In order to improve the accessibility of genetic resources, a core collection needs to be constructed and appropriately evaluated. For Cryptomeria japonica, the most important forestry species in Japan, we constructed a core collection derived from 3,203 plus trees. First, genetic redundancy was removed based on SSR genotypes from the plus tree population. One diploid accession from each of the 539 groups that were identified using information on the original growing location was then selected considering the conservation conditions. We defined this population composed of 539 individuals as a core collection for C. japonica, and then evaluated the collection status of this core collection from multiple viewpoints. This core collection proved to contain on average one entry selected per 10 km radius (314 km2) from 10 × 10 km grid squares with an area of more than 40 % covered with C. japonica, and covered more than 85 % retention of all 12 environmental factors affecting plus trees, while maintaining almost the same genetic diversity as the complete set of plus trees. These methods of evaluation from multiple viewpoints, using a geographic information system and genetic markers, were efficient in determining whether the collection of resources was complete, and, if not, where additional efforts for balancing a deficit should be devoted.
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