Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification

Saccharina japonica , a commercially significant brown alga, has been cultivated for several decades in China. Despite extensive efforts to collect and preserve its germplasms, the absence of genetic data and reliable molecular markers has obstructed their effective utilization, thereby limiting genetic improvement of S. japonica . In this study, we performed genetic analysis on an initial collection, consisting of 226 representative Saccharina germplasm accessions, using approximately 4.60 million SNP markers. The results revealed the presence of two major genetic clusters, with clustering patterns consistent with their genetic backgrounds, indicating the reliability of the source information for the representative accessions. Accordingly, we established a core collection of 91 accessions that encompasses all SNP variations and retains the similar clustering structure as the initial collection. Additionally, we identified a set of 130 core SNP markers, which were successfully used for fingerprinting analysis and individual differentiation of the 91 accessions. Notably, one SNP marker located within a candidate sex-determination region demonstrated potential for identifying the sex of Saccharina japonica gametophyte accessions. This study provides valuable genetic insights and a fundamental framework for improving the efficiency of germplasm conservation and utilization in Saccharina . It also offers a foundation for future applications in cultivar identification, genetic research, and the acceleration of molecular breeding efforts in this economically important species. • Genetic analysis of 226 representative Saccharina accessions were performed using SNPs. • A 91-accession mini-core collection retaining variations was developed. • 130 core SNPs were selected for fingerprinting analysis and germplasm identification. • One SNP marker shows potential for identifying Saccharina gametophyte sex.