The advantages and disadvantages of being polyploid

Key Points

  • The occurrence and behaviour of polyploids — organisms that inherit multiple complete sets of chromosomes — has been studied for nearly a century. Recently, the footprints of ancestral polyploidy have been detected in many eukaryotic genomes, indicating that polyploidization and diploidization can be cyclical.

  • Understanding the effect of polyploidization on gene diversification and genome evolution requires an understanding of the mechanisms that lead to the formation and establishment of polyploidy. The possible incentives and constraints on polyploid formation are discussed.

  • There are three obvious advantages of becoming polyploid: heterosis, gene redundancy (a result of gene duplication) and asexual reproduction. Heterosis causes polyploids to be more vigorous than their diploid progenitors, whereas gene redundancy shields polyploids from the deleterious effect of mutations. Asexual reproduction, for which the mechanistic connection to polyploidy is unclear, enables polyploids to reproduce in the absence of sexual mates.

  • There are several disadvantages, documented or conjectured, of polyploidy. They include the potentially disrupting effects of nuclear and cell enlargement, the propensity of polyploid mitosis and meiosis to produce aneuploid cells, and the epigenetic instability that results in transgressive (non-additive) gene regulation.

  • The amount of experimental evidence that addresses these problems varies considerably. In particular, recent data on gene regulation in polyploids provide interesting but still incomplete information on the genetic responses that are involved in polyploidy and on the role of epigenetic remodelling.

  • Transcriptional remodelling in polyploids has two causes. The first is the interaction of diverged parental genomes that are reunited in the allopolyploid; this interaction has both genetic and epigenetic effects. The second, less characterized causal mechanism is genome duplication.

  • Triploidy and aneuploidy are unstable states that often lead to or result from the more stable polyploidy states such as tetraploidy. Both conditions can have potentially disruptive effects on genome regulation, some of which might result from meiotically unpaired DNA.


Polyploids — organisms that have multiple sets of chromosomes — are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.

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Figure 1: Evolutionary alternation of diploidy and polyploidy.
Figure 2: Polyploid formation and ensuing meiotic and mitotic irregularities.
Figure 3: Contrasting patterns of inheritance in diploids and polyploids.
Figure 4: Ploidy-dependent paramutation.


  1. 1

    Yu, J. et al. The Genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    Paterson, A. H. Polyploidy, evolutionary opportunity, and crop adaptation. Genetica 123, 191–196 (2005).

    Article  CAS  Google Scholar 

  3. 3

    Wong, S., Butler, G. & Wolfe, K. H. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc. Natl Acad. Sci. USA 99, 9272–9277 (2002).

    Article  CAS  Google Scholar 

  4. 4

    Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Becak, M. L. & Kobashi, L. S. Evolution by polyploidy and gene regulation in Anura. Genet. Mol. Res. 3, 195–212 (2004).

    CAS  PubMed  Google Scholar 

  6. 6

    Gu, Z., Cavalcanti, A., Chen, F. C., Bouman, P. & Li, W. H. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19, 256–262 (2002).

    Article  CAS  Google Scholar 

  7. 7

    Christoffels, A. et al. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol. Biol. Evol. 21, 1146–1151 (2004).

    Article  CAS  Google Scholar 

  8. 8

    Van de Peer, Y. & Meyer, A. in The Evolution of the Genome (ed. Gregory, T. R.) 330–363 (Elsevier, San Diego, 2005).

    Google Scholar 

  9. 9

    Stebbins, G. L. Chromosomal Evolution in Higher Plants (Addison–Wesley, Menlo Park, 1970).

    Google Scholar 

  10. 10

    Comai, L. et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12, 1551–1568 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Mayer, V. W. & Aguilera, A. High levels of chromosome instability in polyploids of Saccharomyces cerevisiae. Mutat. Res. 231, 177–186 (1990).

    Article  CAS  Google Scholar 

  12. 12

    Singh, R. J. Plant Cytogenetics (CRC Press, Boca Raton, 2003).

    Google Scholar 

  13. 13

    Ramsey, J. & Schemske, D. W. Neopolyploidy in flowering plants. Annu. Rev. Ecol. Syst. 33, 589–639 (2002).

    Article  Google Scholar 

  14. 14

    Wang, X., Shi, X., Hao, B., Ge, S. & Luo, J. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165, 937–946 (2005).

    Article  CAS  Google Scholar 

  15. 15

    Paterson, A. H., Bowers, J. E. & Chapman, B. A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl Acad. Sci. USA 101, 9903–9908 (2004).

