Optimization of Genotyping-by-sequencing (GBS) in Chrysanthemums: Selecting Proper Restriction Enzymes for GBS Library Construction

Chrysanthemum is one of the most popular ornamental flowers in Korea due to its great diversity of colors and forms. To understand this diversity and to efficiently breed chrysanthemum varieties, a genetic diversity assessment of Korean native chrysanthemum populations using molecular markers is required. Genotyping-by-sequencing (GBS) is a newly developed and widely used next generation sequencing (NGS) method based on the single nucleotide polymorphism (SNP) marker system. In this study, we tested three restriction enzyme combinations (ApeKI, ApeKI/MseI, and ApeKI/MspI) for GBS library construction using eight Korean native Chrysanthemum spp. accessions. Three libraries were constructed and sequenced on the Illumina NextSeq 500 platform and results were analyzed in the Stacks de novo GBS pipeline. Overall, the ApeKI/MseI combination showed the best library quality, highest number of tags, and SNP generation potential.