Abstract：Germplasm resources are foundation for superior cultivar breeding, and essential for improve the economic efficiency for Cornus officinalis, a special herb tree species in China. The current study select C. officinalis core collection in the samples from all over the country by inter-simple sequence repeat (ISSR) markers, for the collection, evaluation, preservation and usage of germplasm. One hundred and twenty nine samples were collected from 11 provinces all over China. Total DNA were extracted by modified cetrimonium trimethyl ammonium bromide (CTAB) method and amplified by 11 ISSR markers. To select the core construction, cluster sampling adopts 2 strategies: Random sampling and site sampling, while genetic distances were estimated in 3 ways: Similar matching (SM) genetic similarity coefficient, Jaccard genetic similarity coefficient or Nei & Li genetic similarity coefficient. T test was carried out on the genetic parameters of the original collection, core collection and germplasm collection, to evaluate the representative and heterogeneity. The heterogeneity of the original germplasm and core collection was tested to confirm the representative of the core collection. Eleven primers amplified 87 bands from 129 samples, all of which were polymorphic, and the average loci number of each primer was 7.91. For the whole 129 samples, the number of alleles (Na) was 2.000 0, the average effective number of alleles (Ne) was 1.438 8, average Nei's genetic diversity index (H) was 0.259 3, the average Shannon's information index (I) was 0.400 6. These parameters showed the samples had high genetic diversity at the DNA level. Cluster analysis showed that geographical isolation and genetic differentiation existed in the populations from different areas. Cluster sampling results under 2 sampling strategies and 3 types of genetic distance were compared, the S1D3 group selected 34 samples by site preferred sampling strategy and Nei & Li genetic distance clustering showed the highest genetic diversity parameters. The number of effective alleles, Nei 's genetic diversity index and Shannon information index of the S1D3 group were significantly higher than the initial collection in the 0.01 level of probability, and the genetic diversity was more abundant than the reserve germplasm. Thirteen phenotypic indicators of the original germplasm and the core collection were compared, except for leaf width, petiole length and dried fruit weight differed at the 0.05 level, other 10 traits had no significant difference with the original germplasm. The phenotypic indicators of the selected core germplasm could represent the original germplasm resources. A C. officinalis core collection including 34 samples were selected from 129 germplasms collected from 11 provinces all over China, contained 26.36% of the original germplasm. By comparing the genetic diversity parameters of the core collection，original germplasm and the reserve germplasm, along with the confirmation by 13 phenotypic traits data, the core collection can represent the genetic diversity of the original germplasm. The result can be used in C. officinalis germplasm resource conservation and superior cultivar breeding.
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