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Tracing ancestor rice of Suriname Maroons back to its African origin

Nature Plants volume 2, Article number: 16149 (2016) Cite this article

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Abstract

African rice (Oryza glaberrima) and African cultivation practices are said to have influenced emerging colonial plantation economies in the Americas1,2. However, the level of impact of African rice practices is difficult to establish because of limited written or botanical records2,3. Recent findings of O. glaberrima in rice fields of Suriname Maroons bear evidence of the high level of knowledge about rice among African slaves and their descendants, who consecrate it in ancestor rituals4,5. Here we establish the strong similarity, and hence likely origin, of the first extant New World landrace of O. glaberrima to landraces from the Upper Guinean forests in West Africa. We collected African rice from a Maroon market in Paramaribo, Suriname, propagated it, sequenced its genome6 and compared it with genomes of 109 accessions representing O. glaberrima diversity across West Africa. By analysing 1,649,769 single nucleotide polymorphisms (SNPs) in clustering analyses, the Suriname sample appears sister to an Ivory Coast landrace, and shows no evidence of introgression from Asian rice. Whereas the Dutch took most slaves from Ghana, Benin and Central Africa7, the diaries of slave ship captains record the purchase of food for provisions when sailing along the West African Coast8, offering one possible explanation for the patterns of genetic similarity. This study demonstrates the utility of genomics in understanding the largely unwritten histories of crop cultures of diaspora communities.

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Figure 1: Logbook entry of the Dutch slave ship D'Eenigheid.
Figure 2: The Surinamese Oryza glaberrima sample (TVA5634) that was propagated to sequence its genome.
Figure 3: Comparison of the Surinamese sample with 109 accessions representing O. glaberrima diversity across West Africa.
Figure 4: Heat map of clustering similarity distances to the Surinamese sample, and clustering tree.

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Acknowledgements

We would like to thank rice farmers in Jawjaw, Mundje Kreek, Mooytaki and Paramaribo for sharing their knowledge on African rice with us. T. Polimé and B. Poeketie facilitated fieldwork in Maroon communities. C.-R. Lee helped us with the TPS analysis. This research was funded by the Biosystematics group of Wageningen University, Naturalis Biodiversity Center (Leiden), as well as support from NSF Plant Genome to R.S.M. (IOS-1202803) and M.D.P. (IOS-1126971), a TKI-Horticulture Grant to M.E.S. and S.A.A., grants from the US National Science Foundation and the NYU Abu Dhabi Research Institute to J.M.F., and the AXA Chair in Genome Biology and Evolutionary Genomics to R.A.W.

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Authors and Affiliations

  1. Biosystematics group, Wageningen University, PO Box 16, 6700 AP, Wageningen, The Netherlands

    Tinde R. van Andel, Saulo A. Aflitos, Margaretha A. Veltman & M. Eric Schranz

  2. Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands

    Tinde R. van Andel

  3. Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, 10003, New York, USA

    Rachel S. Meyer, Jonathan M. Flowers & Michael D. Purugganan

  4. Departmemt of Geography, University of California, Box 951524, Los Angeles, 90095, California, USA

    Judith A. Carney

  5. Arizona Genomics Institute, School of Plant Sciences, University of Arizona, 1657 E. Helen Street, Tucson, 85721, Arizona, USA

    Dario Copetti & Rod A. Wing

  6. Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates

    Jonathan M. Flowers & Michael D. Purugganan

  7. Hortus Botanicus Amsterdam, Plantage Middenlaan 2, 1018 DD, Amsterdam, The Netherlands

    Reinout M. Havinga

  8. Social Sciences Department, Knowledge Technology and Innovation group, Wageningen University, PO Box 8130, 6700 EW, Wageningen, The Netherlands

    Harro Maat

  9. International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines

    Rod A. Wing

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  1. Tinde R. van Andel
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Contributions

T.R.v.A. conducted the fieldwork in Suriname, and wrote the paper with contributions and input from all co-authors. T.R.v.A. and M.E.S. conceived and guided the research. R.M.H. maintained the living collection of Oryza glaberrima from Suriname used in this project. D.C. performed sequencing and assisted with data analysis. R.S.M. and J.M.F. performed alignments, SNP calling, and clustering analyses. S.A.A. and M.A.V. performed phylogenomic and TPS analysis. J.A.C. and H.M. provided background on the geographical and historical aspects of West African rice, slavery and Suriname. R.A.W. and M.D.P. helped to collect the data.

Corresponding authors

Correspondence to Tinde R. van Andel or Rachel S. Meyer.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figure 1-5 (PDF 548 kb)

Supplementary Table 1

Background information on the 110 Oryza glaberrima samples used for analysis, including mean depth of sequencing coverage, accession codes, collection locations and clustering distance to Surinamese sample (suri_glab_SUR). (XLSX 24 kb)

Supplementary Table 2

Per cent heterozygosity of African rice accessions with additional country labels. (XLSX 51 kb)

Supplementary Table 3

Filtering of polymorphisms. Multi Nucleotide Polymorphisms (MNP) were always excluded. Heterozygous (HET) SNPs and regions with no coverage (NC) were tentatively excluded as well but their frequency was too high. (XLSX 8 kb)

Supplementary Table 4

Top 10 EIGENSTRAT principal components of the 110 Oryza glaberrima samples. (XLSX 21 kb)

Supplementary Table 5

Ethnolinguistic information on sample provenances. Ethnolinguistic classification of locations from which the samples were collected. (XLSX 14 kb)

Supplementary Table 6

Genetic distance between the O. glaberrima samples. Kruskal-Wallis multiple comparison tests. A Kruskal-Wallis test showed significant differences in genetic distances to the Surinamese sample by country (where country n>1) (Kruskal-Wallis chi-squared = 53.809, df = 11, p-value = 1.279e-07). Results reported are for the multiple comparison test following Kruskal-Wallis set to Bonferroni significance of alpha = 0.05 after correction for 66 tests (P<0.00075). (XLSX 44 kb)

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van Andel, T., Meyer, R., Aflitos, S. et al. Tracing ancestor rice of Suriname Maroons back to its African origin. Nature Plants 2, 16149 (2016). https://doi.org/10.1038/nplants.2016.149

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