"DNA Explains the History of Rice"


Yo-Ichiro Sato

(Faculty of Agriculture, Shizuoka University, 836 Ohya, Shizuoka, JAPAN 422-8529. Colloquium Paper – no ref. given. Translated by Tomoko Goto; edited by Bryan Gordon)



History of rice cultivation in China

        According to results of archaeological studies, it is assumed that the first rice cultivars appeared along the middle-lower Yangtze Valley (Fig.1) around 6000-9000 BC. Until recently, it was assumed rice origin was in the Assam-Yunnan region, or between southwest China and northeast India. But old remains associated with ancient rice cultivation have not been found in southwest China, including Yunnan, but along the middle-lower Yangtze Valley. Rice cultivation is assumed to have started later because artifacts do not accompany excavated rice cultivars in Yunnan. Recent studies reject Yunnan as an origin of ancient rice.


Fig. 1. The Origin of Japonica (rice) in China

Japonica, originating along the middle-lower Yangtze Valley, spread and settled in the entire Yangtze Valley by 3,000 BC. By this period, rice spread all over China.

Ecological Environment of Rice Origin

        The middle-lower Yangtze River Valley was covered with a deep laurilignosa (laurel) forest, and the river created a wide marshland on lower ground. Between marshland and forest, there was a plain which dried in dry seasons and stored water in rainy seasons, the type of environment assumed to be ideal for the origin of rice (Fig. 2). It is speculated that much wild rice inhabited this region. When rice cultivation expanded, climate shifted from warm to cold, and Yangtze Valley wild rice distribution (to 40 N. Lat.) contracted. As explained later, this wild rice is japonica with a perennial trait. Perennial refers to reproduction not by seeds but by roots; e.g.s, brushwood, reed and Japanese pampas grass. As perennials prefer a stable environment, marshland was suitable, as seed-breeding plants cannot grow under this environment.

Fig. 2 The Origin of rice cultivars from an ecological point of view


Varieties of Rice Cultivars in the Yangtze Valley

        What rice type originated in the middle-lower Yangtze Valley? Several researchers suggest various hypotheses, but many assume both indica and japonica originated there. However, the only ground for this hypothesis is the fact that carbonized rice grains excavated from Yangtze Valley archaeological sites (e.g., Hemudu) are round and thin.

        Originally it was thought indica grain shape differed from japonica; indica was thin and japonica round. But recent studies show grain shape does not differentiate indica and japonica; it is just a popular view with no basis to discriminate indica/japonica from carbonized rice grain shape.


Indica and japonica in DNA analysis

        How do indica and japonica differ? Are they just different types originating in the same species? According to DNA (deoxyribonucleic acid) analyses, it is plausible to say that indica and japonica belong to two different races. Broadly, DNA is a blueprint of biological life activities, and is also a controller. The best DNA trait is the fact it never changes from environmental impact, unlike grass length or quantity, which used to be analyzed.

        DNA is stored mainly in the nucleus, the "conning tower" of cells, but some DNA exists outside the nucleus, as in chlorophyll. In rice, non-nuclear DNA is inherited only via the maternal line. Thus, we can obtain race lineage by tracing DNA rice chlorophyll. As a result, we know there are two maternal rice lines, indica and japonica.

        Nuclear DNA also differs in indica and japonica. By sorting DNA information in many cultivars by computer, relations between races can be expressed by a tree diagram. By adding genetic information, a 3-D genealogical tree divides in two branches: one of indica and the other japonica (Fig. 3). Genealogical studies by Dr. Hikoichi Oka suggest rice originated from one common source, but DNA analysis refutes his theory.


Fig. 3. Gencology of indica and japonica



        "Restructuring" rice evolutionary theory did not end there, and old theories were constantly overturned. Oka’s theory that "wild rice has no indica-japonica differentiation" is precarious, as recent studies show wild rice contains indica-japonica differentiation in chlorophyll and nuclear DNA. In fact, many wild rice lineages have this differentiation from both DNA type and gene nucleus. The explanation until now was that rice divided into wild and cultivated and cultivated rice divided into indica and japonica type. But a new explanation states rice originally differentiated from indica and japonica, with each having wild rice and cultivated rice type. Thus, it is problematic to say indica and japonica are the same type of ‘rice’. Rather, it is more plausible indica and japonica belong to different field crops of different races.