    Article  CAS  Google Scholar 

  16. 16

    Adams, K. L. & Wendel, J. F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8, 135–141 (2005).

    Article  CAS  Google Scholar 

  17. 17

    Taylor, J. S. & Raes, J. in The Evolution of the Genome (ed. Gregory, T. R.) 289–327 (Elsevier, San Diego, 2005).

    Google Scholar 

  18. 18

    Maere, S. et al. Modeling gene and genome duplications in eukaryotes. Proc. Natl Acad. Sci. USA 102, 5454–5459 (2005).

    Article  CAS  Google Scholar 

  19. 19

    Nam, J., Kaufmann, K., Theissen, G. & Nei, M. A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Res. 33, e12 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Langkjaer, R. B., Cliften, P. F., Johnston, M. & Piskur, J. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421, 848–852 (2003).

    Article  CAS  Google Scholar 

  21. 21

    Rastogi, S. & Liberles, D. A. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol. Biol. 5, 28 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Zhang, Z. & Kishino, H. Genomic background predicts the fate of duplicated genes: evidence from the yeast genome. Genetics 166, 1995–1999 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Papp, B., Pal, C. & Hurst, L. D. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661–664 (2004).

    Article  CAS  Google Scholar 

  24. 24

    Langham, R. J. et al. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166, 935–945 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 25

    Lynch, M. & Conery, J. S. The origins of genome complexity. Science 302, 1401–1404 (2003).

    Article  CAS  Google Scholar 

  26. 26

    Ramsey, J. & Schemske, D. W. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29, 467–501 (1998).

    Article  Google Scholar 

  27. 27

    Tate, J. A., Soltis, D. E. & Soltis, P. S. in The Evolution of the Genome (ed. Gregory, T. R.) 372–414 (Elsevier, San Diego, 2005).

    Google Scholar 

  28. 28

    Gregory, T. R. & Mable, B. K. in The Evolution of the Genome (ed. Gregory, T. R.) 428–501 (Elsevier, San Diego, 2005).

    Google Scholar 

  29. 29

    Eiben, B. et al. Cytogenetic analysis of 750 spontaneous abortions with the direct-preparation method of chorionic villi and its implications for studying genetic causes of pregnancy wastage. Am. J. Hum. Genet. 47, 656–663 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Groose, R. W. & Bingham, E. T. Gametophytic heterosis for in vitro pollen traits in alfalfa. Crop Sci. 31, 1510–1513 (1991).

    Article  Google Scholar 

  31. 31

    Butruille, D. V. & Boiteux, L. S. Selection–mutation balance in polysomic tetraploids: impact of double reduction and gametophytic selection on the frequency and subchromosomal localization of deleterious mutations. Proc. Natl Acad. Sci. USA. 97, 6608–6613 (2000).

    Article  CAS  Google Scholar 

  32. 32

    Song, J. L. & Wessel, G. M. How to make an egg: transcriptional regulation in oocytes. Differentiation 73, 1–17 (2005).

    Article  CAS  Google Scholar 

  33. 33

    Ostermeier, G. C., Miller, D., Huntriss, J. D., Diamond, M. P. & Krawetz, S. A. Reproductive biology: delivering spermatozoan RNA to the oocyte. Nature 429, 154 (2004).

    Article  CAS  Google Scholar 

  34. 34

    Tanaka, H. & Baba, T. Gene expression in spermiogenesis. Cell. Mol. Life Sci. 62, 344–354 (2005).

    Article  CAS  Google Scholar 

  35. 35

    Auger, D. L. et al. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169, 389–397 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. 36

    Birchler, J. A., Auger, D. L. & Riddle, N. C. In search of the molecular basis of heterosis. Plant Cell 15, 2236–2239 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Kidwell, K. K., Woodfield, D. R., Bingham, E. T. & Osborn, T. C. Relationships among genetic distance, forage yield and heterozygosity in isogenic diploid and tetraploid alfalfa populations. Theor. Appl. Genet. 89, 323–328 (1994).

    Article  CAS  Google Scholar 

  38. 38

    Bingham, E. T., Groose, R. W. Complementary gene interactions in alfalfa are greater in autotetraploids than diploids. Crop Sci. 34, 823–829 (1994).

