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Polyploidy and Genome Evolution pp 57–76Cite as

Origins of Novel Phenotypic Variation in Polyploids

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Abstract

Polyploid species represent a special type of organism in nature, one that can survive and compete with three or more full sets of homologous chromosomes. While less common in the animal and fungal kingdoms, polyploid species are highly prevalent in the plant kingdom. Indeed, most agricultural crops are polyploids, typically because polyploidy confers greater robustness and therefore higher yields. Among many examples of novel phenotypic variation exhibited by polyploids are the production of larger fruits, reduced tillering, delays in the reproductive transition, and even the creation of visually stunning flower pigmentation patterns coveted by gardeners. The source of this novel variation in polyploids is still largely unclear. However, multiple cellular mechanisms have been proposed, with some supporting evidence, to explain novel variation. We review some of these mechanisms here.

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References

  • Ahloowalia B, Garber F (1961) The genus Collinsia. XIII. Cytogenetic studies of interspecific hybrids involving species with pediceled flowers. Bot Gaz 122:219

    Article  Google Scholar 

  • Akhunova A, Matniyazov R, Liang H, Akhunov E (2010) Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics 11(1):505

    Article  PubMed  CAS  Google Scholar 

  • Albertin W, Balliau T, Brabant P, Chevre A-M, Eber F, Malosse C, Thiellement H (2006) Numerous and rapid Nonstochastic modifications of Gene products in newly synthesized Brassica napus Allotetraploids. Genetics 173(2):1101–1113. doi: 10.1534/genetics.106.057554

    Article  CAS  PubMed  Google Scholar 

  • Bertrand D, Gagnon Y, Blanchette M, El-Mabrouk N (2010) Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss. Paper presented at the Proceedings of the 10th international conference on algorithms in bioinformatics, Liverpool, UK

    Google Scholar 

  • Bingham E (1979) Maximizing heterozygosity in autopolyploids. Basic Life Sci 13:471–489

    CAS  PubMed  Google Scholar 

  • Birchler JA, Bhadra U, Bhadra MP, Auger DL (2001) Dosage-dependent Gene regulation in multicellular Eukaryotes: implications for dosage compensation, Aneuploid syndromes, and quantitative traits. Dev Biology 234(2):275–288. doi: 10.1006/dbio.2001.0262

    Article  CAS  Google Scholar 

  • Bretagnolle F, Thompson J (1995) Tansley review no. 78. Gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of Autopolyploid plants. New Phytol 129:1

    Article  Google Scholar 

  • Buggs RJA, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS, Soltis DE (2009) Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic Allotetraploids. Heredity 103 (1):73–81. doi: http://www.nature.com/hdy/journal/v103/n1/suppinfo/hdy200924s1.html

    Google Scholar 

  • Buggs Richard JA, Zhang L, Miles N, Tate Jennifer A, Gao L, Wei W, Schnable Patrick S, Barbazuk WB, Soltis Pamela S, Soltis Douglas E (2011) Transcriptomic shock generates evolutionary novelty in a newly formed. Natural allopolyploid plant. Curr Biol 21(7):551–556. doi: 10.1016/j.cub.2011.02.016

    Article  CAS  PubMed  Google Scholar 

  • Calarco JP, Martienssen RA (2011) Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr Opin Genet Dev 21(2):134–139. doi: 10.1016/j.gde.2011.01.014

    Article  CAS  PubMed  Google Scholar 

  • Chagué V, Just J, Mestiri I, Balzergue S, Tanguy A-M, Huneau C, Huteau V, Belcram H, Coriton O, Jahier J, Chalhoub B (2010) Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol 187(4):1181–1194. doi: 10.1111/j.1469-8137.2010.03339.x

    Article  PubMed  CAS  Google Scholar 

  • Chang P, Dilkes B, McMahon M, Comai L, Nuzhdin S (2010) Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol 11(12):R125

    Article  CAS  PubMed  Google Scholar 

  • Chaudhary B, Flagel L, Stupar R, Udall J, Verma N, Springer N, Wendel J (2009) Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182:503–517

