Genetic diversity and population structure of a core collection of Mediterranean durum wheat accessions using DArTseq markers

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). 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. 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.