    Article  Google Scholar 

  39. 39

    Yadegari, R. & Drews, G. N. Female gametophyte development. Plant Cell. 16, S133–S141 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. 40

    McCormick, S. Control of male gametophyte development. Plant Cell. 16, S142–S153 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Mable, B. K. & Otto, S. P. Masking and purging mutations following EMS treatment in haploid, diploid and tetraploid yeast (Saccharomyces cerevisiae). Genet. Res. 77, 9–26 (2001).

    Article  CAS  Google Scholar 

  42. 42

    Stadler, I. J. Chromosome number and the mutation rate in Avena and Triticum. Proc. Natl Acad. Sci. USA 15, 876–881 (1929).

    Article  CAS  Google Scholar 

  43. 43

    Moore, R. C. & Purugganan, M. D. The evolutionary dynamics of plant duplicate genes. Curr. Opin. Plant Biol. 8, 122–128 (2005).

    Article  CAS  Google Scholar 

  44. 44

    Prince, V. E. & Pickett, F. B. Splitting pairs: the diverging fates of duplicated genes. Nature Rev. Genet. 3, 827–837 (2002).

    Article  CAS  Google Scholar 

  45. 45

    Miller, J. S. & Venable, D. L. Polyploidy and the evolution of gender dimorphism in plants. Science 289, 2335–2338 (2000).

    Article  CAS  Google Scholar 

  46. 46

    Nasrallah, M. E., Yogeeswaran, K., Snyder, S. & Nasrallah, J. B. Arabidopsis species hybrids in the study of species differences and evolution of amphiploidy in plants. Plant Physiol. 124, 1605–1614 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Entani, T. et al. Relationship between polyploidy and pollen self-incompatibility phenotype in Petunia hybrida Vilm. Biosci. Biotechnol. Biochem. 63, 1882–1888 (1999).

    Article  CAS  Google Scholar 

  48. 48

    Olmo, E. Nucleotype and cell size in vertebrates: a review. Basic Appl. Histochem. 27, 227–256 (1983).

    CAS  PubMed  Google Scholar 

  49. 49

    Melaragno, J. E., Mehrotra, B. & Coleman, A. W. Relationship between endopolyploidy and cell size in epidermal tissue of Arabidopsis. Plant Cell 5, 1661–1668 (1993).

    Article  PubMed  PubMed Central  Google Scholar 

  50. 50

    Fransz, P., De Jong, J. H., Lysak, M., Castiglione, M. R. & Schubert, I. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl Acad. Sci. USA. 99, 14584–14589 (2002).

    Article  CAS  Google Scholar 

  51. 51

    Jasencakova, Z. et al. Histone modifications in Arabidopsis — high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin. Plant J. 33, 471–480 (2003).

    Article  CAS  Google Scholar 

  52. 52

    Corredor, E., Diez, M., Shepherd, K. & Naranjo, T. The positioning of rye homologous chromosomes added to wheat through the cell cycle in somatic cells untreated and treated with colchicine. Cytogenet. Genome Res. 109, 112–119 (2005).

    Article  CAS  Google Scholar 

  53. 53

    Gruenbaum, Y., Margalit, A., Goldman, R. D., Shumaker, D. K. & Wilson, K. L. The nuclear lamina comes of age. Nature Rev. Mol. Cell Biol. 6, 21–31 (2005).

    Article  CAS  Google Scholar 

  54. 54

    Schotta, G., Ebert, A., Dorn, R. & Reuter, G. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 14, 67–75 (2003).

    Article  CAS  Google Scholar 

  55. 55

    Sebillon, P. et al. Expanding the phenotype of LMNA mutations in dilated cardiomyopathy and functional consequences of these mutations. J. Med. Genet. 40, 560–567 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. 56

    Blumenthal, S. S., Clark, G. B. & Roux, S. J. Biochemical and immunological characterization of pea nuclear intermediate filament proteins. Planta 218, 965–975 (2004).

    Article  CAS  Google Scholar 

  57. 57

    Rose, A. et al. Genome-wide identification of Arabidopsis coiled-coil proteins and establishment of the ARABI-COIL database. Plant Physiol. 134, 927–939 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Cavalier-Smith, T. Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. J. Cell Sci. 34, 247–278 (1978).

