Allopolyploid hybridization serves as a major pathway for plant evolution,
but in its early stages it is associated with phenotypic and genomic instab
ilities that are poorly understood. We have investigated allopolyploidizati
on between Arabidopsis thaliana (2n = 2x = 10; n, gametic chromosome number
; x, haploid chromosome number) and Cardaminopsis arenosa (2n = 4x = 32). T
he variable phenotype of the allotetraploids could not be explained by cyto
logical abnormalities. However, we found suppression of 20 of the 700 genes
examined by amplified fragment length polymorphism of cDNA. Independent re
verse transcription-polymerase chain reaction analyses of 10 of these 20 ge
nes confirmed silencing in three of them, suggesting that similar to 0.4% o
f the genes in the allotetraploids are silenced. These three silenced genes
were characterized. One, called K7, is repeated and similar to transposons
. Another is RAP2.1, a member of the large APETALA2 (AP2) gene family, and
has a repeated element upstream of its 5' end. The last, L6, is an unknown
gene close to ALCOHOL DEHYDROGENASE on chromosome 1. CNG DNA methylation of
K7 was less in the allotetraploids than in the parents, and the element va
ried in copy number. That K7 could be reactivated suggests epigenetic regul
ation. L6 was methylated in the C. arenosa genome. The present evidence tha
t gene silencing accompanies allopolyploidization opens new avenues to this
area of research.