Genetic evidence that Chinese chestnut cultivars in Japan are derived from two divergent genetic structures that originated in China

The Chinese chestnut (Castanea mollissima Bl.) was introduced into Japan about 100 years ago. Since then, a number of Chinese chestnut cultivars and Japanese–Chinese hybrid cultivars have been selected by farmers and plant breeders, but little information has been available about their origins and genetic relationships. A classification based on simple sequence repeat markers was conducted using 230 cultivars including Japanese chestnut (Castanea crenata Sieb. et Zucc.) cultivars originated in Japan, Japanese–Chinese hybrid cultivars, and Chinese chestnut cultivars originated in both Japan and China. First, a search for synonyms (cultivars with identical genotypes) revealed 23 synonym groups among the Chinese chestnut cultivars, and all but one cultivar from each synonym group was omitted from further analyses. Second, genetic structure analysis showed a clear division between Japanese and Chinese chestnut, and most of the Japanese and Chinese cultivars had a simple genetic structure corresponding to the expected species. On the other hand, most Japanese–Chinese hybrid cultivars had admixed genetic structure. Through a combination of parentage and chloroplast haplotype analyses, 16 of the 18 hybrid cultivars in this study were inferred to have parent–offspring relationships with other cultivars originated in Japan. Finally, Bayesian clustering and chloroplast haplotype analysis showed that the 116 Chinese chestnut cultivars could be divided into two groups: one originated in the Hebei region of China and the other originated in the Jiangsu and Anhui regions of China. The Chinese chestnut cultivars selected in Japan showed various patterns of genetic structure including Hebei origin, Jiangsu or Anhui origin, and admixed. The chestnut cultivar genetic classifications obtained in this study will be useful for both Japanese and Chinese chestnut breeding programs.