Development of genic SSR markers from an assembled Saccharina japonica genome

Saccharina japonica, a marine brown alga, is an economically important species that has been cultivated in China for approximately a century. We identified 11,973 simple sequence repeats (SSRs) in 58.3 Mb of predicted coding sequence from an assembled S. japonica genome using Illumina paired-end sequencing data. Trinucleotide SSRs were the most abundant motif. Twenty-six loci amplified by the 57 unique primer pairs we designed from trinucleotide genic SSRs (repeat number >10) were polymorphic, among the 55 S. japonica individuals tested. The number of alleles per locus ranged from 2 to 7 (average 3.46). The observed and expected heterozygosity per locus ranged from 0.128 to 0.652 and from 0.130 to 0.676, respectively. Two loci deviated from the Hardy–Weinberg equilibrium and two others were in linkage disequilibrium. We demonstrate that genic SSRs can be efficiently identified from assembled and annotated genomes using Illumina sequencing data. The novel polymorphism markers that we have identified, with informative flanking sequences and unique positional relationships to the genome, should facilitate genetic diversity analysis and further genetic studies in this species.