Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers
Bibliographic record
Abstract
Abstract Plant genebanks contain large numbers of germplasm accessions that likely harbor useful alleles or genes absent in commercial plant breeding programs. Broadening the genetic base of commercial alfalfa germplasm with these valuable genetic variations can be achieved by screening the extensive genetic diversity in germplasm collections and enabling maximal recombination among selected genotypes. In this study, we assessed the genetic diversity and differentiation of germplasm pools selected in northern U.S. latitudes (USDA Plant Hardiness Zone 7 or below) originating from Eurasian germplasm. The germplasm evaluated included four BASE populations (C0) from different geographical origins (Central Asia, Northeastern Europe, Balkans-Turkey-Black Sea, and Siberia/Mongolia), 20 cycle-one populations (C1) derived from each of the four BASE populations selected across five locations in the U.S. and Canada, and four commercial cultivars. Using a panel of 3,000 Diversity Array Technologies (DArTag) marker loci, we retrieved 2,994 target SNPs and approximately 12,000 microhaplotypes. Microhaplotypes exhibited higher genetic diversity values than target SNPs. Principal component analysis and discriminant analysis of principal components revealed significant population structure among the alfalfa populations based on geographical origin, while the check cultivars formed a central cluster. Inbreeding coefficients (F IS ) ranged from − 0.1 to 0.006, with 27 out of 28 populations showing negative F IS values, indicating an excess of heterozygotes. Interpopulation genetic distances were calculated using Rho pairwise distances (F ST adapted for autotetraploid species) and analysis of molecular variance (AMOVA) parameters. All BASE populations showed lower Rho values compared to C1 populations and check cultivars. AMOVA revealed that most of the genetic diversity was among individuals within populations, especially in BASE populations (92.7%). This study demonstrates that individual plants in BASE populations possess high genetic diversity, low interpopulation distances, and minimal inbreeding, characteristics that are essential for base-broadening selection. The populations developed in this project serve as valuable sources of novel alleles for North American alfalfa breeding programs, offering breeders access to diverse, regionally adapted pools for improving various alfalfa traits.
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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 | 0.000 | 0.000 |
| 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) | 0.001 | 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".