ARS | Publication request: Using genomic analysis to trace the introduction of oryza sativa to Africa

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 27, 2012
Publication Date: N/A

Technical Abstract: O. sativa is widely cultivated in various countries throughout Africa with the largest acreage being in West, West Central, and East Africa. It has largely supplanted the locally domesticated African rice (O. glaberrima). O. glaberrima cultivation never spread beyond West Africa, so in the other regions of the continent O. sativa, or Asian rice, is the only rice under cultivation. Asian rice is only one of several introduced crops that have become critical to African agriculture, however the origins, timing and historical processes behind the introduction of O. sativa are poorly understood compared to other introduced crops such as maize, taro and bananas. Rather than focusing on the introduction of Asian rice to Africa, scholars have been more interested in the role of enslaved African rice cultivators in the spread of rice farming to the Americas. There is archeological evidence for the presence of O. sativa on the East African coast by 800. Because other crops that were introduced to Africa in the middle of the first millennium, like bananas and taro, came from Southeast Asia it is generally assumed that the same was true for rice. Bananas and taro diffused rapidly across the continent and are now found in virtually all of high rainfall areas of the continent. Historical evidence suggests that rice did not appear in the interior of East Africa or Central Africa until the 19th century. Thus, the process by which Asian rice spread through Africa was more tentative and gradual than other food crops. Because historical observers could not distinguish between O. glaberrima and O. sativa, it is impossible to tell whether travelers’ reports of rice cultivation in West Africa as early as the 14th century refer to Asian or African rice. Thus the timing and origins of the Asian rice grown in West Africa is unknown. Our project attempted to use genomic analysis to determine the origins Asian rice in Africa and to trace its diffusion within the continent. We selected for analysis 162 O. sativa lines and five glaberrima lines from the USDA National Small Grains collection. We chose landraces whenever possible or lines designated as “cultivated material” in the belief that these varieties would be descendents of populations that were originally introduced to the continent. Our sample included lines from multiple regions of Africa along with those from potential points of introduction in Asia, the Americas, and southern Europe. The samples were analyzed with 50 genome-wide microsatellite markers. Population structure was assigned by the program Structure v2.3.3 and further analyzed with Principal Components Analysis (PCA) and cluster analysis based on genetic distance. The samples grouped into six subpopulations: temperate japonicas, aromatics, aus, indicas, and two discrete subpopulations of tropical japonicas (TRJ1 and TRJ2). In the Mediterranean region, temperate japonicas predominated. East Africa had some indicas, but the TRJ2 group was prominent. West Africa had a cluster of indicas and aus in the Senegambia region but TRJ1 was widespread in the Gulf of Guinea and in Central Africa. TRJ1 was also the predominant group in South America, the Caribbean, and North America. Assuming the germplasm accessions that we have access to today are a reflection of rice that was historically cultivated, we tentatively conclude that Asian rice was introduced to Africa in several independent processes. The temperate japonicas of the Mediterranean region represent one of these and may be part of the introduction of Asian crops to this region associated with the expansion of Islam in the 8th century. The TRJ2 group, which appears in mainland East Africa, Madagascar, South Asia and above all in insular Southeast Asia may be associated with the Austronesian expansion that brought Southeast Asian settlers to Madagascar and bananas and taro to Africa also. The TRJ1 group that is found on both sides of the Atlantic is intriguing. The lines in this group were very closely related despite their wide geographic distribution suggesting a fairly recent introduction. Interestingly, TRJ1 varieties are found in places associated with the slave trade in Africa and the use of slave labor on plantations in the Americas. The TRJ1 population may be a consequence of the post-Columbian opening of sea contacts across the Atlantic and between the Atlantic and Indian Oceans. The close relationships between the members of the TRJ1 group and their geographical distribution offer partial support for the “Black Rice” thesis which contends that enslaved Africans played a central role in the spread of rice cultivation to the Americas. The cluster of indicas and aus in the Senegambia region may represent a fourth introduction of O. sativa to Africa.