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Ha M, Lackey E, Wang J, Chen Z (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

    Article  CAS  PubMed  Google Scholar 

  • Chester M, Gallagher JP, Symonds VV, Cruz da Silva AV, Mavrodiev EV, Leitch AR, Soltis PS, Soltis DE (2012) Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc Nat Acad Sci 109(4):1176–1181. doi: 10.1073/pnas.1112041109

    Article  CAS  PubMed  Google Scholar 

  • Church SA, Spaulding EJ (2009) Gene expression in a wild Autopolyploid sunflower series. J Hered 100(4):491–495. doi: 10.1093/jhered/esp008

    Article  CAS  PubMed  Google Scholar 

  • Clausen J, Keck D, Hiesey W (1945) Experimental studies on the nature of species. II. Plant evolution through Amphiploidy and autoploidy, with examples from the Madiinae. Carnegie Inst Wash Publ 564

    Google Scholar 

  • 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(9):1551–1568. doi: 10.1105/tpc.12.9.1551

    CAS  PubMed  Google Scholar 

  • Darlington CD (1963) Chromosome botany, and the origins of cultivated plants. Allen and Unwin, London

    Google Scholar 

  • Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the Ancestral Vertebrate. PLoS Biol 3(10):e314

    Article  PubMed  CAS  Google Scholar 

  • 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(1):443–461. doi: 10.1146/annurev.genet.42.110807.091524

    Article  CAS  PubMed  Google Scholar 

  • Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316(5833):1862–1866. doi: 10.1126/science.1143986

    Article  CAS  PubMed  Google Scholar 

  • Durán-Figueroa N, Vielle-Calzada J-P (2010) ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis. Plant Signal Behav 5(11):1476–1479

    Article  PubMed  CAS  Google Scholar 

  • Earley K, Lawrence RJ, Pontes O, Reuther R, Enciso AJ, Silva M, Neves N, Gross M, Viegas W, Pikaard CS (2006) Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 20(10):1283–1293. doi: 10.1101/gad.1417706

    Article  CAS  PubMed  Google Scholar 

  • Eigsti OJ (1957) Induced Polyploidy. Am J Bot 44(3):272–279

    Article  Google Scholar 

  • Feldman M, Levy AA (2005) Allopolyploidy—a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109(1–3):250–258

    Article  CAS  PubMed  Google Scholar 

  • Finigan P, Martienssen RA (2008) Nucleolar dominance and DNA methylation directed by small interfering RNA. Mol Cell 32(6):753–754

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Flagel LE, Wendel JF (2010) Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytol 186(1):184–193. doi: 10.1111/j.1469-8137.2009.03107.x

    Article  CAS  PubMed  Google Scholar 

  • 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 Online 19(11):3403–3417. doi: 10.1105/tpc.107.054346

    Article  CAS  Google Scholar 

  • Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Nat Acad Sci U S A 94(13):6809–6814

    Article  CAS  Google Scholar 

  • Grant V (1981) Plant speciation, 2nd edn. Columbia University Press, New York

    Google Scholar 

  • Guo M, Birchler JA (1994) Trans-acting dosage effects on the expression of model Gene systems in Maize Aneuploids. Science 266(5193):1999–2002. doi: 10.1126/science.266.5193.1999

    Article  CAS  PubMed  Google Scholar 

  • Guo M, Davis D, Birchler JA (1996) Dosage effects on Gene expression in a Maize Ploidy series. Genetics 142(4):1349–1355

    CAS  PubMed  Google Scholar 

  • Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang X-J, Chen ZJ (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Nat Acad Sci 106(42):17835–17840. doi: 10.1073/pnas.0907003106

    Article  CAS  PubMed  Google Scholar 

  • Harlan J, deWet J (1975) On Ö. Winge and a prayer: the origins of polyploidy. Bot Rev 41 (4):361–390. doi: 10.1007/bf02860830

    Google Scholar 

  • 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(16):1652–1659. doi: 10.1016/j.cub.2006.06.071

