Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines

Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China

More Information

Corresponding author: E-mail address: baoliu@nenu.edu.cn (Bao Liu)

These authors contributes equally to this work.

摘要

- /
- /
- /
Abstract: Previous studies have shown rapid and extensive genomic instability associated with early stages of allopolyploidization in wheat. However, these studies are based on either a few pre-selected genomic loci or genome-wide analysis of a single plant individual for a given cross combination, thus making the extent and generality of the changes uncertain. To further study the generality and characteristics of allopolyploidization-induced genomic instability in wheat, we investigated genetic and epigenetic changes from a genome-wide perspective (by using the AFLP and MSAP markers) in four sets of newly synthesized allotetraploid wheat lines with various genome constitutions, each containing three randomly chosen individual plants at the same generation. We document that although general chromosomal stability was characteristic of all four sets of allotetraploid wheat lines, genetic and epigenetic changes at the molecular level occurred in all these plants, with both kinds of changes classifiable into two distinct categories, i.e., stochastic and directed. The abundant type of genetic change is loss of parental bands while the prevalent cytosine methylation pattern alteration is hypermethylation at the CHG sites. Our results have extended previous studies regarding allopolyploidization-induced genomic dynamics in wheat by demonstrating the generality of both genetic and epigenetic changes associated with multiple nascent allotetraploid wheat lines, and providing novel insights into the characteristics of the two kinds of induced genomic instabilities.
- allopolyploidy /
- genetic and epigenetic changes /
- genome evolution /
- tetraploid wheat
These authors contributes equally to this work.
注释:

HTML全文

参考文献(54)

