Japan’s archaeological record shows that since the Jomon have been planting and interacting with the soybean plant since the Early Jomon period, and the largest soybeans of ancient times appear to have come from Japan.
According to a Lee & Crawford 2011 study, small seeded soybean appeared in the archaeological record as early as 7000 cal BP in Japan and 9000–8600 cal BP in northern China. Large seed sizes appeared in Japan by 5000 cal BP (Middle Jomon) and in Korea by 3000 cal BP (Early Mumun) (evidenced by direct AMS radiocarbon dates on charred soybean seeds indicating selection). According to the same study, soybean seeds recovered in China from the Shang through Han periods are similar in length to the large Korean and Japanese specimens, but the overall size of the large Middle and Late Jomon, Early Mumun through Three Kingdom seeds is significantly larger than any of the Chinese specimens. The study supported the the view informed by recent phyologenetic research that soybean was domesticated in several locations in East Asia, and further proposed that it is likely that a type (landrace) of large seeded soybean came from Japan and was domesticated in Korea, spreading outwards from there.
Also from the study:
“DNA analysis of charred legumes, not directly dated, from the Early Jomon (ca. 5800–5300 cal BP) component of the Sannai Maruyama site indicates that some may be Glycine sp. . The identification of the seeds as Glycine, however, has been questioned because of their morphology . Nevertheless, the Middle Jomon Shimoyakebe specimens are the largest specimens in East Asia at the time (ca. 5000 cal. BP) (Figures 7, 10). Soybean impressions have also been identified on pottery at the late Early Jomon Tenjin  and the Middle Jomon Sakenomiba and Meotoshi sites . Six soybean impressions on pottery from the Late Jomon in Kyushu  are estimated to be 10.2–11.8 mm by 6.5–7.9 mm wide, the largest soybean seeds in this study. The Jomon soybean archaeological record is poorly known because flotation sampling is only regionally common. Furthermore the 100 Jomon legume reports (usually Vigna sp.) need to be reviewed. Ongoing research indicates that soybean may, indeed, be more extensively represented in the Jomon archaeological record. For example Crawford reexamined an unknown seed from the Late Jomon Usujiri Shogakko site (ca. 3500 cal BP). The seed is soybean (4.5 by 2.3 by 3.1 mm). Soybean has not been reported in the Hokkaido Jomon record previously .
The large deposits of seeds found in Yangshao, Longshan, Chulmun, and Jomon sites indicate a long history of soybean and human interaction. Soybean cultivation and selection for larger seeds occurred by 5000 BP in Japan and at least 3500 BP in Korea and China. Certainly the setting for selection of DRTs is apparent 9000–5000 BP in China, Korea, and Japan.
Historic evidence suggesting that soybean cultivation revolutionized agriculture in the Eastern Zhou Dynasty of China shortly after its introduction around 2510 BP from the northeast  should not be taken to mean that soybean was domesticated in only one location and that it was the Northeast. The earliest appearance of soybean in NE China is at the Xinglonggou site (Locality 3) where it appears shortly after 4000 cal BP . The specimens at Xinglonggou are called “domesticated”  but the criteria for this identification are not clear. Several finds of soybean in Jilin and Heilongjiang provinces indicate that soybean spread throughout the northeast after 3000 BP during the Zhou period . This record, sparse though it is, suggests that soybean was introduced to, rather than from, NE China. Botanical data are consistent with this view too. The highest diversity among modern soybean landraces is found in the Huanghe region so, following Vavilov’s idea of crop origins , Dong et al.  and Li et al.  suggest that soybean was domesticated in one location, the Huanghe valley, rather than somewhere in NE China or elsewhere in East Asia. Seed composition and seed protein electrophoresis  have also been used to support this view. Tian et al.  also favor the Huanghe hypothesis but they only examined Chinese landraces. Furthermore, diversity only indicates that a crop has a long history in a region not that it was domesticated there. However, the early record for soybean and evidence for selection of larger seeded soybean in the Huanghe valley, and the distinct populations in China from 9000 to 3500 cal BP compared to those from Korea and Japan, is consistent with independent domestication there.
Others, based on historical documents, suggest that soybean was domesticated in South China or in multiple centers in and outside China , . Archaeological evidence for soybean is general absent prior to the Han period (2170–1730 cal BP) in southern China. We are aware of only one report from the Bashidang site (8000 cal BP) , but the identification criteria are not outlined . No early written records mention soybean in South China. Sampling is likely not responsible for the general absence of archaeological soybean there. Many waterlogged sites dating to 8000–4000 cal BP in the Yangzi basin (e.g. Kuahuqiao, Hemudu, Luojiajiao, and Chengtoushan) have large quantities of well preserved plant remains. None have yielded confirmed soybean remains. At the moment, we have no archaeological evidence that a domestication of soybean occurred in southern China.
