Genetic diversity and population structure of a core collection of Mediterranean durum wheat accessions using DArTseq markers
Bibliographic record
Abstract
BACKGROUND: Durum wheat was domesticated in the Fertile Crescent and later spread to the Mediterranean, where human and natural selection led to the establishment of local landraces. Since the 1970s, elite durum wheat varieties largely replaced these landraces. However, landraces continue to play an important role in broadening genetic diversity and contributing valuable traits to modern wheat, particularly in the Mediterranean region, which accounts for 45% of global durum wheat production. This study examined the genetic diversity and population structure of 258 durum wheat genotypes, comprising 125 landraces, 54 breeding lines, 43 cultivars, 34 accessions of uncertain improvement status, and two near-isogenic lines. These genotypes originate primarily from various countries in the Mediterranean basin, including Algeria (39 genotypes), Egypt (3), France (45), Israel (2), Italy (54), Jordan (2), Morocco (2), Portugal (51), Spain (50), Tunisia (6), and Turkey (4). RESULTS: The analysis was conducted using 8,015 single nucleotide polymorphism (SNP) markers and 28,200 SilicoDArT markers. Homoeologous A- and B-genome chromosomes exhibited distinct linkage disequilibrium (LD) decay patterns, confirming genetic differences between the two genomes for both SNP and SilicoDArT markers. SNP analysis identified two subpopulations among the tested accessions: Subpopulation 1 contained 34.11% of the accessions, Subpopulation 2 contained 39.53%, and 26.36% were classified as admixture. Similarly, SilicoDArT markers revealed two subpopulations, with 53.10% of accessions in Subpopulation 1, 27.91% in Subpopulation 2, and 18.99% classified as admixture. For SNP markers, Analysis of Molecular Variance (AMOVA) showed that genetic variation was 12.77% between populations, 74.86% among samples within populations, and 12.77% within samples. Discriminant Analysis of Principal Components (DAPC) identified nine groups. AMOVA based on DAPC population assignments indicated that genetic variation was 25.95% between populations, 61.30% among samples within populations, and 12.76% within samples. DAPC was most effective in distinguishing populations based on either their level of improvement or their geographical origin. CONCLUSIONS: This study highlighted the extent of genetic exchange in durum wheat among Mediterranean countries and further supported two primary dispersal pathways: the northern route (north and east of the Mediterranean basin) and the southern route, including North Africa and the Iberian Peninsula. The analyses demonstrated the efficiency of DArTseq markers in differentiating between genotypes and provided a more comprehensive view of available genetic resources, which can be leveraged in breeding programs to introgress beneficial alleles.
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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 | 0.001 |
| 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".