Development of genomic simple sequence repeat (SSR) markers of Pyropia yezoensis (Bangiales, Rhodophyta) and evaluation of genetic diversity of Korean cultivars

Pyropia yezoensis is the most widely cultivated and economically important marine red alga. However, due to its simple morphology, it is not easy to identify P. yezoensis cultivars by phenotype. In the present study, simple sequence repeats (SSRs) were identified in the scaffold-genome sequence of P. yezoensis cultivar SG104. These SSRs were used to develop SSR markers that could be used to study genetic diversity of P. yezoensis and identify P. yezoensis cultivars. A total of 23,120 SSRs that contained di-, tri-, tetra-, penta-, or hexa-nucleotide repeat motifs were identified. Of the 353 SSR markers that were selected for further analysis, 12 SSRs were selected for their ability to distinguish cultivars and assess cultivar genetic diversity. The 12 SSR loci yielded a total of 30 alleles, ranging from two to three alleles per locus. With the exception of cultivars HP2 and HG, all cultivars generated a single allele for each SSR locus. As such, these results demonstrate that these cultivars are double haploid lines. Cluster and STRUCTURE analyses of the SSR marker data indicated that the studied cultivars could be separated into two main clusters, which have different blade types. These SSR markers will be useful for assessing the genetic diversity of P. yezoensis germplasm collections and can be used for the identification and future registration of new cultivars. The findings of the present study will facilitate the fine genetic mapping and quantitative trait loci analysis of P. yezoensis , and, as such, may provide a framework for the molecular breeding of new P. yezoensis cultivars.