Introduction: The domestication bottleneck has reduced genetic diversity in wheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. Objectives: The study aims to explore Genotyping by sequencing to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. Methods: TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie’s and F-statistics (FST) index were used to determine the center of genetic diversity. Results: We found 65% and 47% duplicated accessions in T. timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1). Our results suggest that Israel, Jordan, Syria, and Lebanon as the hub of genetic diversity of wild emmer; Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for the T. timopheevii. Identified core set accessions preserved more than 93% of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. Conclusion: The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
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