    Article  CAS  PubMed  Google Scholar 

  • Hegarty MJ, Hiscock SJ (2008) Genomic clues to the evolutionary success of polyploid plants. Curr Biol: CB 18(10):R435–R444

    Article  CAS  PubMed  Google Scholar 

  • Henry IM, Dilkes BP, Young K, Watson B, Wu H, Comai L (2005) Aneuploidy and genetic variation in the Arabidopsis thaliana Triploid response. Genetics 170(4):1979–1988. doi: 10.1534/genetics.104.037788

    Article  CAS  PubMed  Google Scholar 

  • Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473 (7345):97–100. doi: http://www.nature.com/nature/journal/v473/n7345/abs/10.1038-nature09916-unlocked.html#supplementary-information

    Google Scholar 

  • Jørgensen C (1928) The experimental formation of heteroploid plants in the genus Solanum. J Genet 11:133

    Article  Google Scholar 

  • Josefsson C, Dilkes B, Comai L (2006) Parent-dependent loss of Gene silencing during interspecies hybridization. Curr Biol 16(13):1322–1328. doi: 10.1016/j.cub.2006.05.045

    Article  CAS  PubMed  Google Scholar 

  • Kashkush K, Feldman M, Levy A (2002) Gene loss, silencing and activation in a newly synthesized wheat Allotetraploid. Genetics 160:1651–1659

    CAS  PubMed  Google Scholar 

  • Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces Cerevisiae. Nature 428 (6983):617–624. doi: http://www.nature.com/nature/journal/v428/n6983/suppinfo/nature02424_S1.html

    Google Scholar 

  • Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy AA (2011) Wheat hybridization and Polyploidization results in deregulation of small RNAs. Genetics 188(2):263–272. doi: 10.1534/genetics.111.128348

    Article  CAS  PubMed  Google Scholar 

  • Kerber E (1964) Wheat: reconstitution of the tetraploid component (AABB) of hexaploids. Science 143:53–255

    Article  Google Scholar 

  • Kihara H, Ono T (1926) Chromosomenzahlen und systematische Gruppierung der Rumex-Arten. Z Zellforsch Mikr Anat 4:475

    Article  Google Scholar 

  • Kliebenstein DJ, West MAL, van Leeuwen H, Kim K, Doerge RW, Michelmore RW, St. Clair DA (2006) Genomic survey of Gene expression diversity in Arabidopsis thaliana. Genetics 172(2):1179–1189. doi: 101534/genetics.105.049353

    Article  PubMed  Google Scholar 

  • Lagercrantz U, Lydiate DJ (1996) Comparative genome mapping in Brassica. Genetics 144(4):1903–1910

    CAS  PubMed  Google Scholar 

  • Leitch AR, Leitch IJ (2008) Genomic plasticity and the diversity of polyploid plants. Science 320(5875):481–483. doi: 10.1126/science.1153585

    Article  CAS  PubMed  Google Scholar 

  • Levin DA (1983) Polyploidy and novelty in flowering plants. Am Nat 122(1):1–25

    Article  Google Scholar 

  • Levin DA (2002) The role of chromosomal change in plant evolution. Oxford University Press, Oxford

    Google Scholar 

  • Lexer C, Welch ME, Raymond O, Rieseberg LH (2003) The origin of ecological divergence in Helianthus paradoxus (Asteraceae): selection on transgressive characters in a novel hybrid habitat. Evolution 57(9):1989–2000. doi: 10.1111/j.0014-3820.2003.tb00379.x

    CAS  PubMed  Google Scholar 

  • Li X, Guo W, Wang B, Li X, Chen H, Wei L, Wang Y, Wu J, Long H (2010) Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica Alboglabra Bailey. BMC Plant Biol 10(1):207

    Article  PubMed  CAS  Google Scholar 

  • Liu B, Wendel JF (2003) Epigenetic phenomena and the evolution of plant allopolyploids. Mol Phylogenet Evol 29(3):365–379. doi: 10.1016/s1055-7903(03)00213-6

    Article  CAS  PubMed  Google Scholar 

  • Lukens LN, Pires JC, 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 Physiol 140(1):336–348. doi: 10.1104/pp.105.066308

