The role of siRNAs in genome stability maintaining in the bread wheat introgression lines

  • A. G. Navalikhina
  • M. Z. Antonyuk
  • T. K. Ternovska


Aim. Deviations of the siRNAs levels from the parental ones in the plants with hybrid genomes are associated with the activation of transposable elements (TE). This, in turn, lead to the further genome rearrangements. Introgression lines Triticum aestivum / Amblyopyrum muticum are cytologically stable, however, there are visible signs of genetic and (or) epigenetic restructuring that are still going on. Molecular mechanisms of these processes are the subject of our study. Methods. The levels of siRNAs in the plant lemmas were determined by small RNA-seq. Reads of the small RNA libraries were aligned to the repeats to find siRNA sequences. Results. Introgression lines (ILs) and parental amphidiploid have variable levels of siRNAs regulating MITE and CACTA transposable elements, compared with the parental bread wheat variety. For twelve TE sequences, majority of which are CACTA elements, decrease in the levels of siRNAs in ILs and amphidiploid, compared to the wheat, is statistically significant. Decreased siRNAs levels could lead to the
activation of corresponding TE classes. Conclusions. Variation of siRNA levels in ILs and amphidiploid can be the key factor that cause rearrangements in their genomes. These include activation of TEs, changes in DNA methylation patterns, and gene expression variation. Therefore, detected changes in siRNA levels can be the molecular mechanisms of the processes that occur in studied hybrid genomes.

Keywords: siRNA, transposable elements, amphidiploid, introgression lines.


Liu B., Vega J. M., Segal G. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops.I. Changes in low-copy noncoding DNA sequences. Genome. 1998. Vol. 277. P. 272-277. doi: 10.1139/gen-41-2-272

Ozkan H., Levy A., Feldman M. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. The Plant Cell. 2001. Vol. 13 (8). P. 1735-1747. doi: 10.1105/TPC.010082

Shaked H., Kashkush K., Ozkan H. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. The Plant Cell. 2001. Vol. 13 (8). P. 1749-1759. doi: 10.1105/tpc.13.8.1749

Wang Y., Dong Z., Zhang Z. Extensive de novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics. 2005. Vol. 170. P. 1945-1956. doi: 10.1534/genetics.105.040964

Wang G., Lv J., Zhang J. Genetic and epigenetic alterations of brassica nigra introgression lines from somatic hybridization: A resource for cauliflower improvement. Front Plant Sci. 2016. Vol. 7. P. 1-12.

Liu B., Wendel J.F. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome. 2000. Vol. 880. P. 874-880. doi: 10.1139/g00-058

Shan X., Liu Z., Dong Z. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Molecular biology and evolution. 2005. Vol. 22 (4). P. 976-990. doi: 10.1093/molbev/msi082

Wang N., Wang H., Wang H. Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biology. 2010. Vol. 10 (190). P. 1-15. doi: 10.1186/1471-2229-10-190

Liu Z., Wang Y., Shen Y. Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia. Plant Molecular Biology. 2004. Vol. 54. P. 571-582. doi: 10.1023/B:PLAN.0000038270.48326.7a

Shuwei L., Fei L., Kong L. Genetic and epigenetic changes in somatic hybrid introgression lines between wheat and tall wheatgrass. Genetics. 2015. Vol. 199. P. 1035-1045. doi: 10.1534/genetics.114.174094

Shivaprasad P.V., Dunn R.M., Santos B.A. Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs. The EMBO Journal. 2012. Vol. 31. P. 257-266. doi: 10.1038/emboj.2011.458

Chen Z.J., Ni Z. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays. 2006. Vol. 28 (3). P. 240-252. doi: 10.1002/bies.20374

Chen Z.J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. 2007. Vol. 58. P. 377-406. doi: 10.1146/annurev.arplant.58.032806.103835

Jackson S., Chen Z.J. Genomic and expression plasticity of polyploidy. Current opinion in plant biology. 2010. Vol. 13 (2). P. 153-159. doi: 10.1016/j.pbi.2009.11.004

Michalak P. Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity. 2009. Vol. 102. P. 45-50. doi: 10.1038/hdy.2008.48

Erdmann V., Barciszewski J. Non Coding RNAs in Plants. Berlin: Springer, 2011. doi: 10.1007/978-3-642-19454-2

Iefimenko T.S., Antonyuk M.Z., Martynenko V.S. et al. Introgression of Aegilops mutica genes into common wheat genome. Tsitologiya i Genetika. 2018. Vol. 52 (1). P. 21-30. doi: 10.3103/S0095452718010048

Peng J., Xia Z., Chen L. Rapid and efficient isolation of high-quality small RNAs from recalcitrant plant species rich in polyphenols and polysaccharides. PLoS ONE. 2014. Vol. 9 (5). P. 12-14. doi: 10.1371/journal.pone.0095687

Bioo Scientific Corp. NEXTflex Small RNA-Seq Kit v3 / Bioo Scientific Corporation, 2016.

Wicker T., Matthews D.E., Keller B. TREP: a database for Triticeae repetitive elements. Trends in Plant Science. 2002. Vol. 7 (12). P. 561-562. doi: 10.1016/S1360-1385(02)02372-5

Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nature methods. 2012. Vol. 9 (4). P. 357-359. doi: 10.1038/nmeth.1923

Law C.W., Chen Y., Shi W. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome biology. 2014. Vol. 15. P. 1-17. doi: 10.1186/gb-2014-15-2-r29

Borges F., Martienssen R.A. The expanding world of small RNAs in plants. Nat Rev Mol Cell Biol. 2015. Vol. 16 (12). P. 727-741. doi: 10.1038/nrm4085

Wicker T., Gundlach H., Spannagl M. Impact of transposable elements on genome structure and evolution in bread wheat. Genome biology. 2018. Vol. 19 (1). P. 103. doi: 10.1186/s13059-018-1479-0

Daron J., Glover N., Pingault L. Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome biology. 2014. Vol. 15 (12). P. 546. doi: 10.1186/s13059-014-0546-4