11 Buggs RJ, Chamala S, Wu WEI, Gao LU, May GD, Schnable PS, Soltis DE, Soltis PS, Barbazuk WB (2010). Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol Ecol 19, 132-146.
[7]
12 Chen M, Ha M, Lackey E, Wang JL, Chen ZJ (2008). RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178, 1845-1858.
[8]
13 Chen ZJ (2013). Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet 14, 471- 482.
[9]
14 Chen ZJ, Comai L, Pikaard CS (1998). Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proc Natl Acad Sci USA 95, 14891-14896.
[10]
15 Chen ZJ, Pikaard CS (1997a). Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica . Proc Natl Acad Sci USA 94, 3442-3447.
[11]
16 Chen ZJ, Pikaard CS (1997b). Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes Dev 11, 2124-2136.
[12]
17 Chester M, Gallagher JP, Symonds VV, da Silva AVC, Mavrodiev EV, Leitch AR, Soltis PS, Soltis DE (2012). Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc Natl Acad Sci USA 109, 1176-1181.
[13]
18 Coate JE, Doyle JJ (2010). Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid. Genome Biol Evol 2, 534-546.
[14]
19 Cokus SJ, Feng SH, Zhang XY, Chen ZG, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008). Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219.
[15]
20 Comai L (2000). Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol 43, 387-399.
[16]
21 Comai L (2005). The advantages and disadvantages of being polyploid. Nat Rev Genet 6, 836-846.
[17]
22 Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B (2000). Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12, 1551-1567.
[18]
23 Combes MC, Dereeper A, Severac D, Bertrand B, Lashermes P (2013). Contribution of subgenomes to the transcriptome and their intertwined regulation in the allopolyploid Coffea arabica grown at contrasted temperatures. New Phytol 200, 251-260.
[19]
52 Lewis WH (1980). Polyploidy: Biological Relevance. New York: Plenum. pp. 583.
[20]
53 Li B, Carey M, Workman JL (2007). The role of chromatin during transcription. Cell 128, 707-719.
[21]
54 Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF (2001). Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44, 321-330.
[22]
55 Liu B, Davis TM (2011). Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Ros- aceae). BMC Plant Biol 11, 157.
[23]
56 Madlung A (2013). Polyploidy and its effect on evolutionary success: old questions revisited with new tools. Heredity 110, 99-104.
[24]
57 Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L (2002). Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129, 733-746.
[25]
58 Madlung A, Tyagi AP, Watson B, Jiang H, Kagochi T, Doerge RW, Martienssen R, Comai L (2005). Genomic changes in synthetic Arabidopsis polyploids. Plant J 41, 221-230.
[26]
79 Salmon A, Ainouche ML, Wendel JF (2005). Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14, 1163-1175.
[27]
80 Saze H, Tsugane K, Kanno T, Nishimura T (2012). DNA methylation in plants: relationship to small RNAs and histone modifications, and functions in transposon inactivation. Plant Cell Physiol 53, 766-784.
[28]
104 Zhao JW, Udall JA, Quijada PA, Grau CR, Meng JL, Osborn TC (2006). Quantitative trait loci for resistance to Sclerotinia sclerotiorum and its association with a homeologous non-reciprocal transposition in Brassica napus L. Theor Appl Genet 112, 509-516.
[29]
6 Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, Wohlrab B, von Haeseler A, Scheid OM (2010). Coope- ration of multiple chromatin modifications can generate unanticipated stability of epigenetic states in Arabidopsis. Plant Cell 22, 34-47.
[30]
7 Baulcombe D (2004). RNA silencing in plants. Nature 431, 356-363.
[31]
8 Birchler JA, Newton KJ (1981). Modulation of protein levels in chromosomal dosage series of maize: the biochemical basis of aneuploid syndromes. Genetics 99, 247-266.
[32]
9 Blanc G, Wolfe KH (2004). Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16, 1679-1691.
[33]
10 Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen AC, Elven R (2004). Polyploidy in arctic plants. Biol J Linn Soc 82, 521-536.
[34]
24 Crawford DJ (1990). Plant Molecular Systematics: Macromolecular Approaches. Hoboken: John Wiley & Sons, Inc.
[35]
25 Deal RB, Henikoff S (2011). Histone variants and modifications in plant gene regulation. Curr Opin Plant Biol 14, 116-122.
[36]
26 Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS, Wendel JF (2008). Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42, 443-461.
[37]
27 Edger PP, Pires JC (2009). Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res 17, 699-717.
[38]
28 Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM (1997). Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147, 1381- 1387.
