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

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.