〇Hiroo NASU (Okayama University of Science), Ken NAITO (National Agriculture and Food Research Organization), Ryo ISHIKAWA (Kobe University), Hiroshi SUGA (Prefectural University of Hiroshima), Tatsuya OTA (The Graduate University for Advanced Studies)
The following is a summary of the research results of Group C03 this year for each target plant species. This research is the result of collaboration between the Principal Investigator, Hiroo Nasu, and his research sub-contractors, Hiroshi Suga, Ken Naito, Ryo Ishikawa, Tatsuya Ota, Tatsuhiko Hamada of Group B04, and Yohei Terai of Group C02.
１．Lacquer tree
Although lacquer tree is considered to be a domesticated plant native to China, its history is not well known where and when domestication occurred in China and when it was introduced to the Japanese archipelago. At the Torihama shell mound in Fukui Prefecture, a natural wood of lacquer tree was reported around 12,000 years ago. If this is indeed lacquer tree, it would mean that there was lacquer tree in the Japanese archipelago during the incipient Jomon period. However, the oldest known example of lacquer products was excavated at the Mibiki site in Ishikawa Prefecture around 7,300 years ago, and there is a gap of several thousand years between the finds of natural wood and the beginning of the use of lacquer as sap. This year, Suga, and his co-workers conducted a whole-genome analysis of the present-day lacquer tree, focusing on samples from Hubei Province, China. In addition, we sampled lacquer tree from natural forests around Kyoto, Japan, and conducted whole-genome analysis of these samples as well. Furthermore, as a basic study to advance ancient DNA analysis of lacquer tree, we verified whether current raw lacquer contains DNA or not. In the future, we will examine whether DNA is contained in the coating of lacquer products.
２．Azuki bean
Azuki was previously thought to be a domesticated plant native to China that was introduced to the Japanese archipelago after the Yayoi period. However, numerous carbonized seeds and seed impressions on pottery have been found at Jomon sites, suggesting that domestication may have begun in the Japanese archipelago during the Jomon period. This year, Naito and his colleagues conducted a genome analysis of the present azuki bean and the wild azuki. The results showed that domesticated azuki beans in the Japanese archipelago are most closely related to wild azuki, indicating that azuki is very likely to be a domesticated plant originating from the Japanese archipelago. It was also revealed that the wild species from southern Tohoku to northern Kanto is most closely related to the present domesticated species. Ota conducted a population genetic analysis of Japanese native azuki cultivars to examine changes in the population size (genetic diversity) of native species in the past. The results indicated that the population size of some native species has decreased over the past 1,000 to 2,000 years. I examined changes in size and seed coat thickness of carbonized seeds of the subgenus Azuki, which were excavated from archaeological sites during the Jomon period. This year, I examined carbonized seeds from the Koigakubo site in Tokyo, Japan, dating from the Middle Jomon period, and confirmed that the subgenus azuki had been excavated. However, their size was found to be small, about that of wild species, and smaller than that of the Chubu region of the same period. The results indicate that the increase in azuki seed size began in the Chubu region in the latter half of the Middle Jomon period, and that the rapid increase in size may have occurred in the Late Jomon period, when it spread to the Chugoku region and southern Kanto region. This result differs slightly in region from the presumed place of origin based on genome analysis of the present species, and further mutual verification is needed. Changes in seed coat thickness, which are associated with seed dormancy, were examined at several sites from the Initial Jomon to Yayoi periods. The results showed that seed coat thickness of the subgenus azuki from the Jomon to the Yayoi period was within the variation of wild azuki, and that no trait change in seed coat thickness occurred. In the current domesticated species of azuki "Dainagon," the seed coat is thicker than that of the wild species, and seed water absorption does not occur through the seed coat, but through a micro-crack on the lens, a region located below the hilum. The occurrence of a mutation that causes a crack on the lens leads to increased water absorption (loss of seed dormancy). Next year, we plan to investigate when this trait change occurred.
３．Rice
Thorough verification of the beginning of rice agriculture in the Japanese archipelago, based on recent direct dating of carbonized seeds and impression studies, have revealed that it does not date back to the Tottaimon-type pottery Period at the end of the Final Jomon period. Future issues include the characterization of rice varieties introduced during this period and the evaluation of their productivity. In addition to the question of whether the rice is a tropical japonica or a temperate japonica, we must also examine issues related to the productivity of rice at that time, such as the characteristics of early-ripening or late-ripening rice varieties and the degree of loss of seed shattering. This year, Ishikawa and his colleagues worked to identify the causal genes involved in the loss of rice seed shattering. As a result, it was found that there are at least three genes (sh4, qsh1, and qsh3) that control rice seed shattering, and that the combination of these genes and one gene (SPR3) that controls the opening of panicle causes the loss of seed shattering. Future work is needed to examine whether these mutations are present in rice from the Tottaimon-type pottery period of the end of Final Jomon to the Yayoi period based on both ancient DNA and morphology (seed shattering marks on the spikelet base).
Ancient DNA analysis is being conducted in cooperation with Tatsuhiko Hamada of Group B04 and Yohei Terai of Group C02. This year, Hamada and I collected a large number of uncarbonized rice husks from Yayoi period deposits at the Aoya Kamijichi site in Tottori Prefecture, where they have been excavating. Terai has succeeded in extracting ancient rice DNA from this material and has already determined the 5.2x genome sequence. In the next fiscal year, additional sequencing of this material will yield more than 10x sequences, which will be used by Ota for genome analysis, and with the cooperation of Ishikawa, we plan to clarify the characteristics and origin of the Yayoi period rice. DNA analysis of rice derived from other archaeological sites is also planned.
４．Japanese barnyard millet
Japanese barnyard millet, a grass grain native to East Asia, is another crop that may have begun domestication in the Japanese archipelago, and it is important to elucidate its origin. This year, we searched for carbonized seeds of the genus Japanese barnyard millet at archaeological sites dating from the Initial and Middle Jomon period. At the Iyai rock-shelter site, Gunma Prefecture in the Initial Jomon period, carbonized seeds of wild Japanese barnyard millet, azuki bean, and soybean have been found, and a large number of carbonized seeds of the genus Japanese barnyard millet-were found again this year. The size of the seeds is similar to that of the ancestral wild barnyard grass, indicating that the wild barnyard grass was collected in the Japanese archipelago in the Initial Jomon period. On the other hand, at the Koigakubo site in Tokyo and other sites dating from the Middle Jomon period, subgenus azuki beans were found, but no barnyard grass seeds were found. This suggests that the genus may have been used in the Initial Jomon period, but was no longer used in the Middle Jomon period. Regarding DNA analysis of the present-day Japanese barnyard millet, Naito and his colleagues are currently collecting samples.
５．Chestnut
The chestnut has also been shown to have larger fruits at the Aota site in Niigata Prefecture during the Late Jomon period, raising the question of whether or not domestication occurred during the Jomon Period. In order to obtain basic data for understanding when and how domestication of chestnut occurred, Naito and Ota have been working on the whole genome analysis of the present Japanese cultivated chestnut (Porotan) since this fiscal year.