The hypothesis of multiple domestications in East Asia comes from broad comparative studies of phylogenetic data , , , . For example, the highly differentiated gene pools of Chinese and Japanese soybean point to their separate origins , . Furthermore, distinctions in the chloroplast genomes cannot be explained by pollen flow from wild to domesticated soybean but require that wild plants were taken into cultivation more than once , . The archaeological data are consistent with the multiple origins hypothesis. The archaeological record for soybean in Japan raises a question about a complex issue involving Zhou Dynasty texts . These texts describe soybean as having been introduced from the northeast. This, combined with the absence of a record for soybean in the Huanghe valley at the time, suggested that northeast China was the source of domesticated soybean . Now that we have an extensive record for Neolithic soybean in the Huanghe valley, as well as from Japan and Korea, another interpretation may be worth testing. Could Japan have been a source of a large-seeded landrace of domesticated soybean that spread to Korea and subsequently to China? This record, if it is to be trusted, could be referring to a particular landrace (rather than soybean in general) that would have been quite different from the landraces already grown in China by 2500 BP. We admit that this is highly speculative and difficult to test at this stage of soybean research. Larger Erlitou-Shang soybean remains seem to match the record in Shijing and Xiaxiaozheng indicating a tradition of soybean cultivation in China prior to 3000 BP . Furthermore, soybean-bearing sites are concentrated in the central and eastern Huanghe basin in China where a long history of intensive agriculture and high population density are well documented . Finally, the recent genome sequence comparison of wild and domesticated soybean that points to a complex domestication history for soybean ,  is supported by our analysis.”
Source: Lee G-A, Crawford GW, Liu L, Sasaki Y, Chen X (2011) Archaeological Soybean (Glycine max) in East Asia: Does Size Matter? PLoS ONE 6(11): e26720. https://doi.org/10.1371/journal.pone.0026720
The recently acquired archaeological record for soybean from Japan, China and Korea is shedding light on the context in which this important economic plant became associated with people and was domesticated. This paper examines archaeological (charred) soybean seed size variation to determine what insight can be gained from a comprehensive comparison of 949 specimens from 22 sites. Seed length alone appears to represent seed size change through time, although the length×width×thickness product has the potential to provide better size change resolution. A widespread early association of small seeded soybean is as old as 9000–8600 cal BP in northern China and 7000 cal BP in Japan. Direct AMS radiocarbon dates on charred soybean seeds indicate selection resulted in large seed sizes in Japan by 5000 cal BP (Middle Jomon) and in Korea by 3000 cal BP (Early Mumun). The archaeological record appears to disconfirm the hypothesis of a single domestication of soybean and supports the view informed by recent phyologenetic research that soybean was domesticated in several locations in East Asia.
However, different conclusions pinpointing the origins of fully domesticated soybeans to Central China, were obtained from Yingpeng Han et al.,’s 2015 paper “Domestication footprints anchor genomic regions of agronomic importance in soybeans” New Phytologist 209(2) · October 2015 DOI: 10.1111/nph.13626
“Present-day soybeans consist of elite cultivars and landraces (Glycine max, fully domesticated (FD)), annual wild type (Glycine soja, non-domesticated (ND)), and semi-wild type (semi-domesticated (SD)). FD soybean originated in China, although the details of its domestication history remain obscure. More than 500 diverse soybean accessions were sequenced … The results indicated that the SD group is not a hybrid between the FD and ND groups. The initial domestication region was pinpointed to central China (demarcated by the Great Wall to the north and the Qinling Mountains to the south)”
“The geographical origin of FD soybeans has been the subject of intense debate, with numerous and contradictory domestication hypotheses, including predictions of single and multiple origins (Hymowitz, 1970; Vavilov, 1982; Xu, 1986; Li, 1994; Gai et al., 2000; Xu et al., 2002; Xu & Gai, 2003). The postulated geographical origins of FD soybeans include northeastern China, the Huang-Huai Valley (central China) and southern China (south of the Yangtze River). Based on large-scale sequencing data, our study revealed that the FD group from the Huang-Huai Valley is more closely related to the ND group and possesses higher sequence diversity than the FD groups from northeastern China and southern China. Additionally, the results from an admixture analysis support a model that indicates that the FD group of the Huang-Huai Valley presents greater genetic introgression from the ND group of the Huang-Huai Valley compared with the FD groups from northeastern and southern China. Thus, the results strongly suggest that FD soybeans were initially derived from ND soybeans in the Huang-Huai Valley.
Through genetic distance, sequence diversity and gene flow analyses, we defined the boundaries of the region of origin in the Huang-Huai Valley for FD soybean as the Great Wall to the north and the Qinling Mountains to the south (central China), revealing a region that presents diverse climates and has experienced thousands of years of soybean cultivation history (Zhang & Hu, 1913; Yu & Nan, 2009).”
Finally, a 2017 Zong et al’s paper’s findings on Yellow River soybean samples were as follows:
“Selection for seed composition appears to have occurred as early as 7,500B.P., indicating that soybean domestication and cultivation were occurring by this time. Significant differentiation of soybean is not evident until 4,000 B.P., and by 3,500B.P., during the Shang period, soybean seed size and oil content substantially increased. Soybean likely underwent further selection for large seed size and higher oil and protein content, distinguishing it further from its wild/weedy ancestor that had smaller seeds, less oil, and higher protein25. Importantly, the “hole” structure is a new clue that helps our understanding of soybean domestication.”
“The Yellow River is acknowledged as an important area of agricultural evolution as well as plant and animal domestication during the Late Pleistocene and Early Holocene and appears to be one of at least three regions in East Asia where soybean was domesticated7 . The earliest associations of people and soybean are in Early Holocene Neolithic communities in the region (9,000–7,500 cal B.P.).
Cultivation also likely began at this time, when other crops such as millet and rice were being cultivated13. … Oil content has potential as an archaeologically visible trait that may help resolve when selection for domestication related traits in soybean began.”
Source: Zong Y. et al. Selection for Oil Content During Soybean Domestication Revealed by X-Ray Tomography of Ancient Beans. Scientific Reports. 7. Article number: 43595. 2017. doi:10.1038/srep43595.