Akhunova A R, Matniyazov R T, Liang H Q, Akhunov E D. 2010. Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics, 11, 505.Apashkin V V, Kutueva L I, Vaniushin B F. 2011. Is the cytosine DNA methyltransferase gene MET1 regulated by DNA methylation in Arabidopsis thaliana plants? Genetika, 47, 320–331.Birchler J A, Auger D L, Riddle N C. 2003. In search of the molecular basis for heterosis. The Plant Cell, 15, 2236–2239.Bird A. 2007. Perceptions of epigenetics. Nature, 447, 396–398.Chen Z J. 2007. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review of Plant Biology, 58, 377–406.Chen Z J. 2010. Molecular mechanisms of polyploidy and hybrid vigor. Trends of Plant Science, 15, 57–71.Chen Z J, Ni Z. 2006. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays, 28, 240–252.Chinnusamy V, Zhu J K. 2009. Epigenetic regulation of stress responses in plants. Current Opinion of Plant Biology, 12, 133–139.Doyle J J, Doyle J L. 1990. Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.Feldman M, Levy A A. 2012. Genome evolution due to allopolyploidization in wheat. Genetics, 192, 763–774.Finnegan E J. 2001. Epialleles - a source of random variation in times of stress. Current Opinion of Plant Biology, 5, 101–106.Fulnecek J, Kovarik A. 2014. How to interpret methylation sensitive amplified polymorphism (MSAP) profiles? BMC Genetics, 15, 2–10.Gaeta R T, Pires J C, Iniguez-Luy F, Leon E, Osborn T C. 2007. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. The Plant Cell, 19, 3403–3417.Jackson S, Chen Z J. 2010. Genomic and expression plasticity of polyploidy. Current Opinion of Plant Biology, 13, 153–159.Jiang J J, Shao Y L, Du K, Ran L P, Fang X P, Wang Y P. 2013. Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. BMC Genomics, 14, 72.Jiang J J, Wang Y, Zhu B, Fang T T, Fang Y J, Wang Y P. 2015. Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids. BMC Plant Biology, 15, 22.Kashkush K, Feldman M, Levy A A. 2003. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genetics, 33, 102–106.Keyte A L, Percifield R, Liu B, Wendel J F. 2006. Intraspecific DNA methylation polymorphism in cotton. Journal of Heredity, 97, 444–450.Kong F, Mao S J, Jiang J J, Wang J, Fang X P, Wang Y P. 2011. Proteomic changes in newly synthesized Brassica napus allotetraploids and their early generations. Plant Molecular Biology Reports, 29, 927–935.Law J A, Jacobsen S E. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics, 11, 204–220.Leitch A R, Leitch I J. 2008. Genomic plasticity and the diversity of polyploid plants. Science, 320, 481–483.Li H, Geng M J, Liu Q, Jin C, Zhang Q L, Chen C B, Song W Q, Wang C G. 2014. Characteristics of cytosine methylation status and methyltransferase genes in the early development stage of cauliflower (Brassica oleracea L. var. botrytis). Plant Cell and Tissue Organ Culture, 117, 187–199.Li J, Luo L X, Wang Z, Li J, Chen K R, Ren L, Fang X P. 2010. Resynthesis of Brassica napus with Brassica oleracea or Brassica rapa cytoplasm. Acta Agronomica Sinica, 36, 1280–1285. (in Chinese)Liu B, Brubaker C L, Mergeai G, Cronn R C, Wendel J F. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome, 44, 321–330.Lukens L N, Pires J C, Leon E, Vogelzang R, Oslach L, Osborn T. 2006. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiology, 140, 336–348.Lysak M A, Koch M A, Pecinka A, Schubert I. 2005. Chromosome triplication found across the tribe Brassiceae. Genome Research, 15, 516–525.Madlung A, Masuelli R W, Watson B, Reynolds S H, Davison J, Comai L. 2002. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiology, 129, 733–746.Mason A S, Yan G, Cowling W A, Nelson M N. 2012. A new method for producing allohexaploid Brassica through unreduced gametes. Euphytica, 186, 277–287.Noy-Malka C, Yaari R, Itzhaki R, Mosquna A, Katz A, Ohad N. 2014. A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens. Plant Molecular Biology, 84, 719–735.Pradhan A, Plummer J A, Nelson M N, Cowling W A, Yan G. 2010. Trigenomic hybrids from interspecific crosses between Brassica napus and B. nigra. Crop & Pasture Science, 61, 464–474.Qi B, Huang W, Zhu B, Zhong X F, Guo J H, Zhao N, Xu C M, Zhang H K, Pang J S, Han F P, Liu B. 2010. Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines. Journal of Genetics and Genomics, 37, 737–748.Qi B, Huang W, Zhu B, Zhong X F, Guo J H, Zhao N, Xu C M, Zhang H K, Pang J S, Han F P, Liu B. 2012. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biology, 10, doi: 10.1186/1741-7007-10-3Ramsey J. 2011. Polyploidy and ecological adaptation in wild yarrow. Proceedings of the National Academy of Sciences of the United States of America, 108, 7096–7101.Salmon A, Ainouche M L, Wendel J F. 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology, 14,1163–1175.Shaked H, Kashkush K, Ozkan H, Feldman M, Levy A A. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. The Plant Cell, 13, 1749–1759.Soltis P S, Soltis D E. 2009. The role of hybridization in plant speciation. Annual Review of Plant Biology, 60, 561–588.Song K, Lu P, Tang K, Osborn T C. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences of the United States of America, 92, 7719–7723.Sotgia S, Zinellu A, Pisanu E, Murgia L, Pinna G A, Gaspa L, Deiana L, Carru C. 2010. A hydrophilic interaction ultraperformance liquid chromatography (HILIC-UPLC) method for genomic DNA methylation assessment by UV detection. Analytical and Bioanalytical Chemistry, 396, 2937–2941.Tang X M, Tao X, Wang Y, Ma D W, Li D, Yang H, Ma X R. 2014. Analysis of DNA methylation of perennial ryegrass under drought using the methylation-sensitive amplification polymorphism (MSAP) technique. Molecular Genetics and Genomics, 289, 1075–1084.Udall J A, Quijada P A, Osborn T C. 2005. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics, 169, 967–979.Wang H B, Jiang J F, Chen S M, Qi X Y, Fang W M, Guan Z Y, Teng N J, Liao Y, Chen F D. 2014. Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium× Leucanthemum paludosum hybrids (Asteraceae). Genome and Biological Evolution, 6, 247–259.Wang J L, Tian L, Lee H S, Wei N E, Jiang H M, Watson B, Madlung A, Osborn T C, Doerge R W, Comai L, Chen Z J. 2006. Genome wide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics, 172, 507–517. Wang X G, Duan C G, Tang K, Wang B S, Zhang H M, Lei M G, Lu K, Mangrauthia S K, Wang P C, Zhu G H, Zhao Y, Zhu J K. 2013. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proceedings of the National Academy of Sciences of the United States of America, 38, 15467–15472.Wu X L, Liu Z H, Hu Z H, Huang R Z. 2014. BNWRI1 coordinates fatty acid biosynthesis and photosynthesis pathways during oil accumulation in rapeseed. Journal of Integrative Plant Biology, 56, 582–593.Xiong L Z, Xu C G, Saghai M A, Zhang Q. 1999. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Molecular Genetics and Genetics, 261, 439–446.Xu Y H, Zhong L, Wu X M, Fang X P, Wang J B. 2009. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta, 229, 471–483.Yoo M J, Szadkowski E, Wendel J F. 2013. Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity, 11, 171–180.Zhang X L, Ge X H, Shao Y J, Sun G, Li Z Y. 2013. Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations. PLOS ONE, 8, e56346.Zhao N, Zhu B, Li M, Wang L, Xu L, Zhang H, Zheng S, Qi B, Han F, Liu B. 2011. Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics, 188, 499–510.Zhao Q, Zou J, Meng J L, Mei S Y, Wang J B. 2013. Tracing the transcriptome changes in synthetic trigenomic allohexaploids of Brassica using an RNA-seq approach. PLOS ONE, 8, e68883. |