    CAS  Google Scholar 

  59. 59

    Akerlund, T., Nordstrom, K. & Bernander, R. Analysis of cell size and DNA content in exponentially growing and stationary-phase batch cultures of Escherichia coli. J. Bacteriol. 177, 6791–6797 (1995). This analysis of ploidy and growth conditions in E. coli addresses the question of why certain cells become endopolypoid; it goes a long way towards demonstrating the generality of the connection between metabolic activity and DNA content.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Bresler, V., Montgomery, W. L., Fishelson, L. & Pollak, P. E. Gigantism in a bacterium, Epulopiscium fishelsoni, correlates with complex patterns in arrangement, quantity, and segregation of DNA. J. Bacteriol. 180, 5601–5611 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61

    Kondorosi, E., Roudier, F. & Gendreau, E. Plant cell-size control: growing by ploidy? Curr. Opin. Plant Biol. 3, 488–492 (2000).

    Article  CAS  Google Scholar 

  62. 62

    Sugimoto-Shirasu, K. & Roberts, K. “Big it up”: endoreduplication and cell-size control in plants. Curr. Opin. Plant Biol. 6, 544–553 (2003).

    Article  CAS  Google Scholar 

  63. 63

    Triantaphyllou, A. C. & Hirschmann, H. Evidence of direct polyploidization in the mitotic parthenogenetic Meloidogyne microcephala through doubling of its somatic chromosome number. Fundam. Appl. Nematol. 20, 385–391 (1997).

    Google Scholar 

  64. 64

    Flemming, A. J., Shen, Z. Z., Cunha, A., Emmons, S. W. & Leroi, A. M. Somatic polyploidization and cellular proliferation drive body size evolution in nematodes. Proc. Natl Acad. Sci. USA 97, 5285–5290 (2000).

    Article  CAS  Google Scholar 

  65. 65

    Fankhouser, G. Maintenance of normal structure in heteroploid salamander larvae, through compensation of changes in cell size by adjustment of cell number and cell shape. J. Exp. Zool. 100, 445–455 (1945).

    Article  Google Scholar 

  66. 66

    Henery, C. C., Bard, J. B. & Kaufman, M. H. Tetraploidy in mice, embryonic cell number, and the grain of the developmental map. Dev. Biol. 152, 233–241 (1992).

    Article  CAS  Google Scholar 

  67. 67

    Andreassen, P. R., Lohez, O. D., Lacroix, F. B. & Margolis, R. L. Tetraploid state induces p53-dependent arrest of nontransformed mammalian cells in G1. Mol. Biol. Cell 12, 1315–1328 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Borel, F., Lohez, O. D., Lacroix, F. B. & Margolis, R. L. Multiple centrosomes arise from tetraploidy checkpoint failure and mitotic centrosome clusters in p53 and RB pocket protein-compromised cells. Proc. Natl Acad. Sci. USA 99, 9819–9924 (2002). This article shows that polyploidy can cause a mitotic crisis.

    Article  CAS  Google Scholar 

  69. 69

    Klinner, U. & Bottcher, F. Mitotically unstable polyploids in the yeast Pichia guilliermondii. J. Basic Microbiol. 32, 331–338 (1992).

    Article  CAS  Google Scholar 

  70. 70

    Lin, H. et al. Polyploids require Bik1 for kinetochore-microtubule attachment. J. Cell Biol. 155, 1173–1184. (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. 71

    Chan, J., Calder, G., Fox, S. & Lloyd, C. Localization of the microtubule end binding protein EB1 reveals alternative pathways of spindle development in Arabidopsis suspension cells. Plant Cell 17, 1737–1748 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. 72

    Schmit, A. C. Acentrosomal microtubule nucleation in higher plants. Int. Rev. Cytol. 220, 257–289 (2002).

    Article  CAS  Google Scholar 

  73. 73

    Risso-Pascotto, C., Pagliarini, M. S. & do Valle, C. B. Multiple spindles and cellularization during microsporogenesis in an artificially induced tetraploid accession of Brachiaria ruziziensis (Gramineae). Plant Cell Rep. 23, 522–527 (2005).

    Article  CAS  Google Scholar 

  74. 74

    Santos, J. L. et al. Partial diploidization of meiosis in autotetraploid Arabidopsis thaliana. Genetics 165, 1533–1540 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75

    Weiss, H. & Maluszynska, J. Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana. Hereditas 133, 255–261 (2000).

    Article  CAS  Google Scholar 

  76. 76

    Mastenbroek, I., deWet, J. M. J. & Lu, C. -Y. Chromosome behavior in early and advanced generation of tetraploid maize. Caryologia 35, 463–470 (1982).

    Article  Google Scholar 

  77. 77

    Doyle, G. G. Aneuploidy and inbreeding depression in random mating and self-fertilizing autotetraploid populations. Theor. Appl. Genet. 72, 799–806 (1986).