    Article  CAS  PubMed  Google Scholar 

  • Lumaret R (1988) Adaptive strategies and ploidy levels. Acta Oecol Oecol Plant 9:83

    Google Scholar 

  • 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(2):733–746. doi: 10.1104/pp.003095

    Article  CAS  PubMed  Google Scholar 

  • Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y (2005) Modeling gene and genome duplications in Eukaryotes. Proc Nat Acad Sci U S A 102(15):5454–5459. doi: 10.1073/pnas.0501102102

    Article  CAS  Google Scholar 

  • Martienssen RA (2010) Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol 186(1):46–53. doi: 10.1111/j.1469-8137.2010.03193.x

    Article  CAS  PubMed  Google Scholar 

  • Matzke MA, Scheid OM, Matzke AJM (1999) Rapid structural and epigenetic changes in polyploid and aneuploid genomes. BioEssays 21(9):761–767. doi: 10.1002/(sici)1521-1878(199909)21:9<761:aid-bies7>3.0.co;2-c

    Article  CAS  PubMed  Google Scholar 

  • McStay B (2006) Nucleolar dominance: a model for rRNA gene silencing. Genes Dev 20(10):1207–1214. doi: 10.1101/gad.1436906

    Article  CAS  PubMed  Google Scholar 

  • Meins F, Thomas M (2003) Meiotic transmission of epigenetic changes in the cell-division factor requirement of plant cells. Development 130(25):6201–6208. doi: 10.1242/dev.00856

    Article  CAS  PubMed  Google Scholar 

  • Meyer A, Schartl M (1999) Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr Opin Cell Biol 11(6):699–704. doi: 10.1016/s0955-0674(99)00039-3

    Article  CAS  PubMed  Google Scholar 

  • Meyer A, Van de Peer Y (2005) From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). BioEssays 27(9):937–945. doi: 10.1002/bies.20293

    Article  CAS  PubMed  Google Scholar 

  • Mohan Jain S (2001) Tissue culture-derived variation in crop improvement. Euphytica 118(2):153–166. doi: 10.1023/a:1004124519479

    Article  Google Scholar 

  • Müntzing A (1936) The evolutionary significance of Autopolyploidy. Hereditas 21(2–3):363–378. doi: 10.1111/j.1601-5223.1936.tb03204.x

    Google Scholar 

  • Müntzing A (1937) The effects of chromosomal variation in Dactylis. Hereditas 23:113

    Article  Google Scholar 

  • Newton W, Pellew C (1929) Primula kewensis and its derivatives. J Genet 20:405

    Article  Google Scholar 

  • Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ (2011) Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity. doi: http://www.nature.com/hdy/journal/vaop/ncurrent/suppinfo/hdy201192s1.html

  • Ni Z, Kim E-D, 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 (7227):327–331. doi: http://www.nature.com/nature/journal/v457/n7227/suppinfo/nature07523_S1.html

    Google Scholar 

  • Noggle G (1946) The physiology of polyploidy in plants. Lloydia 9:153

    CAS  Google Scholar 

  • Ohno S (1970) Evolutoin by gene duplication. Springer, Berlin

    Google Scholar 

  • Olmedo-Monfil V, Duran-Figueroa N, Arteaga-Vazquez M, Demesa-Arevalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA, Vielle-Calzada J-P (2010) Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature 464 (7288):628–632. doi: http://www.nature.com/nature/journal/v464/n7288/suppinfo/nature08828_S1.html

    Google Scholar 

  • Osborn T, Pires J, Birchler J, Auger D, Chen Z, Lee H, Comai L, Madlung A, Doerge R, Colot V, Martienssen R (2003) Understanding mechanisms of novel gene expression in polyploids. Trends Genet 19:141–147

    Article  CAS  PubMed  Google Scholar 

  • Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien M-A, Ainouche M (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184(4):1003–1015. doi: 10.1111/j.1469-8137.2009.03029.x

    Article  CAS  PubMed  Google Scholar 

  • Phillips RL, Kaeppler SM, Olhoft P (1994) Genetic instability of plant tissue cultures: breakdown of normal controls. Proc Nat Acad Sci U S A 91(12):5222–5226

