Genomic sequence and copy number evolution during hybrid crop development in sunflowers
Why this work is in the frame
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Bibliographic record
Abstract
Abstract Hybrid crops, an important part of modern agriculture, rely on the development of male and female heterotic gene pools. In sunflowers, heterotic gene pools were developed through the use of crop‐wild relatives to produce cytoplasmic male sterile female and branching, fertility restoring male lines. Here, we use genomic data from a diversity panel of male, female, and open‐pollinated lines to explore the genetic changes brought during modern improvement. We find the male lines have diverged most from their open‐pollinated progenitors and that genetic differentiation is concentrated in chromosomes, 8, 10 and 13, due to introgressions from wild relatives. Ancestral variation from open‐pollinated varieties almost universally evolved in parallel for both male and female lines suggesting little or no selection for heterotic overdominance. Furthermore, we show that gene content differs between the male and female lines and that differentiation in gene content is concentrated in high F ST regions. This means that the introgressions that brought branching and fertility restoration to the male lines, brought with them different gene content from the ancestral haplotypes, including the removal of some genes. Although we find no evidence that gene complementation genomewide is responsible for heterosis between male and female lines, several of the genes that are largely absent in either the male or female lines are associated with pathogen defense, suggesting complementation may be functionally relevant for crop breeders.
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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 | 0.000 |
| Science and technology studies | 0.001 | 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 it