[39]
29 Feschotte C, Jiang N, Wessler SR (2002). Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3, 329-341.
[40]
30 Flagel L, Udall J, Nettleton D, Wendel J (2008). Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol 6, 16.
[41]
31 Frieman M, Chen ZJ, Saez-Vasquez J, Shen LA, Pikaard CS (1999). RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: tests of transcription factor involvement in nucleolar dominance. Genetics 152, 451-460.
[42]
32 Gaeta RT, Pires JC, Iniguez-Luy F, Leon E, Osborn TC (2007). Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19, 3403-3417.
[43]
33 Galili G, Feldman M (1984). Intergenomic suppression of endosperm protein genes in common wheat. Can J Genet Cytol 26, 651-656.
[44]
34 Gottlieb LD (1982). Conservation and duplication of iso- zymes in plants. Science 216, 373-380.
[45]
35 Guo M, Davis D, Birchler JA (1996). Dosage effects on gene expression in a maize ploidy series. Genetics 142, 1349-1355.
[46]
36 Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ, Chen ZJ (2009). Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci USA 106, 17835- 17840.
[47]
37 Ha M, Pang MX, Agarwal V, Chen ZJ (2008). Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta 1779, 735-742.
[48]
38 Harberd NP, Flavell RB, Thompson RD (1987). Identification of a transposon-like insertion in a Glu-1 allele of wheat. Mol Gen Genet 209, 326-332.
[49]
39 Hegarty MJ, Barker GL, Wilson ID, Abbott RJ, Edwards KJ, Hiscock SJ (2006). Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr Biol 16, 1652-1659.
[50]
40 Ilic K, SanMiguel PJ, Bennetzen JL (2003). A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes. Proc Natl Acad Sci USA 100, 12265-12270.
42 Jenuwein T, Allis CD (2001). Translating the histone code. Science 293, 1074-1080.
[53]
43 Kashkush K, Feldman M, Levy AA (2002a). Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160, 1651-1659.
[54]
44 Kashkush K, Feldman M, Levy AA (2002b). Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33, 102-106.
[55]
45 Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melam- ed-Bessudo C, Feldman M, Levy AA (2011). Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188, 263-272.
[56]
46 Kihara H, Ono T (1926). Chromosomenzahlen und systematische gruppierung der Rumex-Arten. Cell Tissue Res 4, 475-481.
[57]
47 Koh J, Chen SX, Zhu N, Yu FH, Soltis PS, Soltis DE (2012). Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytol 196, 292-305.
[58]
48 Lai JS, Ma JX, Swigoňová Z, Ramakrishna W, Linton E, Llaca V, Tanyolac B, Park YJ, Jeong OY, Bennetzen JL, Messing J (2004). Gene loss and movement in the maize genome. Genome Res 14, 1924-1931.
[59]
49 Lee HS, Chen ZJ (2001). Protein-coding genes are epigene- tically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98, 6753-6758.
[60]
50 Leitch AR, Leitch IJ (2008). Genomic plasticity and the diversity of polyploid plants. Science 320, 481-483.
[61]
51 Leitch IJ, Bennett MD (2004). Genome downsizing in polyploid plants. Biol J Linn Soc 82, 651-663.
[62]
59 Marmagne A, Brabant P, Thiellement H, Alix K (2010). Analysis of gene expression in resynthesized Brassica napus allotetraploids: transcriptional changes do not explain differential protein regulation. New Phytol 186, 216- 227.
[63]
60 Martienssen RA, Colot V (2001). DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293, 1070-1074.
[64]
61 Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP (2011). Recently formed polyploid plants diversify at lower rates. Science 333, 1257-1257.
[65]
62 McClintock B (1984). The significance of responses of the genome to challenge. Science 226, 792-801.
[66]
63 Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei FS, Fuks G, Soderlund CA, Mayer KFX, Wing RA (2004). Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101, 14349-14354.
[67]
64 Mok DWS, Peloquin SJ (1975). The inheritance of three mechanisms of diplandroid (2 n pollen) formation in diploid potatoes. Heredity 35, 295-302.
[68]
65 Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ (2012). Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 108, 419-430.
[69]
66 Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ (2009). Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457, 327-331.
[70]
67 Osborn TC, Butrulle DV, Sharpe AG, Pickering KJ, Parkin IA, Parker JS, Lydiate DJ (2003a). Detection and effects of a homeologous reciprocal transposition in Brassica napus . Genetics 165, 1569-1577.
[71]
68 Osborn TC, Chris Pires J, Birchler JA, Auger DL, Jeffery Chen Z, Lee HS, Comai L, Madlung A, Doerge RW, Colot V, Martienssen RA (2003b). Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19, 141-147.
[72]
69 Ozkan H, Tuna M, Arumuganathan K (2003). Nonadditive changes in genome size during allopolyploidization in the wheat ( Aegilops-Triticum ) group. J Hered 94, 260-264.
