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| Status |
Public on Nov 01, 2015 |
| Title |
Transcriptome modification to the BBAA subgenomes of common wheat since allohexaploidization is largely irreversible |
| Platform organism |
Triticum aestivum |
| Sample organisms |
Triticum aestivum; Triticum turgidum subsp. durum; Triticum turgidum; Aegilops tauschii; Triticum dicoccoides; Triticum carthlicum |
| Experiment type |
Expression profiling by array
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| Summary |
The three subgenomes (B, A and D) of common wheat (2n=6x=42) are largely intact, which makes extraction of the BBAA subgenomes as organismally independent genomes possible. Availability of such novel extracted tetraploid wheat (Extracted-tetra) provides a unique opportunity to study whether and to what extent the BBAA subgenomes of common wheat have been irreversibly modified, as well as its attendant biological consequences, during their evolutionary trajectory as allohexaploidy. We report here that the extracted-tetra is stable in karyotype but with severely deteriorated phenotypes. Microarray-based transcriptome analysis revealed a substantial portion of differentially expressed genes (down- or up-regulation) between extracted and natural tetraploid wheat, Triticum turgidum, which exceeded the transcriptome divergence at tetraploid level, implying reinforced effects of allopolyploidization and domestication at the allohexaploid level. Great majority of the differentially expressed genes showed additive expression in a resynthesized allohexaploid wheat (parented by Extracted-tetra), indicating transcriptome modifications to the BBAA subgenomes are largely irreversible. Analysis of a newly synthesized allohexaploid wheat (parented by T. turgidum) suggests that whereas most of the modified genes are accrued evolutionary changes, some showed immediate regulation post-allohexaploidization and evolutionary perseverance. Homeologue-specific pyrosequencing of 44 genes revealed either concordant or independent expression changes to the B and A homeologues. The Extracted-tetra vs.T. turgidum down-regulated genes showed enrichment for distinct GO categories.
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| Overall design |
Structurally, the three constituent subgenomes of common wheat, BB, AA and DD, are largely intact with only a few inter-subgenomic translocations. Because of these unique attributes, it is feasible to extract the BBAA subgenomes from the common wheat BBAADD genome by hybridization to a durum line and repeated back-crossing to the hexaploid parent, restituting a novel type of extracted tetraploid wheat, namely Extracted-tetr, with a genome constitution BBAA, virtually identical to the subgenomes BBAA of its common wheat donor. Availability of the extracted-tetra, the resynthesized allohexaploid wheat parented by the extracted-tetra, and newly synthesized allohexaploid wheat parented by natural tetraploid wheat, T. turgidum, provides an excellent system to address the issues of whether and to what extent transcriptome modifications to the BBAA subgenomes of common wheat have occurred since its formation ca. 10,000 years ago, timing of the modifications, and their biological consequences. Here, we have addressed these issues by microarray-based transcriptome analysis.
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| Contributor(s) |
Liu B, Qi B, Zhang H, Zhu B |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jun 03, 2013 |
| Last update date |
Dec 04, 2018 |
| Contact name |
bao qi |
| E-mail(s) |
qibao3712@163.com
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| Organization name |
northeast normal university
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| Street address |
5268, renmindajie
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| City |
changchun |
| State/province |
jilin province |
| ZIP/Postal code |
130024 |
| Country |
China |
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| Platforms (1) |
| GPL3802 |
[wheat] Affymetrix Wheat Genome Array |
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| Samples (33)
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| GSM1153334 |
Allo-960S7, biological rep 1 |
| GSM1153335 |
Allo-960S7, biological rep 2 |
| GSM1153336 |
Allo-960S7, biological rep 3 |
| GSM1153337 |
Allo-960 mix, biological rep 1 |
| GSM1153338 |
Allo-960 mix, biological rep 2 |
| GSM1153339 |
Allo-960 mix, biological rep 3 |
| GSM1153340 |
Blackbird, biological rep 1 |
| GSM1153341 |
Blackbird, biological rep 2 |
| GSM1153342 |
Blackbird, biological rep 3 |
| GSM1153343 |
Extracted-tetra, biological rep 1 |
| GSM1153344 |
Extracted-tetra, biological rep 2 |
| GSM1153345 |
Extracted-tetra, biological rep 3 |
| GSM1153346 |
TAA10, biological rep 1 |
| GSM1153347 |
TAA10, biological rep 2 |
| GSM1153348 |
TAA10, biological rep 3 |
| GSM1153349 |
TD265, biological rep 1 |
| GSM1153350 |
TD265, biological rep 2 |
| GSM1153351 |
TD265, biological rep 3 |
| GSM1153352 |
TQ18, biological rep 1 |
| GSM1153353 |
TQ18, biological rep 2 |
| GSM1153354 |
TQ18, biological rep 3 |
| GSM1153355 |
TTR13, biological rep 1 |
| GSM1153356 |
TTR13, biological rep 2 |
| GSM1153357 |
TTR13, biological rep 3 |
| GSM1153358 |
XX329, biological rep 1 |
| GSM1153359 |
XX329, biological rep 2 |
| GSM1153360 |
XX329, biological rep 3 |
| GSM1153361 |
XX329 mix, biological rep 1 |
| GSM1153362 |
XX329 mix, biological rep 2 |
| GSM1153363 |
XX329 mix, biological rep 3 |
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| Relations |
| BioProject |
PRJNA206520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47617_RAW.tar |
150.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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