Development and characterization of microsatellite markers from an enriched genomic library of Saccharina japonica

Saccharina (Laminaria) is an important economic seaweed. Simple sequence repeat (SSR) markers were developed for S. japonica from an SSR-enriched genomic library using a modified magnetic-bead enrichment protocol. Sequence analysis of 2,853 randomly picked recombinant colonies indicated that 1,092 of the colonies contained microsatellites. After filtration, the remaining 593 unique sequences were examined for their suitability and 266 primer pairs were ultimately designed. Among them, 179 could be used for genetic study by practicability tests. Then, 23 pairs of core primers with good representativeness were selected to analyze 13 Saccharina (Laminaria) gametophyte lines, which are widely used in breeding and economic cultivation in China. A total of 72 alleles were detected with an average of 3.13 alleles per locus. The Nei’s (1973) gene diversity (H) of these markers ranged from 0.1420 to 0.7222. Cluster analysis was generated from genetic distance by the Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) which resolved the 13 lines into two main groups in accord with their geographic distribution. These results indicated that the SSR markers developed in this study were informative and would be useful for genetic analysis and germplasm management in Saccharina (Laminaria).