Integration and imputation of GBS-derived and DArTseq-derived SNP markers in assessing genetic diversity of bread wheat genotypes

Overview

This study integrated single nucleotide polymorphism (SNP) markers derived from two distinct genotyping platforms—Genotyping-by-Sequencing (GBS) and Diversity Array Technology sequencing (DArTseq)—to comprehensively assess genetic diversity within Iranian bread wheat germplasm. The research addressed the technical challenge of unifying molecular marker datasets from heterogeneous genotyping sources through imputation methodology, enabling consolidated analysis of 357 wheat accessions with complementary marker information.

Methods and approach

The analysis employed sequential imputation of missing genotypic data to integrate GBS-derived and DArTseq-derived SNP markers. Initial imputation of missing data for 357 Iranian bread wheat accessions genotyped via GBS substantially increased the number of usable SNP markers from the GBS platform. Subsequent imputation utilized a reference panel of 90 accessions genotyped with DArTseq technology to impute markers for remaining genotypes. The consolidated dataset comprised 46,876 GBS-derived SNP markers and 3,417 DArTseq-derived SNP markers of high quality. Genetic diversity was assessed through cluster analysis, and selection signatures were detected via fixation index (Fst) calculations to identify genomic regions exhibiting elevated differentiation between populations. Functional annotation of candidate regions under selection examined gene ontology enrichment.

Results

The integrated marker dataset effectively distinguished cultivars from landraces and stratified the 357 genotypes into three discrete cluster groups. High complementarity between the two marker systems was demonstrated through concordant patterns of diversity assessment. Fst-based analysis identified genomic regions exhibiting signatures of natural and artificial selection. Genes located within these selection signature regions were predominantly involved in DNA transcriptional regulation, cell wall organization, protein phosphorylation, and biotic stress defense mechanisms—pathways particularly relevant to population differentiation under environmental pressure. In contrast, genes associated with DArTseq-derived SNP markers demonstrated enrichment in broader functional categories including transcriptional regulation and cell structural processes, suggesting potentially lower directional selection sensitivity for this platform. Despite this differential functional profile, DArTseq-derived markers identified distinct selection signatures, demonstrating their complementary contribution to genomic analysis.

Implications

The methodological framework developed here provides a general approach for integrating multi-platform SNP marker datasets through imputation, addressing a substantial technical barrier in comparative genomic studies where samples have been genotyped through heterogeneous platforms. The resulting consolidated dataset represents a foundational genomic resource for downstream applications in wheat germplasm analysis, including genome-wide association studies and genomic prediction of agronomic traits relevant to breeding objectives. The differential functional enrichment patterns observed between GBS and DArTseq selection signatures indicate platform-specific sensitivity to different categories of selection pressure, suggesting that concurrent deployment of complementary genotyping platforms may enhance detection of selection signatures operating across variable genomic contexts.