Variability in predicted deleterious mutations among barley accessions conserved ex situ
Bibliographic record
Abstract
Abstract Understanding the genetic cost for long‐term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide requires knowledge about the extent and variation of deleterious mutations within and among conserved germplasm collections. Our recent study revealed a wide range of mutations predicted to be deleterious to gene function and averaged sample‐wise mutation burden per deleterious locus across barley, wheat, oat, soybean, maize, rapa, and sunflower germplasm collections. Here we report the extent and variation of predicted deleterious mutations among nine accessions of a barley ( Hordeum vulgare L.) collection from an RNA‐Seq analysis of 16 individual samples of each accession. The assayed accessions were found to vary significantly in the number and proportion of single nucleotide polymorphisms (SNPs) predicted to be deleterious mutations (ranging from 242 to 314 with a mean of 270 and from 0.00073 to 0.00099 with a mean of 0.00086, respectively). Similarly, a significant variation was also observed in the averaged sample‐wise mutation burden estimates per deleterious locus, ranging from 0.541 to 0.747 with a mean of 0.681. Cultivar accessions had higher averages in the proportions of the predicted deleterious SNPs and in the averaged sample‐wise mutation burden estimates than landrace accessions (0.00090 vs. 0.00082 and 0.695 vs. 0.663, respectively). The estimates of deleterious base‐substitution mutations (×10 −8 ) for the nine accessions varied from 0.313 to 0.406 with a mean of 0.349. These within‐collection findings are useful for understanding the genetic cost in conserved germplasm and have implications for long‐term germplasm management and conservation.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 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".