Genotyping-by-sequencing -based genome-wide SNP profiling and DNA fingerprinting of Saudi Arabian faba bean germplasm

Gene banks play a vital role in conserving plant genetic resources (PGR), yet the limited genetic characterization of many collections restricts their effective utilization in breeding and crop improvement. Faba bean (Vicia faba L.) is an important food legume in Saudi Arabia, but its conserved germplasm has remained largely uncharacterized. This study presents the first genome-wide SNP-based assessment of 21 faba bean accessions conserved at the Seed Center and PGR Bank, Ministry of Environment, Water and Agriculture (MEWA), Riyadh, Saudi Arabia.

Genotyping by sequencing (GBS) generated 17,170 high quality SNPs distributed across the six chromosomes of faba bean. SNP based population structure analysis, neighbour-joining (NJ) phylogeny, and principal component analysis (PCA) consistently revealed clear genetic differentiation among accessions, forming distinct clusters independent of geographical origin. Several accessions showed close genetic relationships or redundancy, while Saudi landraces displayed broad genetic diversity. Using a genetic algorithm, we identified a core set of 150 highly informative SNPs and constructed DNA fingerprints for all accessions. Accessions F2 (Egypt) and F4 (Saudi Arabia) shared identical SNP profiles, suggesting potential synonymy, while F15 showed the highest allelic diversity. Several Saudi landraces (F1, F3, F6, F7, F8, F12, F13) also displayed notable genetic variation, highlighting both redundancy and unique diversity within the collection.

This work highlights the first SNP-based DNA fingerprinting platform for faba bean accessions in Saudi Arabia, providing a valuable genomic resource for germplasm authentication, distinctness-uniformity-stability testing, varietal protection, and strategic conservation. The genomic insights and DNA fingerprints developed here will enhance the utilization of conserved germplasm and support future faba bean breeding and sustainable crop improvement efforts.