    Article  CAS  Google Scholar 

  78. 78

    Randolph, L. F. Cytogenetics of tetraploid maize. J. Agric. Res. 50, 591–605 (1935).

    Google Scholar 

  79. 79

    Muntzing, A. Cytogenetic properties and practical value of tetraploid rye. Hereditas 37, 17–84 (1951).

    Article  Google Scholar 

  80. 80

    Burnham, C. R. Discussions in Cytogenetics (Burgess, Minneapolis, 1962).

    Google Scholar 

  81. 81

    Sears, E. R. Genetic control of chromosome pairing in wheat. Annu. Rev. Genet. 10, 31–51 (1976).

    Article  CAS  Google Scholar 

  82. 82

    Prieto, P., Shaw, P. & Moore, G. Homologue recognition during meiosis is associated with a change in chromatin conformation. Nature Cell Biol. 6, 906–908 (2004).

    Article  CAS  Google Scholar 

  83. 83

    Jenczewski, E. et al. PrBn, a major gene controlling homeologous pairing in oilseed rape (Brassica napus) haploids. Genetics 164, 645–653 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Henry, I. M. et al. Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response. Genetics 170, 1979–1988 (2005). This paper shows that ploidy can “segregate as a trait” in a cross; it also highlights the relationship between polyploidy, triploidy and aneuploidy, and the effect of genetic background.

    CAS  Google Scholar 

  85. 85

    Papp, I. et al. Structural instability of a transgene locus in tobacco is associated with aneuploidy. Plant J. 10, 469–478 (1996).

    Article  CAS  Google Scholar 

  86. 86

    Matzke, M. A., Mette, M. F., Kanno, T. & Matzke, A. J. Does the intrinsic instability of aneuploid genomes have a causal role in cancer? Trends Genet. 19, 253–256 (2003).

    Article  CAS  Google Scholar 

  87. 87

    Birchler, J. A., Riddle, N. C., Auger, D. L. & Veitia, R. A. Dosage balance in gene regulation: biological implications. Trends Genet. 21, 219–226 (2005).

    Article  CAS  Google Scholar 

  88. 88

    Guo, M., Davis, D. & Birchler, J. A. Dosage effects on gene expression in a maize ploidy series. Genetics 142, 1349–1355 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. 89

    Jones, R. N. & Rees, H. Genotypic control of chromosome behaviour in rye. XI. The influence of B chromosomes on meiosis. Heredity 22, 333–347 (1967).

    Article  Google Scholar 

  90. 90

    Camacho, J. P. M. in The Evolution of the Genome (ed. Gregory, T. R.) 223–286 (Elsevier, San Diego, 2005).

    Google Scholar 

  91. 91

    Galitski, T., Saldanha, A. J., Styles, C. A., Lander, E. S. & Fink, G. R. Ploidy regulation of gene expression. Science 285, 251–254 (1999). A microarray analysis of the transcriptome in a yeast ploidy series.

    Article  CAS  Google Scholar 

  92. 92

    Albertin, W. et al. Autopolyploidy in cabbage (Brassica oleracea L.) does not alter significantly the proteomes of green tissues. Proteomics 5, 2131–2139 (2005).

    Article  CAS  Google Scholar 

  93. 93

    Adams, K. L. & Wendel, J. F. Novel patterns of gene expression in polyploid plants. Trends Genet. 21, 539–543 (2005).

    Article  CAS  Google Scholar 

  94. 94

    Mittelsten Scheid, O., Afsar, K. & Paszkowski, J. Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nature Genet. 34, 450–454 (2003).

    Article  CAS  Google Scholar 

  95. 95

    Mittelsten Scheid, O., Jakovleva, L., Afsar, K., Maluszynska, J. & Paszkowski, J. A change of ploidy can modify epigenetic silencing. Proc. Natl Acad. Sci. USA 93, 7114–7119 (1996). A compelling demonstration of epigenetic remodelling that is associated with autopolyploidization.

    Article  CAS  Google Scholar 

  96. 96

    Ye, F. & Signer, E. R. RIGS (repeat-induced gene silencing) in Arabidopsis is transcriptional and alters chromatin configuration. Proc. Natl Acad. Sci. USA 93, 10881–10886 (1996).

    Article  CAS  Google Scholar 

  97. 97

    Wang, J. et al. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167, 1961–1973 (2004). A good example of the epigenetic instability found in neoallopolyploids.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. 98

    Madlung, A. et al. Genomic changes in synthetic Arabidopsis polyploids. Plant J. 41, 221–230 (2005).

