Ploidy Variation in Plants


Evidence from genome sequences of many plant species indicate that all plants have had a cyclical history of doubling of chromosome numbers, followed by gene deletions back to a near diploid level. Recent cases of increases in genome copy number are generally considered to comprise ploidy variation. Ploidy variation involves changes in the number of whole sets of chromosomes. Aneuploid variation involves changes in the number of individual chromosomes. The two types of chromosomal changes have different consequences for gene expression patterns.

Key concepts:

  • An increase in whole genome chromosome sets is a recurring process in plant evolution followed by deletion of genes back to a near diploid level.

  • Recent genome doubling can consist of genomes from slightly diverged species and are referred to as allopolyploids.

  • Recent genome doubling within a species is referred to as autopolyploids.

  • Allopolyploids and autopolyploids have different genetic behaviours.

  • Cell size increases with the number of genomes present, as does gene expression in general.

  • Aneuploidy is the change in copy number of part of the genome.

  • Aneuploidy produces greater changes in gene expression than does ploidy variation.

Keywords: ploidy; aneuploidy; chromosomes; genomes; gene expression


Barker MS, Kane NC, Matvienk M et al. (2008) Multiple paleopolyploidizations during the evolution of the compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25: 2445–2455.

Birchler JA (1979) A study of enzyme activities in a dosage series of the long arm of chromosome one in maize. Genetics 92: 1211–1229.

Birchler JA (1981) The genetic basis of dosage compensation of Alcohol dehydrogenase1 in maize. Genetics 97: 625–637.

Birchler JA and Newton KJ (1981) Modulation of protein levels in chromosomal dosage series of maize: the biochemical basis of aneuploid syndromes. Genetics 99: 247–266.

Blakeslee AF (1921) Types of mutations and their possible significance in evolution. American Naturalist 55: 254–267.

Blakeslee AF (1924) Distinction between primary and secondary chromosomal mutants in Datura. Proceedings of the National Academy of Sciences of the United States of America 10: 109–116.

Blakeslee AF (1934) New jimson weeds from old chromosomes. Journal of Heredity 25: 80–108.

Blakeslee AF (1941) Effect of induced polyploidy in plants. American Naturalist 75: 117–135.

Blakeslee AF and Avery AG (1937) Methods of inducing doubling of chromosomes in plants. Journal of Heredity 28: 393–411.

Blakeslee AF, Belling J and Farnham ME (1920) Chromosomal duplication and Mendelian phenomena in Datura mutants. Science 52: 388–390.

Bowers JE, Chapman BA, Rong J and Paterson AH (2003) Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433–438.

Church SA and Spaulding EJ (2009) Gene expression in a wild autopolyploid sunflower series. Journal of Heredity 100: 491–495.

Clausen RE and Cameron DR (1944) Inheritance in Nicotiana tabacum. XVIII. Monosomic analysis. Genetics 29: 447–477.

Coe EH (1959) A line of maize with high haploid frequency. American Naturalist 93: 381–382.

DeRocher J, Harkins KR, Galbraith DW and Bohnert H (1990) Developmentally regulated systemic endopolyploidy in succulents with small genomes. Science 250: 99–101.

Freeling M and Thomas BC (2006) Gene‐balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Research 16: 805–814.

Grafi G and Larkins BA (1995) Endoreduplication in maize: involvement of M phase‐promoting factor inhibition and induction of S phase‐related kinases. Science 269: 1262–1264.

Guo M and Birchler JA (1994) Trans‐acting dosage effects on the expression of model gene systems in maize aneuploids. Science 266: 1999–2002.

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

Henry IM, Dilkes BP, Tyagi AP, Lin HY and Comai L (2009) Dosage and parent‐of‐origin effects shaping aneuploid swarms in A. thaliana. Heredity doi 10.1038/hdy.2009.81.

Kato A and Birchler JA (2006) Induction of tetraploid derivatives of maize inbred lines by nitrous oxide gas treatment. Journal of Heredity 97: 39–44.

Kermicle JL (1969) Androgenesis conditioned by a mutation in maize. Science 166: 1422–1424.

Khush GS and Rick CM (1966) The origin, identification and cytogenetic behavior of tomato monosomics. Chromosoma 18: 407–420.

Khush GS and Rick CM (1969) Tomato secondary trisomics: origin, identification, morphology, and use in cytogenetic analysis of the genome. Heredity 24: 129–146.

Kihara H (1930) Genomanalyse bei Triticum und Aegilops. Cytologia 1: 263–270.

Kimber G and Riley R (1963) Haploid angiosperms. Botanical Review 29: 480–531.

Lee HS and Chen ZJ (2001) Protein‐coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Academy of Sciences of the United States of America 98: 6753–6758.

Lilienfeld FA (1951) H. Kihara: Genome analysis in Triticum and Aegilops. Concluding review. Cytologia 16: 101–123.

McClintock B (1929) A cytological and genetical study of triploid maize. Genetics 14: 180–227.

Nagl W (1969) Banded polytene chromosomes in the legume Phaseolus vulgaris. Nature 221: 70–71.

Punyasingh K (1947) Chromosome numbers in crosses of diploid, triploid and tetraploid maize. Genetics 32: 541–554.

Rober FK, Gordillo GA and Geiger HH (2005) In vivo haploid induction in maize‐performance of new inducers and significance of doubled haploid lines in hybrid breeding. Maydica 50: 275–284.

Redei G (1964) Crossing experiences with polyploids. Arabidopsis Information Service 1: 13.

Riddle NC and Birchler JA (2008) Comparative analysis of heterosis in diploid and tetraploid maize. Theoretical and Applied Genetics 116: 563–576.

Satina S, Blakeslee AF and Avery AG (1938) Chromosome behavior in triploid Datura. III. The seed. American Journal of Botany 25: 595–602.

Sears ER (1944) Cytogenetic studies with polyploid species of wheat. II. Additional chromosomal aberrations in Triticum vulgare. Genetics 29: 232–246.

Sears ER (1953) Nullisomic analysis in common wheat. American Naturalist 87: 245–252.

Simillion C, Vandepoole K, Montagu MC, Zabeau M and Van der Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 99: 13627–13632.

Wang J, Tian L, Madlung A et al. (2004) Stochastic and epigenetic changes in gene expression in Arabidopsis polyploids. Genetics 167: 1961–1973.

Weber DF (1991) Monosomic analysis in maize and other diploid crop plants. In: Gupta PK and Tsuchiya T (eds) Chromosome Engineering in Plants: Genetics, Breeding and Evolution, Part A, pp. 181–209. Amsterdam: Elsevier.

Further Reading

Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review of Plant Biology 58: 377–406.

Doyle JJ, Flagel LE, Paterson AH et al. (2008) Evolutionary genetics of genome merger and doubling in plants. Annual Review of Genetics 42: 443–461.

Otto SP and Whitton J (2000) Polyploid incidence and evolution. Annual Review of Genetics 34: 401–437.

Soltis DE and Soltis PS (1993) Molecular data and the dynamic nature of polyploidy. Critical Reviews in Plant Sciences 12: 243–273.

Wendel JF (2000) Genome evolution in polyploids. Plant Molecular Biology 42: 225–249.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Birchler, James A(Dec 2009) Ploidy Variation in Plants. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0002017.pub2]