Molecular analyses and present distribution of wild and weedy populations as well as recent archaeological findings suggest that azuki bean has been domesticated first in Japan. Comparative genomic analyses for azuki bean, rice bean, mungbean, and black gram revealed genetic background for major domestication traits, i.e., (A) seed size, (B) pod dehiscence, and (C) water absorption by seeds. The increase of seed size is a genetically complex process and attained by mutations of at least 5 to 7 genes, and the loss of pod dehiscence has simply attained by mutations of 1 or 2 genes for a given species, while the loss of dormancy and/or water absorption by seed is brought by mutations on different numbers and sets of genes among beans. Recent identification of domestication genes and studies on associated changes of phenotypes among beans are discussed. Most changes of domestication traits revealed are due to loss-of-function mutations, which have been selected by farmers. This might explain the reason why domestication could occur rapidly compared with evolution. Based on these findings, we try to develop a new crop by inducing artificial loss-of-function mutations on domestication genes of stress tolerant wild species. This plant breeding strategy is named “Neo-domestication”.

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This paper overviews the study trends on legume cultivation in the East Asian archaeology. In East Asia, cultivation of legumes, such as species of Glycine and Vigna subgen. Ceratotropis, seems to have begun in multiple regions in the middle latitude area, including China, Korea, and Japan, ca. 7000-6000 years ago. Enlargement of the seed size is one feature of the domestication syndrome that demonstrates cultivation. Because cultivation without the enlargement of the seed sie is argued, several approaches are tried to demonstrate the cultivation of legumes. Now, the studies mainly focus on the beginning of cultivation rather than the proof of its existence. An increase in the study of pottery impressions has significantly contributed to clarifying the utilization history of legumes in prehistoric Japan. Pottery impressions of legume seeds not only allowed more critical argument about the enlargement of the seed size with more correct dating, but also identified legumes as synanthropic plants in prehistoric times. Moreover, the difference in species embedded in the pottery between Chinese and Korean Neolithic and Jomon in Japan indicated the existence of an original plant cultivation system in Jomon, that includes no cereal plants, but places legumes as one of the staple plant foods.

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In this paper, after reviewing previous studies on the morphological and trait changes of Glycine max seeds during the Jomon period, I analyzed the temporal changes in seed size and epidermal structure from the Early to Middle Jomon periods, using materials found at the Sekiguchi site, Yamanashi Prefecture, as a case study. The results showed that, during the seed enlargement phase in the first half of the Middle Jomon period, almost no changes in the epidermal structure known as bloom occurred. This observation suggests that the timing of changes in the luster phenotype and epidermal structure was delayed compared to that of seed enlargement, a component of the domestication syndrome. Results of previous studies and this analysis indicated that, in the central highlands of the Japanese archipelago, soybean seeds began to enlarge about 5500–5100 years ago, that their epidermal structure changed since about 5100–4900 years ago, and that their morphology diversified since about 4900–4400 years ago. Temporal difference in the changes of multiple traits of soybeans, i.e., seed size, seed morphology, and epidermal structure, seems to show a process of domestication of soybean (Glycine max) in the Jomon period.

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The recognition of seed impressions of legumes, Glycine and Vigna, on the surface of Jomon pottery has led to an animated discussion on the possibility of cultivation and domestication of these legumes in the Jomon period. Some archaeologists are, however, criticizing the discussion as focusing only on the size of excavated charred legumes and legume impressions, that are the only archaeologically available evidences of ancient legumes. Because lack of the genetic information of ancient legumes restricts the discussion of legume cultivation and domestication in the Jomon period, a broader comparison between legume use, subsistence activities, and other phenomena, such as composition of stone tools and vegetation change around Jomon settlements, seems necessary to examine legume cultivation and domestication. In this paper, based on the Jomon pottery chronology, the author presented the diachronic change in the seed length of legumes over seven thousand years from the initial to final Jomon periods for further comparison between legume use and cultural phenomena through these periods.

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Animal and plant remains from archaeological sites can be used for historical ecology as well as human ecology. Although archaeology has been regarded as human ecology (or human history) in Japan, this study also highlights the role of archaeology as historical ecology that purposes to reveal the history of animals and plants. From the human ecological viewpoint, this study discusses the definition of domestication, an issue in agriculture, based on soybean and adzuki bean, and the significance of legume plants in human history. The use of animal and plant remains as materials for historical ecology is not necessarily common in Japanese archaeology, yet this study suggests that it can greatly contribute to revealing the history not only of domesticated species but of wild species by collaborating phylogenetic studies. Moreover, the significance of the founder effect, genetic drift, and inbreeding should be taken into consideration for examining the domestication syndromes of isolated plant populations by humans. Finally, although only indirect evidence is currently available for addressing the issue, the author examined the importance of the fermentation process in the history of both humans and pulse plants.

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