    Article  CAS  Google Scholar 

  • Pignatta D, Dilkes BP, Yoo S-Y, Henry IM, Madlung A, Doerge RW, Jeffrey Chen Z, Comai L (2010) Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling. New Phytol 186(1):194–206. doi: 10.1111/j.1469-8137.2010.03198.x

    Article  CAS  PubMed  Google Scholar 

  • Pires JC, Zhao J, Schranz ME, 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(4):675–688. doi: 10.1111/j.1095-8312.2004.00350.x

    Article  Google Scholar 

  • Pontes O, Neves N, Silva M, Lewis MS, Madlung A, Comai L, Viegas W, Pikaard CS (2004) Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc Nat Acad Sci U S A 101(52):18240–18245. doi: 10.1073/pnas.0407258102

    Article  CAS  Google Scholar 

  • Preuss S, Pikaard CS (2007) rRNA gene silencing and nucleolar dominance: insights into a chromosome-scale epigenetic on/off switch. Biochimica et Biophysica Acta (BBA)—Gene structure and expression 1769 (5–6):383–392. doi: 10.1016/j.bbaexp.2007.02.005

  • Preuss SB, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KD, Carrington JC, Baulcombe DC, Viegas W, Pikaard CS (2008) Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell 32(5):673–684. doi: 10.1016/j.molcel.2008.11.009

    Article  CAS  PubMed  Google Scholar 

  • Pumphrey M, Bai J, Laudencia-Chingcuanco D, Anderson O, Gill B (2009) Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 181:1147–1157

    Article  CAS  PubMed  Google Scholar 

  • Ramsey J, Schemske DW (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst 29(1):467–501. doi: 10.1146/annurev.ecolsys.29.1.467

    Article  Google Scholar 

  • Ramsey J, Schemske DW (2002) Neopolyploidy in flowering plants. Annu Rev Ecol Syst 33(1):589–639. doi: 10.1146/annurev.ecolsys.33.010802.150437

    Article  Google Scholar 

  • Randolph L (1941) An evaluation of induced polyploidy as a method of breeding crop plants. Am Nat 75:347

    Article  Google Scholar 

  • Rapp R, Udall J, Wendel J (2009) Genomic expression dominance in allopolyploids. BMC Biol 7:18

    Article  PubMed  CAS  Google Scholar 

  • Riddle N, Jiang H, An L, Doerge R, Birchler J (2010) Gene expression analysis at the intersection of ploidy and hybridity in maize. Theor Appl Genet 120(2):341–353. doi: 10.1007/s00122-009-1113-3

    Article  CAS  PubMed  Google Scholar 

  • Santos JL, Alfaro D, Sanchez-Moran E, Armstrong SJ, Franklin FCH, Jones GH (2003) Partial diploidization of meiosis in Autotetraploid Arabidopsis thaliana. Genetics 165(3):1533–1540

    CAS  PubMed  Google Scholar 

  • Schnable JC, Springer NM, Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Nat Acad Sci 108(10):4069–4074. doi: 10.1073/pnas.1101368108

    Article  CAS  PubMed  Google Scholar 

  • Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C (2005) Role of FRIGIDA and flowering locus c in determining variation in flowering time of Arabidopsis. Plant Physiol 138(2):1163–1173. doi: 10.1104/pp.105.061309

    Article  CAS  PubMed  Google Scholar 

  • Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144(1):329–338

    CAS  PubMed  Google Scholar 

  • Simpson GG, Dean C (2002) Arabidopsis, the rosetta stone of flowering time? Science 296(5566):285–289. doi: 10.1126/science.296.5566.285

    Article  CAS  PubMed  Google Scholar 

  • Singh M, Goel S, Meeley RB, Dantec C, Parrinello H, Michaud C, Leblanc O, Grimanelli D (2011) Production of viable gametes without Meiosis in Maize deficient for an ARGONAUTE protein. Plant Cell Online 23(2):443–458. doi: 10.1105/tpc.110.079020

