Dual-color fluorescence in situ hybridization with combinatorial labeling probes enables a detailed karyotype analysis of Saccharina japonica

Saccharina japonica is an economically and ecologically important alga. In recent decades, cytogenetic researches have promoted the large-scale farming of this kelp. However, no reliable cytological landmarks have been developed to distinguish chromosomes and help establish the precise karyotype of S. japonica. In this study, the simple sequence repeat (SSR) (GCT)7 motif with high occupancy level and polymorphism, and a specific SSR (GCT)7 were screened from the genome of S. japonica with all together bioinformatics tools. The existence of (GCT)7 motif and the specific SSR (GCT)7 in the genomic DNA of S. japonica were verified by PCR and southern blot analyses. Fluorescence in situ hybridization (FISH) analysis of the specific SSR (GCT)7 demonstrated that it was stably inherited and co-dominant. With the combined probes of SSR (GCT)7 motif and telomere DNA repeats, dual FISH was conducted for the karyotyping analysis of S. japonica. In agreement with the bioinformatics analysis results, FISH signals of the probe of (GCT)7 motif distributed on all the metaphase chromosomes of the gametophyte of S. japonica with different patterns, and 31 chromosomes were identified. Correspondingly, 31 pairs of homologous chromosomes were distinguished in the sporophyte of S. japonica on the basis of the co-localization of probes of (GCT)7 motif and telomere DNA repeats, as well as the size of metaphase chromosomes. This is the first report of the precise karyotype of S. japonica, which would contribute to the genomic physical mapping and the further genetic breeding of this important brown alga. •Simple sequence repeats (SSRs) are useful markers in chromosome identification and molecular karyotyping.•SSR (GCT)7 motif with high polymorphism was screened and identified in the genome of Saccharina japonica.•The specific SSR (GCT)7 was verified to be stably inherited and co-dominant.•Dual-color FISH was processed with combinatorial labeling probes of Arabidopsis-type telomere and SSR (GCT)7 motif.•The detailed karyotype of S. japonica was established for the first time.