Abstract
During the process of alien germplasm introduced into wheat genome by chromosome engineering, extensive genetic variations of genome structure and gene expression in recipient could be induced. In this study, we performed GISH (genome in situ hybridization) and AFLP (amplified fragment length polymorphism) on wheat-rye chromosome translocation lines and their parents to detect the identity in genomic structure of different translocation lines. The results showed that the genome primary structure variations were not obviously detected in different translocation lines except the same 1RS chromosome translocation. Methylation sensitive amplification polymorphism (MSAP) analyses on genomic DNA showed that the ratios of fully-methylated sites were significantly increased in translocation lines (CN12, 20.15%; CN17, 20.91%; CN18, 22.42%), but the ratios of hemimethylated sites were significantly lowered (CN12, 21.41%; CN17, 23.43%; CN18, 22.42%), whereas 16.37% were fully-methylated and 25.44% were hemimethylated in case of their wheat parent. Twenty-nine classes of methylation patterns were identified in a comparative assay of cytosine methylation patterns between wheat-rye translocation lines and their wheat parent, including 13 hypermethylation patterns (33.74%), 9 demethylation patterns (22.76%) and 7 uncertain patterns (4.07%). In further sequence analysis, the alterations of methylation pattern affected both repetitive DNA sequences, such as retrotransposons and tandem repetitive sequences, and low-copy DNA.
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Saze H, Mittelsten Scheid O, Paszkowski J. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet, 2003, 34(1): 65–69
Guimil S, Dunand C. Patterning of Arabidopsis epidermal cells: Epigenetic factors regulate the complex epidermal cell fate pathway. Trends Plant Sci, 2006, 11(12): 601–609
Madlung A, Masuelli R W, Watson B, et al. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol, 2002, 129: 733–746
Chan S W L, Henderson I R, Jacobsen S E. Gardening the genome: DNA methylation Arabidopsis thaliana. Nat Rev Genet, 2005, 6: 351–360
Xiao W, Custard K D, Brown R C, et al. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell, 2006, 18(4): 805–814
Jullien P E, Kinoshita T, Ohad N, et al. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell, 2006, 18(6): 1360–1372
Adams K L, Percifield R, Wendel J F. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics, 2004, 168: 2217–2226
Salmon A, Ainouche M L, Wendel J F. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol, 2005, 14: 1163–1175
Liu Z, Wang Y, Shen Y, et al. Extensive alterations in DNA methylation and transcription in rice caused by introgression from Zizania latifolia. Plant Mol Biol, 2004, 54(4): 571–582
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, 2006, 113: 196–205
Schob H, Grossniklaus U. The first high-resolution DNA “methylome”. Cell, 2006, 126(6): 1025–1028
Ren Z L. Introduction of rye chromatin into wheat and its breeding behavior. Scientia Agricultura Sinica, 1991, 24(3): 18–25
Ren Z L. Effect of wheat genetic background on the expression of the rye gene Lr26 for resistance to leaf rust in wheat. Acta Genetica Sinica, 1993, 20(4): 312–316
Ren Z L, Zhang H Q. Induction of small-segment-translocation between wheat and rye chromosomes. Sci China Ser C-Life Sci, 1997, 27(3): 258–263
Reyna-Lopez G E, Simpson J, Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol Gen Genet, 1997, 253: 703–710
Tang Z X, Ren Z L, Wu F, et al. The selection of transgenic recipients from new elite wheat cultivars and study on its plant regeneration system. Agri Sci China, 2006, 5(6): 417–427
Murray M G, Thompson W F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res, 1980, 8(19): 4321–4325
Zhang Y, Zhang S G, Qi L W, et al. Chromosome microdissection, cloning and painting of the chromosome 1 in poplar (Populus tremula). Silvae Genetica, 2005, 54(4–5): 211–217
Froidmont D. A co-dominant marker for the 1BL/1RS wheat-rye translocation via multiplex PCR. J Cereal Sci, 1998, 27: 229–232
Chai J F, Zhou R H, Jia J Z, et al. Development and application of a new codominant PCR marker for detecting 1BL/1RS wheat-rye chromosome translocations. Plant Breed, 2006, 125: 302–304
Vos P, Hogers R, Bleeker M, et al. AFLP: A new techique for DNA fingerprinting. Nucleic Acids Res, 1995, 23: 4407–4414
Bassam B J, Caetano-Anolles G, Gresshoff P M. Fast and sensitive silver straining of DNA in polyacrylamide gels. Anal Biochem, 1991, 196: 80–83
Xiong L Z, Xu C G, Maroof M A S, et al. Patterns of cytosine methylation in an elicite hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Genet Genomics, 1999, 26: 439–446
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, 2001, 13: 1749–1759
He P, Friebe B R, Gill B S, et al. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol, 2003, 52: 401–414
Ma X F, Fang P, Gustafson J P. Polyploidization-induced genome variation in triticale. Genome, 2004, 47: 839–848
Zhao X X, Chai Y, Liu B. Epigenetic inheritance and variation of DNA methylation level and pattern in maize intra-specific hybrids. Plant Sci, 2007, 172: 930–938
Cheng C, Daigen M, Hirochika H. Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genomics, 2006, 276(4): 378–390
Uauy C, Distelfeld A, Fahima T, et al. A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science, 2006, 314: 1298–1301
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Supported by the National Natural Science Foundation of China (Grants No. 30671136 and 30730065), the China Postdoctoral Science Foundation (Grant No. 20070411158), the Program for New Century Excellent Talents in University from Ministry of Education, China (Grant No. NCET-06-0810) and the Youth Foundation of University of Electronic Science and Technology of China (Grant No. L08010901JX0677)
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Zhang, Y., Liu, Z., Liu, C. et al. Analysis of DNA methylation variation in wheat genetic background after alien chromatin introduction based on methylation-sensitive amplification polymorphism. Chin. Sci. Bull. 53, 58–69 (2008). https://doi.org/10.1007/s11434-008-0049-3
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DOI: https://doi.org/10.1007/s11434-008-0049-3