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Japanese chestnut (Castanea crenata Siebold et Zucc.) is the only fruit tree species to have been domesticated in Japan, and
it has been a part of human life since ancient times. Gene flow from cultivars to natural stands is common in Castanea species,
which hinders a correct interpretation of genetic diversity. To clarify the genetic relationships and breeding history of
chestnut, we analyzed its population structure, direction(s) of gene flow, and demography using 4 cultivar populations and
41 wild populations. The hierarchical population structure analysis revealed that the populations were roughly divided into
Kyushu, southwest, and northeast clusters at K = 3, and cultivar clusters arose at K = 4. Bi-directional gene flow between
cultivars and wild individuals was detected in Kanto region, whereas flow in only one direction — from cultivars to wild
populations — was detected in Tanba region. The most likely scenario estimated by approximate Bayesian computation
was that the Kyushu cluster diverged first, and then the southwest, northeast, and cultivar clusters separated simultaneously.
Assuming a generation time of 20 years, the first divergence was around 50,000 years ago, which was before the Last Glacial
Maximum (LGM, 21,000–18,000 years ago). The other clusters diverged around 20,000 years ago, during the LGM,
which indicates a long breeding history for cultivars. The results obtained in this study provide new insight into the history
of chestnut and would be useful for both breeding and conservation of Japanese chestnut.
Research papers (academic journals)
