Phenotypic Instability and Rapid Gene Silencing in Newly Formed Arabidopsis Allotetraploids

Abstract

Allopolyploid hybridization serves as a major pathway for plant evolution, but in its early stages it is associated with phenotypic and genomic instabilities that are poorly understood. We have investigated allopolyploidization between Arabidopsis thaliana (2n = 2x = 10; n, gametic chromosome number; x, haploid chromosome number) and Cardaminopsis arenosa (2n = 4x = 32). The variable phenotype of the allotetraploids could not be explained by cytological abnormalities. However, we found suppression of 20 of the 700 genes examined by amplified fragment length polymorphism of cDNA. Independent reverse transcription-polymerase chain reaction analyses of 10 of these 20 genes confirmed silencing in three of them, suggesting that approximately 0.4% of 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 varied in copy number. That K7 could be reactivated suggests epigenetic regulation. L6 was methylated in the C. arenosa genome. The present evidence that gene silencing accompanies allopolyploidization opens new avenues to this area of research.

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

“…(15) Indeed, transposons including DNA transposons and retrotransposons are reactivated in wheat and Arabidopsis allotetraploids. (42,61,68) In wheat, activation of Wis 2-1A retrotransposons leads to the production of readout transcripts from neighboring genes in both sense and antisense orientations. (68) Using transposon display with template cDNA, Kashkush et al (2003) found that >7% of the Wis 2-1 A-containing transcripts are novel in the amphidiploids (synonymous with allotetraploids) but absent in both parents or absent in the amphidiploids but present in one or both parents.…”

“…(21) How are orthologous protein-coding genes regulated in synthetic interspecific hybrids and allotetraploids? To address this question, several groups took AFLP-cDNA display approaches to uncover novel gene expression patterns in synthetic Arabidopsis allotetraploids and natural A. seucica, (42,70) cotton (31) and wheat (68,82) allotetraploids. Synthetic Arabidopsis allotetraploids were produced by direct hybridization between an A. thaliana Ler autotetraploid and A. arenosa, a naturally outcrossing tetraploid.…”

“…Synthetic Arabidopsis allotetraploids were produced by direct hybridization between an A. thaliana Ler autotetraploid and A. arenosa, a naturally outcrossing tetraploid. (20,42) A. suecica is a natural allotetraploid that was formed through interspecific hybridization between A. thaliana and A. arenosa ancestral species, from $20,000 years (50) to $1.5 million years. (83) The initial survey of gene expression variation indicated $2.5% of gene expression differences in A. suecica relative to A. thaliana and A. arenosa.…”

“…1C) as demonstrated in the production of new Arabidopsis allotetraploids. (42)(43)(44) Fusion of unreduced gametes may be the predominate mode because almost every plant species produces a variable but small amount of unreduced gametes via first or second division meiotic restitution, (45) and many plant species are autotetraploids. (24,41) It is notable that autopolyploids may be formed via either model, except that a single species is involved.…”

“…A relatively low frequency ($1%) of genomic changes was detected in Arabidopsis allotetraploids. (42,44) However, meiotic abnormalities can be as high as 36%, which correlates with pollen sterility and low seed set in synthetic Arabidopsis allotetraploids (61) and rapid rearrangements in some specific genomic regions such as rDNA loci. (62) The various levels of genomic changes observed among different allotetraploids may be due to selection for the surviving allotetraploid individuals that can overcome meiotic abnormalities and reproductive barriers.…”