    Article  CAS  Google Scholar 

  • Skalinska M (1946) Polyploidy in valeriana officinalis Linn. In relation to its ecology and distribution. J Linn Soc London, Bot 53:159

    Article  Google Scholar 

  • Slotkin RK, Vaughn M, Borges F, Tanurdzic M, Becker JD, Feijo JA, Martienssen RA (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136 (3):461–472. doi: S0092-8674(08)01644-9 [pii] 10.1016/j.cell.2008.12.038

    Google Scholar 

  • Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, dePamphilis CW, Wall PK, Soltis PS (2009) Polyploidy and angiosperm diversification. Am J Bot 96(1):336–348. doi: 10.3732/ajb.0800079

    Article  PubMed  Google Scholar 

  • Soltis DE, Rieseberg LH (1986) Autopolyploidy in Tolmiea menziesii (Saxifragaceae): genetic insights from enzyme electrophoresis. Am J Bot 73(2):310–318

    Article  CAS  Google Scholar 

  • Soltis DE, Soltis PS (1999) Polyploidy: recurrent formation and genome evolution. Trends Ecol Evol 14(9):348–352. doi: 10.1016/s0169-5347(99)01638-9

    Article  PubMed  Google Scholar 

  • Soltis DE, Soltis PS, Schemske DW, Hancock JF, Thompson JN, Husband BC, Judd WS (2007) Autopolyploidy in angiosperms: have we grossly underestimated the number of species? Taxon 56(1):13–30

    Google Scholar 

  • Soltis PS, Soltis DE (2009) The role of hybridization in plant speciation. Annu Rev Plant Biol 60(1):561–588. doi: 10.1146/annurev.arplant.043008.092039

    Article  CAS  PubMed  Google Scholar 

  • Song K, Lu P, Tang K, Osborn TC (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Nat Acad Sci 92(17):7719–7723

    Article  CAS  PubMed  Google Scholar 

  • Song K, Tang K, Osborn T (1993) Development of synthetic Brassica amphidiploids by reciprocal hybridization and comparison to natural amphidiploids. Theor Appl Genet 86:811

    Article  Google Scholar 

  • Stebbins G (1947) Types of polyploids: their classification and significance. Adv Genet 1:403

    Article  PubMed  Google Scholar 

  • Stebbins GL (1950) Variation and evolution in plants. Columbia University Press, New York

    Google Scholar 

  • Stebbins GL (1971) Chromosomal evolution in higher plants [by] G. Ledyard Stebbins. Contemporary biology, vol Accessed from http://nla.gov.au/nla.cat-vn1859678. Edward Arnold, London

  • Storchova Z, Breneman A, Cande J, Dunn J, Burbank K, O’Toole E, Pellman D (2006) Genome-wide genetic analysis of polyploidy in yeast. Nature 443 (7111):541–547. doi: http://www.nature.com/nature/journal/v443/n7111/suppinfo/nature05178_S1.html

    Google Scholar 

  • Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J (2007) Phenotypic and Transcriptomic changes associated with Potato Autopolyploidization. Genetics 176(4):2055–2067. doi: 10.1534/genetics.107.074286

    Article  CAS  PubMed  Google Scholar 

  • Tanurdzic M, Vaughn MW, Jiang H, Lee T-J, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 6(12):e302. doi: 10.1371/journal.pbio.0060302

    Article  CAS  Google Scholar 

  • Tate JA, Symonds VV, Doust AN, Buggs RJA, Mavrodiev E, Koh J, Soltis PS, Soltis DE (2009) Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 50 + years after Ownbey’s discovery. Am J Bot 96:979–988

    Article  PubMed  Google Scholar 

  • Tate JA, Ni Z, Scheen A-C, Koh J, Gilbert CA, Lefkowitz D, Chen ZJ, Soltis PS, Soltis DE (2006) Evolution and expression of Homeologous Loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 173(3):1599–1611. doi: 10.1534/genetics.106.057646

    Article  CAS  PubMed  Google Scholar 

  • Valvekens D, Montagu MV, Lijsebettens MV (1988) Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Nat Acad Sci U S A 85(15):5536–5540

