*E-mail: z.tarekegn@cgiar.org

The impact of breeding period and geographical origin on the genetic makeup of wheat populations is a subject of considerable interest in agricultural genetics. In this study, the diversity panel included 908 genotypes sourced from the N.I. Vavilov Institute of Plant Genetic Resources, Consultative Group on International Agricultural Research (CGIAR), and national wheat research programs were investigated using 19,070 polymorphic DArTseq SNP markers to explore the genetic diversity, population structure, and selection signatures.

The population structure analysis divided the study panel into five subpopulations, revealing clear groupings based on breeding periods and environmental adaptation. Principal component analysis (PCA) further confirmed the clustering pattern between modern (clusters 1 and 2) and historical (clusters 4 and 5) wheat populations.

Cluster 3 was intermediate and comprised of genotypes from all breeding improvement periods. Regression analysis between the PCA clustering pattern and year of release revealed a correlation of 0.72. Additionally, clusters 4 and 5 were distinctly grouped based on environmental gradients, with a regression coefficient of 0.30 between PCA and the altitude of the source country of the genotypes. Genotypes in Cluster 4 were primarily sourced from drier regions, such as India and Pakistan, whereas those in Cluster 5 originated from cooler regions, including Russia, Armenia, Ukraine, and China.

Pairwise population differentiation statistics (FST) indicated significant genetic differentiation between modern and historical wheat populations (FST range: 0.034 - 0.190). Linkage disequilibrium (LD) decay revealed a slower LD decay in modern wheat compared to historical (LD decay: 1.53 Mb vs. 0.97 Mb with r2=0.23), which is one of the possible influences of modern breeding. This difference was clearly reflected in the haplotype block analysis, which showed significant variations in the number and size of the blocks between the two populations.

Using eigenGWAS approaches, 186 haplotype block regions were identified under selection, and some of the genomic regions were in proximity to known adaptation, quality, and disease resistance genes. Overall, this study highlights the impact of breeding period and environmental gradient on wheat genetic diversity. Furthermore, exploring landraces based on beneficial haplotype blocks will help enrich the genetic diversity of modern wheat populations in response to changing environmental conditions.