    Article  CAS  Google Scholar 

  99. 99

    Pontes, O. et al. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome. Proc. Natl Acad. Sci. USA 101, 18240–18245 (2004).

    Article  CAS  Google Scholar 

  100. 100

    Shaked, H., Kashkush, K., Ozkan, H., Feldman, M. & Levy, A. A. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13, 1749–1759 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. 101

    Madlung, A. et al. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129, 733–746 (2002). This paper reports on the activation of some transposable elements in neopolyploids of the Arabidopsis genus.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. 102

    Kashkush, K., Feldman, M. & Levy, A. A. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160, 1651–1169 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. 103

    He, P., Friebe, B. R., Gill, B. S. & Zhou, J. M. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol. Biol. 52, 401–414 (2003).

    Article  CAS  Google Scholar 

  104. 104

    Kashkush, K., Feldman, M. & Levy, A. A. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nature Genet. 33, 102–106 (2003). This report connects the regulation of repeated elements to that of genes in newly formed allopolyploids.

    Article  CAS  Google Scholar 

  105. 105

    Salmon, A., Ainouche, M. L. & Wendel, J. F. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol. 14, 1163–1175 (2005).

    Article  CAS  Google Scholar 

  106. 106

    Wang, J. et al. Genome-wide non-additive gene regulation in Arabidopsis allotetraploids. Genetics. The first microarray-based comparison of newly formed allopolyploids and their parents.

  107. 107

    Bean, C. J., Schaner, C. E. & Kelly, W. G. Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans. Nature Genet. 36, 100–105 (2004).

    Article  CAS  Google Scholar 

  108. 108

    Baarends, W. M. et al. Silencing of unpaired chromatin and histone H2A ubiquitination in mammalian meiosis. Mol. Cell. Biol. 25, 1041–1053 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. 109

    Turner, J. M. et al. Silencing of unsynapsed meiotic chromosomes in the mouse. Nature Genet. 37, 41–47 (2005).

    Article  CAS  Google Scholar 

  110. 110

    Shiu, P. K., Raju, N. B., Zickler, D. & Metzenberg, R. L. Meiotic silencing by unpaired DNA. Cell 107, 905–916 (2001).

    Article  CAS  Google Scholar 

  111. 111

    Brochmann, C. et al. Polyploidy in arctic plants. Biol. J. Linn. Soc. 82, 521–536 (2004).

    Article  Google Scholar 

  112. 112

    Jackson, J. A. & Tinsley, R. C. Parasite infectivity to hybridising host species: a link between hybrid resistance and allopolyploid speciation? Int. J. Parasitol. 33, 137–144 (2003).

    Article  CAS  Google Scholar 

  113. 113

    Sall, T., Jakobsson, M., Lind-Hallden, C. & Hallden, C. Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica. J. Evol. Biol. 16, 1019–1029 (2003).

    Article  CAS  Google Scholar 

  114. 114

    Adams, K. L., Percifield, R. & Wendel, J. F. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168, 2217–2226 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. 115

    Veitia, R. A. Paralogs in polyploids: one for all and all for one? Plant Cell 17, 4–11 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. 116

    Bicknell, R. A. & Koltunow, A. M. Understanding apomixis: recent advances and remaining conundrums. Plant Cell 16, S228–S245 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. 117

    Koltunow, A. M. & Grossniklaus, U. Apomixis: a developmental perspective. Annu. Rev. Plant Biol. 54, 547–574 (2003).

    Article  CAS  Google Scholar 

  118. 118

    Richards, A. J. Apomixis in flowering plants: an overview. Philos. Trans. R. Soc. Lond. B 358, 1085–1093 (2003).

    Article  CAS  Google Scholar 

  119. 119

    Joly, S. & Bruneau, A. Evolution of triploidy in Apios americana (Leguminosae) revealed by genealogical analysis of the histone H3-Dgene. Evolution 58, 284–295 (2004).

    Article  CAS  Google Scholar 

  120. 120

    van Dijk, P. J. & Bakx-Schotman, J. M. Formation of unreduced megaspores (diplospory) in apomictic dandelions (Taraxacum officinale, s. l.) is controlled by a sex-specific dominant locus. Genetics 166, 483–492 (2004). This is a good example of studies that have shown linkage between a dominant apomictic gene and a heterochromatic B chromosome.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. 121

    Yamauchi, A., Hosokawa, A., Nagata, H. & Shimoda, M. Triploid bridge and role of parthenogenesis in the evolution of autopolyploidy. Am. Nat. 164, 101–112 (2004).