    Article  CAS  Google Scholar 

  • Van de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10(10):725–732

    Article  PubMed  CAS  Google Scholar 

  • Vaughn MW, Tanurdzic M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5 (7):e174. doi: 06-PLBI-RA-2115 [pii] 10.1371/journal.pbio.0050174

  • Walia H, Josefsson C, Dilkes B, Kirkbride R, Harada J, Comai L (2009) Dosage-dependent deregulation of an AGAMOUS-LIKE gene cluster contributes to interspecific incompatibility. Curr Biol: CB 19(13):1128–1132

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Chai Y, Chu X, Zhao Y, Wu Y, Zhao J, Ngezahayo F, Xu C, Liu B (2009) Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability. BMC Plant Biol 9(1):63

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Tian L, Lee H-S, Chen ZJ (2006a) Nonadditive regulation of FRI and FLC Loci mediates flowering-time variation in Arabidopsis Allopolyploids. Genetics 173(2):965–974. doi: 10.1534/genetics.106.056580

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Tian L, Lee H-S, Wei NE, Jiang H, Watson B, Madlung A, Osborn TC, Doerge RW, Comai L, Chen ZJ (2006b) Genomewide nonadditive Gene regulation in Arabidopsis Allotetraploids. Genetics 172(1):507–517. doi: 10.1534/genetics.105.047894

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Tian L, Madlung A, Lee H-S, 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(4):1961–1973. doi: 10.1534/genetics.104.027896

    Article  CAS  PubMed  Google Scholar 

  • Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42(1):225–249. doi: 10.1023/a:1006392424384

    Article  CAS  PubMed  Google Scholar 

  • Winge O (1917) The chromosomes: their number and general importance. C.R. Trav Lab, Carlsberg

    Google Scholar 

  • Winge Ö (1932) On the origin of constant species-hybrids. Sven Bot Tidskr 26:107

    Google Scholar 

  • Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286(5439):481–486. doi: 10.1126/science.286.5439.481

    Article  CAS  PubMed  Google Scholar 

  • Xiong Z, Gaeta RT, Pires JC (2011) Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proc Nat Acad Sci 108(19):7908–7913. doi: 10.1073/pnas.1014138108

    Article  CAS  PubMed  Google Scholar 

  • Xu Y, Zhong L, Wu X, Fang X, Wang J (2009) Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 229(3):471–483. doi: 10.1007/s00425-008-0844-8

    Article  CAS  PubMed  Google Scholar 

  • Yaakov B, Kashkush K (2011) Massive alterations of the methylation patterns around DNA transposons in the first four generations of a newly formed wheat allohexaploid. Genome 54(1):42–49. doi: 10.1139/g10-091

    Article  CAS  PubMed  Google Scholar 

  • Yao H, Kato A, Mooney B, Birchler J (2011) Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43. Plant Mol Biol 75(3):237–251. doi: 10.1007/s11103-010-9722-4

    Article  CAS  PubMed  Google Scholar 

  • Yu Z, Haberer G, Matthes M, Rattei T, Mayer KFX, Gierl A, Torres-Ruiz RA (2010) Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc Nat Acad Sci 107(41):17809–17814. doi: 10.1073/pnas.1000852107

    Article  CAS  PubMed  Google Scholar 

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  1. Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA

    Patrick Finigan, Milos Tanurdzic & Robert A. Martienssen

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  1. Patrick Finigan
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  2. Milos Tanurdzic
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Correspondence to Robert A. Martienssen .

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  1. , Florida Museum of Natural History, University of Florida, Museum Road, Gainesville, 32611, Florida, USA

    Pamela S. Soltis

  2. , Florida Museum of Natural History, University of Florida, Museum Road, Gainesville, 32611, Florida, USA

    Douglas E. Soltis

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Finigan, P., Tanurdzic, M., Martienssen, R.A. (2012). Origins of Novel Phenotypic Variation in Polyploids. In: Soltis, P., Soltis, D. (eds) Polyploidy and Genome Evolution. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31442-1_4

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