Development of a 10K breeder-friendly SNP chip for faba bean

Introduction Faba bean breeding and genomics have seen steady progress in recent years, supported by genome sequences and high-density genotyping platforms. These tools have been valuable for trait mapping, diversity assessment, and genomic research, but they have limited routine use in breeding programs due to their relatively high cost. Recent progress in establishing an optimized, cost-efficient genotyping-by-sequencing protocol tailored to the large and complex faba bean genome has created the foundation for a more accessible genotyping solution. Methods Using this approach, we explored the genetic diversity of faba bean germplasm from various panels, providing a comprehensive representation of the crop’s genetic landscape. From this dataset, we identified and selected a high-quality set of informative SNP markers that are evenly distributed across the genome. Building on these resources, we designed a breeder-friendly 10K SNP chip. Results The 10K SNP chip delivers high accuracy, broad genomic coverage, and affordability. The chip was validated across diverse germplasm panels, demonstrating strong clustering performance, high reproducibility, and applicability to breeding-relevant germplasm. Discussion This platform offers a cost-effective alternative to higher-density arrays, enabling its integration into genomic selection, marker-assisted breeding, and diversity monitoring, ultimately supporting accelerated genetic gain and the delivery of improved varieties to farmers.