[1]	Adams, K.L., Wendel, J.F. Polyploidy and genome evolution in plants Cur. Opin. Plant Biol., 8 (2005),pp. 135-141
[2]	Axelsson, T., Bowman, C.M., Sharpe, A.G. et al. Genome, 43 (2000),pp. 679-688
[3]	Baumel, A., Ainouche, M., Kalendar, R. et al. Mol. Biol. Evol., 19 (2002),pp. 1218-1227
[4]	Bento, M., Pereira, H.S., Rocheta, M. et al. Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in triticale PLoS One, 3 (2008),p. e1402
[5]	Boyko, A., Kovalchuk, I. Epigenetic control of plant stress response Environ. Mol. Mutagen., 49 (2008),pp. 61-72
[6]	Cao, X., Jacobsen, S.E. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes Proc. Natl. Acad. Sci. USA, 99 (2002),pp. 16491-16498
[7]	Cao, X., Aufsatz, W., Zilberman, D. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation Curr. Biol., 13 (2003),pp. 2212-2217
[8]	Chagué, V.J.J., Mestiri, I., Balzergue, S. et al. Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids New Phytol., 186 (2010),pp. 161-174
[9]	Chelaifa, H., Monnier, A., Ainouche, M. New Phytol., 186 (2010),pp. 161-174
[10]	Chen, Z.J., Ni, Z. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids BioEssays, 28 (2006),pp. 240-252
[11]	Comai, L. The advantages and disadvantages of being polyploid Nat. Rev. Genet., 6 (2005),pp. 836-846
[12]	Comai, L., Tyagi, A.P., Winter, K. et al. Plant Cell, 12 (2000),pp. 1551-1567
[13]	Dong, Y.Z., Liu, Z.L., Shan, X.H. et al. Allopolyploidy in wheat induces rapid and heritable alterations in DNA methylation patterns of cellular genes and mobile elements Russ. J. Genet., 41 (2005),pp. 890-896
[14]	Dong, Z.Y., Wang, Y.M., Zhang, Z.J. et al. Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb Theor. Appl. Genet., 113 (2006),pp. 196-205
[15]	Doyle, J.J., Flagel, L.E., Paterson, A.H. et al. Evolutionary genetics of genome merger and doubling in plants An. Rev. Genet., 42 (2008),pp. 443-461
[16]	Dubcovsky, J., Dvorak, J. Genome plasticity a key factor in the success of polyploid wheat under domestication Science, 316 (2007),pp. 1862-1866
[17]	Feldman, M.
[18]	Feldman, M., Levy, A.A. Allopolyploidy-A shaping force in the evolution of wheat genomes Cytogenet. Genome Res., 109 (2005),pp. 250-258
[19]	Feldman, M., Levy, A.A. Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes J. Genet. Genomics, 36 (2009),pp. 511-518
[20]	Feldman, M., Lupton, F.G.H., Miller, T.E.
[21]	Flagel, L.E., Wendel, J.F. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation New Phytol., 186 (2010),pp. 184-193
[22]	Gaeta, R.T., Pires, J.C., Iniguez-Luy, F. et al. Plant Cell, 19 (2007),pp. 3403-3417
[23]	Han, F., Liu, B., Fedak, G. et al. Theor. Appl. Genet., 109 (2004),pp. 1070-1076
[24]	Han, F., Fedak, G., Guo, W. et al. Rapid and repeatable elimination of a parental genome-specific repeat (pGc1R-1a) in newly synthesized wheat allopolyploids Genetics, 170 (2005),pp. 1239-1245
[25]	Han, F.P., Fedak, G., Ouellet, T. et al. Rapid genomic changes in interspecific and intergeneric hybrids and allopolyploids of Triticeae Genome, 46 (2003),pp. 716-723
[26]	Hegarty, M.J., Barker, G.L., Brennan, A.C. et al. Philosoph. Transac. Royal Soc. B: Biol. Sci., 363 (2008),pp. 3055-3069
[27]	Hufton, A.L., Panopoulou, G. Polyploidy and genome restructuring: a variety of outcomes Cur. Opin. Genet. Develop., 19 (2009),pp. 600-606
[28]	Jackson, S., Chen, Z.J. Genomic and expression plasticity of polyploidy Cur. Opin. Plant Biol., 13 (2010),pp. 153-159
[29]	Levy, A.A., Feldman, M. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization Biol. J. Lin. Soc., 82 (2004),pp. 607-613
[30]	Liu, B., Wendel, J.F. Epigenetic phenomena and the evolution of plant allopolyploids Mol. Phylogenet. Evol., 29 (2003),pp. 365-379
[31]	Liu, B., Brubaker, C.L., Mergeai, G. et al. Polyploid formation in cotton is not accompanied by rapid genomic changes Genome, 44 (2001),pp. 321-330
[32]	Liu, B., Vega, J.M., Segal, G. et al. Genome, 41 (1998),pp. 272-277
[33]	Liu, B., Vega, J.M., Feldman, M. Genome, 41 (1998),pp. 535-542
[34]	Liu, B., Xu, C., Zhao, N. et al. Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement J. Genet. Genomics, 36 (2009),pp. 519-528
[35]	Ma, X.F., Gustafson, J.P. Genome evolution of allopolyploids: a process of cytological and genetic diploidization Cytogenet. Genome Res., 109 (2005),pp. 236-249
[36]	Ma, X.F., Gustafson, J.P. Allopolyploidization-accommodated genomic sequence changes in triticale Ann. Bot., 101 (2008),pp. 825-832
[37]	McClelland, M., Nelson, M., Raschke, E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases Nucleic Acids Res., 22 (1994),pp. 3640-3659
[38]	Madlung, A., Tyagi, A.P., Watson, B. et al. Plant J., 41 (2005),pp. 221-230
[39]	McClintock, B. The significance of responses of the genome to challenge Science, 226 (1984),pp. 792-801
[40]	Otto, S.P., Whitton, J. Polyploid incidence and evolution Ann. Rev. Genet., 34 (2000),pp. 401-437
[41]	Otto, S.P. The evolutionary consequences of polyploidy Cell, 131 (2007),pp. 452-462
[42]	Ozkan, H., Levy, A.A., Feldman, M. Plant Cell, 13 (2001),pp. 1735-1747
[43]	Parisod, C., Salmon, A., Zerjal, T. et al. New Phytol., 184 (2009),pp. 1003-1015
[44]	Paun, O., Fay, M.F., Soltis, D.E. et al. Genetic and epigenetic alterations after hybridization and genome doubling Taxon, 56 (2007),pp. 649-656
[45]	Pumphrey, M., Bai, J., Laudencia-Chingcuanco, D. et al. Non-additive expression of homoeologous genes is established upon polyploidization in hhexaploid wheat Genetics, 181 (2009),pp. 1147-1157
[46]	Salmon, A., Ainouche, M.L., Wendel, J.F. Mol. Ecol., 14 (2005),pp. 1163-1175
[47]	Shaked, H., Kashkush, K., Ozkan, H. et al. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat Plant Cell, 13 (2001),pp. 1749-1759
[48]	Song, K., Lu, P., Tang, K. et al. Proc. Natl. Acad. Sci. USA, 92 (1995),pp. 7719-7723
[49]	Suzuki, K., Suzuki, I., Leodolter, A. et al. Global DNA demethylation in gastrointestinal cancer is age dependent and precedes genomic damage Cancer Cell, 9 (2006),pp. 199-207
[50]	Vos, P., Hogers, R., Bleeker, M. et al. AFLP: a new technique for DNA fingerprinting Nucleic Acids Res., 23 (1995),pp. 4407-4414
[51]	Wang, J., Tian, L., Lee, H.-S. et al. Genomewide nonadditive gene regulation in arabidopsis allotetraploids Genetics, 172 (2006),pp. 507-517
[52]	Wang, Y.-M., Dong, Z.-Y., Zhang, Z.-J. et al. Genetics, 170 (2005),pp. 1945-1956
[53]	Wendel, J.F. Genome evolution in polyploids Plant Mol. Biol., 42 (2000),pp. 225-249
[54]	Xu, Y., Zhong, L., Wu, X. et al. Planta, 229 (2009),pp. 471-483