Study of genomic variation in bread wheat collection based on next generation sequencing data

Genotyping by Sequencing (GBS) is a Next Generation Sequencing (NGS) technique widely applied in plant breeding that uses restriction enzymes to reduce the complexity of the genome. In the current study the genomic diversity of 87 local and introduced bread wheat genotypes was evaluated using GBS technology. A total of 411 single-nucleotide polymorphisms (SNPs) were obtained for three genomes. The SNP range within each genome was 15–29, 10–36 and 3–17 for A, B and D genome, respectively. The highest number of SNP markers was recorded on the B (48.8%) and the lowest on the D genome (14%). In total, 70.2% of SNPs were transitions (Ts) and 29.8% transversions (Tv). The largest Delta K value was recorded at K = 2, indicating the existence of 2 groups in the collection. The I group contained 68.5% of the introduced accessions, whereas 82% of local genotypes fell into the II group. The average ancestral contribution of the genotypes in I and II groups were 86.4% and 83.6%, respectively. The results of cluster and PCoA analyses were consistent with the STRUCTURE, indicating a sharp differentiation between local and introduced germplasm. Other factors determining the grouping of samples were traits of botanical varieties and genealogy. The SNP markers, revealed in the current study will be used as a genetic source for genotyping and marker-trait association analyzes. The data can be successfully applied in the development and implementation of new strategies for subsequent genetic analysis and breeding