Rice archaeological remains and the possibility of DNA archaeology: examples from Yayoi and Heian periods of Northern Japan

Japanese rice cultivation in paddy fields has 2,400∼3,000 years of history. Most of modern Japanese rice varieties are classified as Temperate-japonica (Tm-J). Few landraces are recognized as Tropical-japonica (Tr-J) only in southwestern Japan. However, ancient DNA studies and phytolith analysis suggest that Tr-J strains were more popular in the past than now. Maekawa is a complex archaeological site composed of paddies dated from the Yayoi (2,100 years BP) to the Heian (1,100 years BP) periods. Phytolith analysis indicates that intensive rice cultivation was practiced in both periods, but there was no cultivation in the intervening period. Morphological features of bulliform phytoliths suggest that Tr-J was cultivated during both periods. Locally, rice cultivation during the Heian period was brought to a close by a flood event, in which immature rice plants were pulled down and buried in silt to be preserved in a quasi-carbonized/ waterlogged state. Ancient DNA (aDNA) analysis of the carbonized plant culm from Heian Maekawa recovered chloroplast DNA sequences of the 6C7A plastid subtype, which is common to both Tr-J and Tm-J, whereas two plastid subtypes, such as 6C7A and also 7C6A, were found in aDNA of carbonized grains from the Tareyanagi site of the Yayoi period. The latter plastid subtype was specific only to Tr-J. In order to better characterize the past rice populations, modern landraces collected in the local area were classified with morphophysiological traits. Some of the landraces were found to carry several traits of Tr-J, including bulliform phytolith types, but mixed with Tm-J traits. Based on the discontinuous distribution of rice phytoliths between the Yayoi and the Heian period, the early introduction of rice cultivation may have been discontinuous and locally reintroduced after a ∼1,000-year hiatus, but with a genetically different rice population. Such populations were composed from Tr-J like strains as shown by landraces but with reduced diversity in plastid types. Through such changes, since the Yayoi era, Tr-J was largely replaced by Tm-J, although ancient Tr-J continued to participate in the genetic makeup of later rice populations and may have aided the local adaptation of introduced Tm-J.