MEASURING OF THE ALTERATION OF RETROTRANSPOSITION IN THE RESPONSE OF SALINITY STRESS USING IRAP AND SCOT MARKERS

Abstract

Retrotransposons comprise the major part of eukaryotic genomes. They have the ability to replicate themselves through RNA intermediate via reverse transcription process. During normal development, these elements become quiescent, but they are stimulated by stresses. The availability of PCR-based techniques to detect the variation in retrotransposition rate due to salinity was tested. IRAP and SCoT markers were applied in two salinity-tolerant eukaryotic genomes: Yeast (Saccharomyces cerevisiae L.) and Barley (Hordeum vulgare L.). The genomes of the yeast strain EMCC49 and two barley cultivars Giza-123 and Giza2000 were extracted. Five IRAP primers with two combinations and nine SCoT primers were applied. The yeast strain was grown in the YPG media with 0.5 M, 1 M, 1.5 M NaCl or the control. The barley cultivars were irrigated with 0.25 M, 0.6 M NaCl or just distilled water. IRAP technique developed three markers in the yeast under the different levels of salinity. ScM1 IRAP primer showed a band with molecular size of 456 bp in the yeast under 0.5 and 1.5 M only. Another band with molecular size of 409 bp appeared under the control and disappeared in all salinity treatments. The third IRAP marker was shown by the ScM2 primer with molecular size of 1952 bp under the 0.5 M treatment. While, two IRAP markers appeared in barley due to high salt conditions. The 5'LTR IRAP primer showed an 886 bp band in the barley cultivar Giza2000 under the control condition only. Sukkula IRAP primer displayed the second IRAP marker in the cultivar Giza-2000 of barley with molecular size of 330 bp under the 0.6 M only. SCoT markers showed 17 markers in the response of salinity stress in yeast with molecular sizes ranged from 1911 to 271 bp with SCoT 31 and SCoT 26 primers, respectively. SCoT 26 primer gave the highest number of markers per SCoT primer (five different markers). In barley, 18 SCoT markers were detected under high salt conditions. They molecular sizes were between 1762 (SCoT 26) and 281 bp (SCoT 7). SCoT 32 primer showed five markers in barley under salinity as the highest number of markers per SCoT primer. The results showed different patterns between control and treatments and the high levels of salinity led to new retrotransposition. This study confirmed that PCR techniques; like IRAP and SCoT can exhibit the activation of retrotransposition due to high salt conditions. Good positive results were obtained and we recommend using these techniques for different molecular purposes due to their advantage; easy, fast, cheap and effectiveness.