Abstract
The merging of two different genomes occurs during the formation of amphidiploids, and the merged regulatory networks have the potential to generate a new gene expression pattern. We examined the genome-wide gene expression of two newly synthesized amphidiploids between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera. 1,137 (4.7%) and 1,316 (5.4%) of probesets showed differential gene expression in A. thaliana–A. halleri and A. thaliana–A. lyrata hybrids respectively, compared to the mid parent value and of these, 489 were in common. Genes that differed in expression between the parental lines tended to have an expression level in both hybrids differing from the mid parent value. In contrast to protein coding genes, there is little differential expression of transposons. Genes in the categories of chloroplast-targeted and response to stress were overrepresented in the non-additively expressed genes in both amphidiploids. As these genes have the potential to contribute directly to the plant phenotype, we suggest that rapid changes of gene expression in amphidiploids might be important for producing greater biomass.
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Acknowledgments
We thank Dr. Tetsuji Kakutani because this work originally started in his laboratory at National Institute of Genetics. We thank Dr. Candice Sheldon and Dr. Michael Groszmann for critical comments on the manuscript and Dr. Masahiro Fujita for his technical advice. This work is supported by Research Fellowship of the Japan Society for the Promotion of Science (JSPS) for Young Scientists and Excellent Young Researcher Overseas Visit Program of the JSPS to R. Fujimoto.
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Microarray data have been deposited with GEO under GSE23318.
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11103_2011_9820_MOESM1_ESM.ppt
Figure S1. Scatter plot of relative signal intensity. Relative signal intensity of each spot from 6 experiments was plotted. Two lines, #39-1 and #39-2, of the artificially synthesized amphidiploid between A. thaliana and A. halleri had highly correlated expression levels (shown in bold letters). Two lines, #77-1 and #77-2, of the artificially synthesized amphidiploid between A. thaliana and A. lyrata also had highly correlated expression levels (shown in bold letters). At–Al Hyb, hybrid between A. thaliana and A. lyrata; At–Ah Hyb, hybrid between A. thaliana and A. halleri. MPV At–Ah, mid parent value between A. thaliana and A. halleri; MPV At–Al, mid parent value between A. thaliana and A. lyrata; r, correlation coefficient. Supplementary material 1 (PPT 195 kb)
11103_2011_9820_MOESM2_ESM.ppt
Figure S2. GO classification. The ratio of the up- and down- regulated genes in At–Al hybrid detected by perfect match probeset. The relative ratios were calculated by dividing the percentage of all annotated genes in A. thaliana. Supplementary material 2 (PPT 88 kb)
11103_2011_9820_MOESM3_ESM.ppt
Figure S3. Verification of four transposons detected in microarrays (Array data) by RT-PCR. At, A. thaliana; Al, A. lyrata; Ah, A. halleri; AtAl, hybrid between A. thaliana and A. lyrata; AtAh, hybrid between A. thaliana, and A. halleri. Right panels are the results of PCR using genomic DNA as a template. Supplementary material 3 (PPT 103 kb)
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Fujimoto, R., Taylor, J.M., Sasaki, T. et al. Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis . Plant Mol Biol 77, 419 (2011). https://doi.org/10.1007/s11103-011-9820-y
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DOI: https://doi.org/10.1007/s11103-011-9820-y