Population structure and genome-wide linkage disequilibrium (LD)were investigated in a Cryptomeria japonica core collection consisting of 510 individuals and providing comprehensive coverage of the natural distribution range of the species, using 4,896 SNP markers. Both Bayesian clustering and principal coordinate analyses clearly subdivided the sample into two distinct groups corresponding to the Japan Sea side and the Pacific Ocean side of Japan. The clustering analysis also detected two subgroups located in Northern Tohoku and Yakushima Island, as was also the case in the natural population. This finding is in accord with the ecogeographical origin of the cultivars; however, the spatial distribution of these clusters was slightly different between the natural population and the core collection, especially in the Chugoku district, an effect which might have resulted from historical human activity. The genetic diversity of the core collection is comparable to, or a little higher than, that of natural populations, indicating that the individuals in the core collection have not suffered from diversity losses caused by a domestication bottleneck. LD analysis with mapped markers indicated that the LD decays rapidly, within approximately 5 cM, in both the core collection and natural populations. The results show that the population described here is a valuable resource for both basic and applied research on C. japonica.
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