Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat
Bibliographic record
Abstract
Synthetic hexaploid wheat (SHW) lines are created as pre-breeding germplasm to diversify the D subgenome of hexaploid wheat and capitalize upon the untapped genetic diversity of the Aegilops tauschii gene pool. However, the phenotypes observed in the Ae. tauschii parents are not always recovered in the SHW lines, possibly due to inter-subgenome interactions. To elucidate this post-polyploidization genome reprogramming phenomenon, we performed RNA-seq of four SHW lines and their corresponding tetraploid and diploid parents, across ten tissues and three biological replicates. Homoeologue expression bias (HEB) analysis using more than 18,000 triads suggests massive suppression of homoeoalleles of the D subgenome in SHWs. Comparative transcriptome analysis of the whole-genome gene set further corroborated this finding. Alternative splicing analysis of the high-confidence genes indicates an additional layer of complexity where all five splice events are identified, and retained intron is predominant. Homoeologue expression upon resynthesis of hexaploid wheat has implications to the usage and handling of this germplasm in breeding as it relates to capturing the effects of epistatic interaction across subgenomes upon polyploidization. Special considerations must be given to this germplasm in pre-breeding activities to consider the extent of the inter-subgenome interactions on gene expression and their impact on traits for crop improvement.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.003 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".