Genetic diversity and structure within and between wild and cultivated Saccharina japonica (Laminariales, Phaeophyta) revealed by SSR markers

In the present study, we selected the sporophytes of eight representative cultivars and four wild populations as specimens to assess their genetic diversity level and investigate their population genetic structure using the simple sequence repeat (SSR) markers. The genetic diversity analysis showed that the average genetic diversity of the wild populations from Russia Far East was higher than that of the wild populations from Northern Japan, which was in turn higher than that of the cultivars from China. The wild populations harboring higher genetic diversity level than the cultivars implied that S. japonica domestication might be accompanied by genetic diversity decrease. The four wild populations and the eight cultivars were taken as two groups respectively. Analysis of molecular variance (AMOVA) results indicated that there was significant genetic differentiation between the two groups (ФCT = 0.212, P < 0.01), and the differentiations among populations or cultivars within group were also significant (ФSC = 0.115, P < 0.01). Intensive artificial selection, cultivation method and dispersal model together affected the population genetic structure, and the artificial selection was the main factor caused the significant genetic differentiation between wild and cultivated S. japonica. In addition, the four wild populations and eight cultivars were divided into three genetic groups by Bayesian model-based cluster analysis. The proportion of the genetic variations contained by each genetic group was 39.12%, 32.18% and 28.70% respectively. These discoveries will shed light on the effects of historical and ongoing domestication and cultivation on population genetic structure and diversity of S. japonica, and also provide the foundation for high-efficiency utilization of S. japonica germplasm resources in S. japonica breeding practice.

► Genetic diversity and structure of S. japonica populations were characterized.
► The genetic diversity of wild populations was higher than that of cultivars.
► The S. japonica populations have significant genetic structure differentiation.
► Selection, cultivation and dispersal model affected the population structure.