Development of EST-SSR markers derived from transcriptome of Saccharina japonica and their application in genetic diversity analysis

Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers were developed and characterized for Saccharina japonica using transcriptome data. A total of 98,627 ESTs were screened for SSRs using microsatellite search module (MISA) tool. From those, 9688 SSRs in 8039 ESTs were identified and trinucleotides accounted for 57.69% were the predominant types. Among these EST-SSRs, 1120 SSR primer pairs were ultimately designed and 146 could be used for genetic study by polymorphism tests using four Saccharina DNAs as templates. In the present study, 52 EST-SSR markers with good representativeness were selected to conduct genetic analyses of ten Chinese strains. A total of 139 alleles were detected and alleles per locus ranged from 2 to 5. The percentage of polymorphic loci (P) per strain ranged from 28.85 to 73.08%, Nei’s genetic diversity (H) ranged from 0.1207 to 0.3376 and Shannon’s information index (I) from 0.1819 to 0.5267. Genetic identity and cluster analysis of Saccharina strains were also performed based on the obtained EST-SSR data in our work. As shown by genetic structure analysis, ten strains could be classified into three groups which associated with their parental origin. These obtained EST-SSR markers will be helpful for genetic analysis and molecular marker assisted breeding in Saccharina.