Accumulating Heterozygous Deleterious Mutations in Conserved Soybean Germplasm over Successive Regenerations
Bibliographic record
Abstract
More than 5.9 million plant germplasm accessions currently conserved in over 850 national genebanks worldwide will accumulate deleterious mutations over long-term conservation. However, little is known about how mutations accumulate in germplasm under long-term conservation. An attempt was made using seed-based RNA-Seq analysis to identify and characterize deleterious genetic variants in 190 diverse soybean accessions that were conserved since 1972 and were regenerated up to 10 cycles. The analysis identified 588 deleterious variants, which were widely distributed across 20 soybean chromosomes, mostly present in 10 or fewer samples, associated with diverse biological processes, and largely predicted to be weakly and mildly detrimental. Significant differences in estimates of three mutation burdens (total, heterozygous, and homozygous) were found among the samples, including sample groups representing different countries of origin. Total and heterozygous mutation burden estimates were found to increase significantly with the number of conservation years since accession acquisition and the number of germplasm regenerations, but homozygous mutation burden estimates were not correlated with these two conservation-related accession features. Total mutation burden estimates were negatively correlated with expressed gene counts and RNA integrity numbers (RINs) and marginally positively associated with averaged gene expression levels. Correlations were also found among expressed gene count, averaged gene expression level, and RIN value. No significant differences were detected between seed-based and leaf-based estimates of total mutation burden, expressed gene count, averaged expression level, and RIN. These findings provide the first empirical evidence that total mutation burden increased primarily through the accumulation of heterozygous, rather than homozygous, deleterious mutations over successive soybean germplasm regenerations. This insight is useful for conducting informative assessments of deleterious mutation accumulation and enhancing the management and conservation of plant germplasm.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| 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 source (direct Gemma or distilled Codex), 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".