[73]
70 Pecinka A, Fang W, Rehmsmeier M, Levy AA, Scheid OM (2011). Polyploidization increases meiotic recombination frequency in Arabidopsis. BMC Biol 9, 24.
[74]
71 Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (2004). SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans -acting siRNAs in Arabidopsis. Genes Dev 18, 2368-2379.
[75]
72 Pikaard CS (1999). Nucleolar dominance and silencing of transcription. Trends Plant Sci 4, 478-483.
[76]
73 Pikaard CS (2001). Genomic change and gene silencing in polyploids. Trends Genet 17, 675-677.
[77]
74 Pires JC, Zhao JW, Schranz M, Leon EJ, Quijada PA, Lukens LN, Osborn TC (2004). Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc 82, 675-688.
[78]
75 Pumphrey M, Bai JF, Laudencia-Chingcuanco D, Ander- son O, Gill BS (2009). Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 181, 1147-1157.
[79]
76 Ramsey J, Schemske DW (2002). Neopolyploidy in flowering plants. Annu Rev Ecol Evol Syst 33, 589-639.
[80]
77 Rastogi S, Liberles DA (2005). Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol 5, 28.
[81]
78 Roose ML, Gottlieb LD (1980). Biochemical properties and level of expression of alcohol dehydrogenases in the allotetraploid plant Tragopogon miscellus and its diploid progenitors. Biochem Genet 18, 1065-1085.
[82]
81 Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC (2002). Characterization and effects of the replicated flowering time gene FLC in Brassica rapa . Genetics 162, 1457-1468.
[83]
82 Shen HS, He H, Li JG, Chen W, Wang XC, Guo L, Peng ZY, He GM, Zhong SW, Qi YJ, Terzaghi W, Deng XW (2012). Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24, 875-892.
[84]
83 Shitsukawa N, Tahira C, Kassai KI, Hirabayashi C, Shimizu T, Takumi S, Mochida K, Kawaura K, Ogihara Y, Murai K (2007). Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat. Plant Cell 19, 1723-1737.
[85]
84 Soltis DE, Soltis PS (1990). Isozymes in Plant Biology. Berlin: Springer.
[86]
85 Stebbins GL (1971). Chromosomal Evolution in Higher Plants. London: Edward Arnold.
[87]
86 Stephens SG (1951). Possible significance of duplication in evolution. Adv Genet 4, 247-265.
[88]
87 Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang JM (2007). Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176, 2055-2067.
[89]
88 Szadkowski E, Eber F, Huteau V, Lodé M, Coriton O, Jenczewski E, Chèvre AM (2011). Polyploid formation pathways have an impact on genetic rearrangements in resynthesized Brassica napus . New Phytol 191, 884-894.
[90]
89 Szadkowski E, Eber F, Huteau V, Lodé M, Huneau C, Belcram H, Coriton O, Manzanares-Dauleux MJ, Delourme R, King GJ, Chalhoub B, Jenczewski E, Chèvre AM (2010). The first meiosis of resynthesized Brassica napus , a genome blender. New Phytol 186, 102- 112.
[91]
90 The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana . Nature 408, 796-815.
[92]
91 Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crété P (2004). Endogenous trans -acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16, 69-79.
[93]
92 Veitia RA, Bottani S, Birchler JA (2008). Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet 24, 390-397.
[94]
93 Wang JL, Tian L, Lee HS, Chen ZJ (2006a). Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids. Genetics 173, 965-974.
[95]
94 Wang JL, Tian L, Lee HS, Wei NE, Jiang HM, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ (2006b). Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172, 507-517.
[96]
95 Wang JL, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ (2004). Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167, 1961-1973.
97 Wolfe KH (2001). Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet 2, 333-341.
[99]
98 Wood TE, Takebayashi N, Barker MS, Mayrose I, Green- spoon PB, Rieseberg LH (2009). The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci USA 106, 13875-13879.
[100]
99 Wright KM, Pires JC, Madlung A (2009). Mitotic instability in resynthesized and natural polyploids of the genus Arabidopsis (Brassicaceae). Am J Bot 96, 1656-1664.
[101]
100 Xiong ZY, Gaeta RT, Pires JC (2011). Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus . Proc Natl Acad Sci USA 108, 7908-7913.
[102]
101 Xu ZY, John ZY, Cho J, Yu J, Kohel RJ, Percy RG (2010). Polyploidization altered gene functions in cotton ( Gossypium spp.). PLoS One 5, e14351.
[103]
102 Zeng ZX, Zhang T, Li GR, Liu C, Yang ZJ (2012). Phenotypic and epigenetic changes occurred during the autopolyploidization of Aegilops tauschii . Cereal Res Commun 40, 476-485.
[104]
103 Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009). Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana . Genome Biol 10, R62.