    Article  Google Scholar 

  122. 122

    Verduijn, M. H., Van Dijk, P. J. & Van Damme, J. M. The role of tetraploids in the sexual-asexual cycle in dandelions (Taraxacum). Heredity 93, 390–398 (2004).

    Article  CAS  Google Scholar 

  123. 123

    Sharbel, T. F., Mitchell-Olds, T., Dobes, C., Kantama, L. & de Jong, H. Biogeographic distribution of polyploidy and B chromosomes in the apomictic Boechera holboellii complex. Cytogenet. Genome Res. 109, 283–292 (2005).

    Article  CAS  Google Scholar 

  124. 124

    Saura, A., Lokki, J. & Suomalainen, E. Origin of polyploidy in parthenogenetic weevils. J. Theor. Biol. 163, 449–456 (1993).

    Article  Google Scholar 

  125. 125

    Quarin, C. L., Espinoza, F., Martinez, E. J., Pessino, S. C. & Bovo, O. A. A rise of ploidy level induces the expression of apomixis in Paspalum notatum. Sex. Plant Reprod. 13, 243–249 (2001).

    Article  Google Scholar 

  126. 126

    Nogler, G. A. Genetics of apospory in Ranunculus auricomus. V. Conclusions. Bot. Helv. 94, 411–422 (1984).

    Google Scholar 

  127. 127

    Noyes, R. D. & Rieseberg, L. H. Two independent loci control agamospermy (apomixis) in the triploid flowering plant Erigeron annuus. Genetics 155, 379–390 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. 128

    Grimanelli, D. et al. Non-Mendelian transmission of apomixis in maize–Tripsacum hybrids caused by a transmission ratio distortion. Heredity 80, 40–47 (1998).

    Article  Google Scholar 

  129. 129

    Manning, J. T. & Dickson, D. P. E. Asexual reproduction, polyploidy and optimal mutation rates. J. Theor. Biol. 118, 485–589 (1986).

    Article  Google Scholar 

  130. 130

    Roche, D., Hanna, W. W. & Ozias-Akins, P. Is supernumerary chromatin involved in gametophytic apomixis of polyploid plants? Sex. Plant Reprod. 13, 343–349 (2001).

    Article  Google Scholar 

  131. 131

    Henikoff, S., Ahmad, K. & Malik, H. S. The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293, 1098–1102 (2001).

    Article  CAS  Google Scholar 

  132. 132

    Fishman, L. & Willis, J. H. A novel meiotic drive locus almost completely distorts segregation in mimulus (monkeyflower) hybrids. Genetics 169, 347–353 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. 133

    Sharbel, T. F. & Mitchell-Olds, T. Recurrent polyploid origins and chloroplast phylogeography in the Arabis holboellii complex (Brassicaceae). Heredity 87, 59–68 (2001).

    Article  CAS  Google Scholar 

  134. 134

    Larkins, B. A. et al. Investigating the hows and whys of DNA endoreduplication. J. Exp. Bot. 52, 183–192 (2001).

    Article  CAS  Google Scholar 

  135. 135

    Zhimulev, I. F. et al. Polytene chromosomes: 70 years of genetic research. Int. Rev. Cytol. 241, 203–275 (2004).

    Article  CAS  Google Scholar 

  136. 136

    Weiss, H. & Maluszynska, J. Molecular cytogenetic analysis of polyploidization in the anther tapetum of diploid and autotetraploid Arabidopsis thaliana plants. Ann. Bot. 87, 729–735 (2001).

    Article  CAS  Google Scholar 

  137. 137

    Comai, L., Tyagi, A. P. & Lysak, M. A. FISH analysis of meiosis in Arabidopsis allopolyploids. Chromosome Res. 11, 217–226 (2003).

    Article  CAS  Google Scholar 

  138. 138

    Leach, T. J., Chotkowski, H. L., Wotring, M. G., Dilwith, R. L. & Glaser, R. L. Replication of heterochromatin and structure of polytene chromosomes. Mol. Cell. Biol. 20, 6308–6316 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. 139

    Makunin, I. V. et al. The Drosophila suppressor of underreplication protein binds to late-replicating regions of polytene chromosomes. Genetics 160, 1023–1134 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  140. 140

    Satina, S. & Blakeslee, A. F. Chromosome behavior in triploids of Datura stramonium. I. The male gametophyte. Am. J. Bot. 24, 519–621 (1938).

