Plant Molecular Biology 43: 387–399, 2000.
M.A. Matzke and A.J.M. Matzke (Eds.), Plant Gene Silencing.
© 2000 Kluwer Academic Publishers. Printed in the Netherlands.
Genetic and epigenetic interactions in allopolyploid plants
Department of Botany, Box 355325, University of Washington, Seattle, WA 98195-5325, USA (e-mail: co-
Key words: chromosome evolution, gene silencing, heterochromatin, interspeciﬁc hybridization, recombination,
Allopolyploid plants are hybrids that contain two copies of the genome from each parent. Whereas wild and
cultivated allopolyploids are well adapted, man-made allopolyploids are typically unstable, displaying homeotic
transformation and lethality as well as chromosomal rearrangements and changes in the number and distribution
of repeated DNA sequences within heterochromatin. Large increases in the length of some chromosomes has been
documented in allopolyploid hybrids and could be caused by the activation of dormant retrotransposons, as shown
to be the case in marsupial hybrids. Synthetic (man-made) allotetraploids of Arabidopsis exhibit rapid changes
in gene regulation, including gene silencing. These regulatory abnormalities could derive from ploidy changes
and/or incompatible interactions between parental genomes, although comparison of auto- and allopolyploids
suggests that intergenomic incompatibilities play the major role. Models to explain intergenomic incompatibilities
incorporate both genetic and epigenetic mechanisms. In one model, the activation of heterochromatic transposons
(McClintock’s genomic shock) may lead to widespread perturbation of gene expression, perhaps by a silencing in-
teraction between activated transposons and euchromatic genes. Qualitatively similar responses, of lesser intensity,
may occur in intraspeciﬁc hybrids. Therefore, insight into genomefunctiongainedfromthestudyofallopolyploidy
may be applicable to hybrids of any type and may even elucidate positive interactions, such as those responsible
for hybrid vigor.
Abbreviations: AFLP-cDNA, ampliﬁed fragment length polymorphism of copy DNA; HDGS, homology-
dependent gene silencing; LTR, long terminal repeat; RFLP, restriction fragment length polymorphism; RT-PCR,
reverse transcriptase polymerase chain reaction; WU-BLASTN, Washington University Basic Local Alignment
Search Tool, nucleotide comparison algorithm.
Whereas wild and cultivated allopolyploid plants are
well adapted, man-made allopolyploids are typically
unstable. Instability refers to the appearance of unex-
pected changes in phenotype, such as homeotic trans-
formation and lethality, and in genome structure, such
as chromosomal rearrangements and changes in the
number and distribution of repeated DNA sequences
within heterochromatin. These instabilities are pre-
sumably eliminated by evolutionary adaptations giv-
ing rise to stable species. However, the molecular
mechanisms underlying these adaptive steps remain
obscure. This review provides examples of instability
and considers the genetic and epigenetic mechanisms
that may be responsible for instability.
Interspeciﬁc hybrids between distant relatives are
usually sterile. In 1912, Digby found a fertile plant
that appeared spontaneously among the sterile hybrids
generated in a cross between two primrose species;
this plant had twice the number of chromosomesof its
sterile sibs (Digby, 1912). While the signiﬁcance of
chromosome doubling eluded Digby, Winge, unaware
of Digby’s results, speculated that speciation could