons and DNA transposons in a host genome can be activated by tissue culture stresses, thus these elements can be both the cause of and useful markers for genomic variation. In this study, Hordeum-specific and Phoenix-specific inter-retrotransposon amplified polymorhism (IRAP) markers together with Phoenix-specific miniature inverted-repeat transposable element (MITE) markers were used to investigate the activation of DNA transposons and retrotransposons by somaclonal variation. Ty3/gypsy-like LTR retotransposons and MITE DNA transposon sequences were extracted from P. dactylifera cv. Khalas. Phoenix-specific primers were designed from the long terminal repeat (LTR) region of Ty3/gypsy-like LTR retotransposons and MITE DNA transposons. Both IRAP and MITE markers were able to detect somaclonal variants among date palms grown in open field trials. DNA marker analyses support that the transposability of both LTR retrotransposon and MITEs in the date palm genome is activated during the tissue culture process, leading to new insertion events in somaclonal variants. This study demonstrated a simple PCR-based method for the screening of somaclonal variants in tissue cultured date palm plants and establishes the application of transposible element based DNA markers for clonal identification.

Key message

This study demonstrated a simple PCR-based method for the screening of somaclonal variants in tissue cultured date palm plants and establishes the application of transposable element-based DNA markers for clonal identification.

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Acknowledgements

This work was supported by the Higher Education Commission (HEC), Islamabad, Pakistan and CEBAR grant RU006-2017, from the University of Malaya, Malaysia.

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Correspondence to Jennifer Ann Harikrishna.

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Communicated by Maria Margarida Oliveira.

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Figure S1 IRAP primer design. A) IRAP primers (PdGy01F and PdGy01R) designed from the 5’-end of PdGy01 Ty3/gypsy-like LTR retrotransposon; B) IRAP primers (PdGyChromo01F and PdGyChromo01R) designed from 3’-end of PdGyChromo01 Ty3/gypsy-like LTR retrotransposon (JPEG 747.5 kb)

Figure S2 IRAP profile for date palm plants of P. dactylifera cv. Gulistan showing monomorphic bands among mother plant (M) and tissue culture regenerants (1-30; 46-47). L: GeneRuler 1 kb DNA Ladder; C: negative control (JPEG 804.9 kb)

Figure S3 MITE profile for date palm of P. dactylifera cv. Gulistan showing monomorphic bands among mother plant (M) and tissue culture regenerants (1-30; 46-47). L: GeneRuler 1 kb DNA Ladder; C: negative control (JPEG 615.3 kb)

Figure S4 IRAP profile for date palm of P. dactylifera cv. Kashuwari showing monomorphic bands among mother plant (M) and tissue culture regenerants (1-15; 31-50). L: GeneRuler 1 kb DNA Ladder; C: negative control (JPEG 770.2 kb)

Figure S5 MITE profile for date palm of P. dactylifera cv. Kashuwari showing monomorphic bands among mother plant (M) and tissue culture regenerants (1-15; 31-50). L: GeneRuler 1 kb DNA Ladder; C: negative control (JPEG 655.2 kb)

Figure S6 Dendrogram of P. dactylifera cv. Gulistan showing control (mother plant), normal tissue cultured (TC) plants and somaclonal variant tissue cultured (TC) plants. (JPEG 124.7 kb)

Figure S7 Dendrogram of P. dactylifera cv. Kashuwari showing control (mother plant), normal tissue cultured (TC) plants and somaclonal variant tissue cultured (TC) plants. (JPEG 120.4 kb)

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Mirani, A.A., Teo, C.H., Markhand, G.S. et al. Detection of somaclonal variations in tissue cultured date palm (Phoenix dactylifera L.) using transposable element-based markers. Plant Cell Tiss Organ Cult (2020). https://doi.org/10.1007/s11240-020-01772-y

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Keywords

  • Date palm
  • Somaclonal variation
  • Micropropagation
  • MITEs
  • IRAP
  • Retrotransposons