    Google Scholar 

  141. 141

    Satina, S. & Blakeslee, A. F. Chromosome behavior in triploid Datura. II. The female gametophyte. Am. J. Bot. 24, 621–627 (1938).

    Article  Google Scholar 

  142. 142

    Satina, S., Blakeslee, A. F. & Avery, A. G. Chromosome behavior in triploid Datura. III. The seed. Am. J. Bot. 24, 595–602 (1938).

    Article  Google Scholar 

  143. 143

    Janick, J. & Stevenson, E. C. The effects of polyploidy on sex expression in the spinach. J. Heredity 46, 151–156 (1955).

    Article  Google Scholar 

  144. 144

    Burton, T. L. & Husband, B. C. Fecundity and offspring ploidy in matings among diploid, triploid and tetraploid Chamerion angustifolium (Onagraceae): consequences for tetraploid establishment. Heredity 87, 573–582 (2001).

    Article  CAS  Google Scholar 

  145. 145

    Steinitz-Sears, L. M. Chromosome studies in Arabidopsis thaliana. Genetics 48, 483–490 (1963).

    CAS  PubMed  PubMed Central  Google Scholar 

  146. 146

    Stock, M. et al. A bisexually reproducing all-triploid vertebrate. Nature Genet. 30, 325–328 (2002). A recently discovered example of fixed sexual triploidy.

    Article  Google Scholar 

  147. 147

    Norrmann, G. A. & Quarin, C. L. Permanent odd polyploidy in a grass (Andropogon ternatus). Genome 29, 340–344 (1987).

    Article  Google Scholar 

  148. 148

    Smith-White, S. Polarised segregation in the pollen mother cells of a stable triploid. Heredity 2, 119–129 (1948).

    Article  CAS  Google Scholar 

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I wish to thank three anonymous reviewers for their suggestions. I also gratefully acknowledge funding by the National Science Foundation Plant Genome Program.

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A polyploid that has been produced by artificially inducing chromosome doubling.


Gradual conversion from polyploidy to diploidy through genetic changes that differentiate duplicated loci.


Retention by duplicated genes of different components of the original common function.


Acquisition of novel function by a duplicated gene.


A mitotically stable change in gene expression that depends not on a change in DNA sequence, but on covalent modifications of DNA or chromatin proteins such as histones.


The increase in performance displayed by hybrids compared with their inbred parents. Because performance can be a subjective trait (for example, age of reproduction), a more precise definition is non-additive inheritance in which a trait in the F1 transgresses both parental values.


Sterility or other deleterious trait of an F1 hybrid that results from incompatibilities between parental genomes.


A polyploid that is generated through hybridization and thus combines different types of chromosome sets; by contrast, an autopolyploid arises through the multiplication of the same chromosome set.


Duplicated genes or chromosomes that are derived from different parental species and are related by ancestry.


Meiotic association of more than two chromosomes, resulting in synapsis and recombination between partners.


The property of having a chromosome number that is not an exact multiple of X.


The microtubule-organizing centre that divides to organize the two poles of the mitotic spindle and directs assembly of the cytoskeleton, so controlling cell division, motility and shape.


The loss of vigour and fitness that is observed when genome-wide heterozygosity is decreased by inbreeding.


The action of chemical, physical and biological agents that damage DNA.


Successive rounds of DNA replication without cytokinesis.


The property of cells in certain developmental stages of an organism of having more chromatid sets or, less frequently, more chromosome sets than the germ line.


Species that produce embryos from maternal tissues, bypassing normal meiosis and sexual fusion of egg and sperm.


Departure from the expected gametic ratio of alleles that is observed in the progeny of a cross, usually caused by preferential loss of certain chromosomes during gametogenesis (meiotic drive) or by selection on gametes and zygotes.


The ability of the same genotype to change and adapt its phenotype in response to different environmental conditions.


An organism or cell that has a balanced set of chromosomes.


Supernumerary chromosomes that differ from the normal complement by being dispensable, often heterochromatic and exhibiting unusual meiotic behaviour.


A strain of a species, usually classified from the geographical site of isolation. In the Arabidopsis genus it is also known as an ecotype.


Allelic composition over a contiguous chromosome stretch.


The concomitant and widespread misregulation and activation of suppressed heterochromatic elements, leading to genomic remodelling.


A fertilization-derived, triploid nutritive tissue that is found in the seeds of flowering plants.

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Comai, L. The advantages and disadvantages of being polyploid. Nat Rev Genet 6, 836–846 (2005).

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