A Theory: Japonica originated in the Yangtze Valley


        As aforementioned, I assumed indica and japonica have different origins, with no reason to think both originated in the same region. From this point of view, I presented "A theory of japonica origin from the Yangtze Valley" in 1991 (Fig. 4).

Fig. 4. A Theory of japonica origin from the Yangtze Valley


        In order to confirm this theory, the authors wrote a discriminant function based on easy DNA chlorophyll differentiation of indica and japonica from DNA derived from carbonized rice grains. When studies were carried out on carbonized rice grains excavated from several sites near the Yangtze River, we found each grain carries its own DNA trait derived from japonica. Although the result is unconfirmed due to the number of grains and excavation sites used, it is suggested that japonica was cultivated ca. 4000-5000 BC, strengthening our theory that japonica originated in the Yangtze Valley.

        Chinese civilization is mainly characterized as Yellow River Civilization, with the Yangtze Valley regarded as undeveloped, but an hypothesis of an unknown much earlier Yangtze Valley civilization exists.

        As described earlier, many of the oldest rice cultivation sites have been found in the middle and lower Yangtze Valley in the past 10 years, especially between coastal Zhejiang to SE Jiangsu, i.e., Tai Lake region (Fig.1). The capital of Zhejiang, various Liangzhu locations, western Hangzhou and western Henan are current popular sites. The size and quantity of ancient artifacts in these sites suggest an ancient state. The Liangzhu site dates 3,000 BC, while Henan sites date 4,000 BC. Rice cultivation spread over the Yangtze Valley at 4000-3000 BC. If a suggested ancient city then were true, it would be surprising, and it could be said Yangtze Valley Civilization was based on japonica.

The Origin of indica

        We must begin seeking the origin of indica. It has been generally regarded SE and S Asia are places where indica originated. But rice cultivation sites do not pre-date 2,000 BC and onset of rice cultivation would have been very late compared to China.

        The reason may be derived from different Chinese and tropical ecosystems. Under favorable tropical or warm Hypsithermal climate, people obtained food without cultivation, presumably as hunter-gatherers. Different tropical and temperate climates encouraged the beginning of rice cultivation and its rapid growth in China. Problems of a cooling climate and preservation of gathered food were past.

The Yangtze Valley Civilization and the Laurel (laurilignosa) Forest

        I assume that a base of Yangtze Valley Civilization was the "Laurel (laurilignosa) Forest Culture". Then, a thick laurel forest grew near the Yangtze Valley, with Spring and Autumn Dynasty coffins from cemeteries and canoes of this wood supporting this idea, as do excavated pieces of silk cloth and lacquered vessels.

        Alternately, Yellow River Civilization was a cereal civilization based on mainly cultivated millet. Now desert-like, this region earlier was warmer, with more trees. Forest species are uncertain, but likely were deciduous broad-leafed trees originating in eastern Japan, like Quercus glandulifera (young oak) and Fagaceae (beech). Forests sustained both Yangtze Valley and Yellow Valley Civilizations, corresponding to forest analogies in western and eastern Japan.

Why did the Yangtze Valley Civilization disappear?

        Both civilizations maintained their independence to some extent, but when they matured and their territories grew closer, intervention began, with serious opposition between differing cultural elements peaking in the Spring and Autumn period. I suggest this long conflict divided China into south and north.

        After the Spring and Autumn period, the Yellow River Civilization successor destroyed the southern state and its culture, but interestingly, it adapted to rice and its cultivation. Probably, high rice stability and productivity met its managerial style. Rice reaching this evolution is japonica (temperate) and currently domesticated in Japan. This rice is suited to paddy field controlled cultivation. Temperate japonica and the paddy field system could have evolved via Yellow River Civilization.

        Many southerners were oppressed and deprived of their living by south-north opposition in the Spring and Autumn period. Some may have been exiled to various regions by ascending the Yangtze River to the Yunnan mountains, then descending to lowland with a tropical climate, carrying their rice and ancestral culture with them. Recently, the area between Assam to Yunnan is seen as the center of the Laurel Forest Culture, and it is speculated that a large-scale cultural movement occurred in the Spring and Autumn period.