Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population
Why this work is in the frame
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Bibliographic record
Abstract
Alfalfa (Medicago sativa L.) is a widely planted perennial forage legume grown throughout temperate and dry subtropical regions in the world. Long breeding cycles limit genetic improvement of alfalfa, particularly for complex traits such as biomass yield. Genomic selection (GS), based on predicted breeding values obtained using genome-wide molecular markers, could enhance breeding efficiency in terms of gain per unit time and cost. In this study, we genotyped tetraploid alfalfa plants that had previously been evaluated for yield during two cycles of phenotypic selection using genotyping-by-sequencing (GBS). We then developed prediction equations using yield data from three locations. Approximately 10,000 single nucleotide polymorphism (SNP) markers were used for GS modeling. The genomic prediction accuracy of total biomass yield ranged from 0.34 to 0.51 for the Cycle 0 population and from 0.21 to 0.66 for the Cycle 1 population, depending on the location. The GS model developed using Cycle 0 as the training population in predicting total biomass yield in Cycle 1 resulted in accuracies up to 0.40. Both genotype × environment interaction and the number of harvests and years used to generate yield phenotypes had effects on prediction accuracy across generations and locations, Based on our results, the selection efficiency per unit time for GS is higher than phenotypic selection, although accuracies will likely decline across multiple selection cycles. This study provided evidence that GS can accelerate genetic gain in alfalfa for biomass yield.
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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 | 0.000 | 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 it