An extensive analysis of the African rice genetic diversity through a global genotyping


Key message

We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species.


Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.

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Authors want to thank Dr MN Ndjiondjop from AfricaRice Center (Cotonou, Benin) for her help in the African rice accessions choice, Dr Laurence Albar and Valérie Poncet for useful discussions, Mme Christine Tranchant for her informatics support, and Dr Timothy Tranbarger for his help in English corrections. All the analyses were performed on the Bioinformatics platform from IRD ( This project was supported by a Grant from Agropolis Foundation (ArCad program) and from GRiSP project (MENERGEP NewFrontier program).

Conflict of interest

The authors declare no conflict of interest.

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Corresponding author

Correspondence to François Sabot.

Additional information

J. Orjuela and F. Sabot contributed equally to the work.

Communicated by Takuji Sasaki.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental Fig. 1. STRUCTURE analysis for 279 O. glaberrima, 101 O. barthii accessions and 54 O. sativa estimated from 235 SNP loci, from K = 2 to K = 6.

Supplemental Fig. 2. Plots of log-likelihood and ΔK, from STRUCTURE analysis of the full set of sampled O. sativa, O. glaberrima and O. barthii (a, b); only for African accessions (c, d); O. barthii (e, f) and O. glaberrima (g, h).

Supplemental Fig. 3. STRUCTURE analysis for 266 O. glaberrima and 101 O. barthii accessions estimated from 235 SNP loci, from K = 2 to K = 6.

Supplemental Fig. 4. a STRUCTURE analysis estimated from 235 SNP loci for 101 O. barthii accessions, from K = 2 to K = 8. b Relationship between O. barthii accessions based on 70 % of ancestry between the 3 populations.

Supplemental Fig. 5. STRUCTURE analysis estimated from 235 SNP loci for 266 O. glaberrima, from K = 2 to K = 7.

Supplemental Table 1. Individual accessions used in the bulked sequencing.

Supplemental Table 2. Position and nature of the 384 SNPs used in the present study. The positions are based on the Oryza sativa ssp japonica cv Nipponbare MSU 6.1 sequence.

Supplemental Table 3. Origin, names and synonymic names of the plant material used in the current study. The accessions used in Li et al. (2011) are shown.

Supplementary material 1 (PDF 945 kb)

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Orjuela, J., Sabot, F., Chéron, S. et al. An extensive analysis of the African rice genetic diversity through a global genotyping. Theor Appl Genet 127, 2211–2223 (2014).

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  • African Species
  • Asian Rice
  • African Rice
  • Clear Geographical Pattern
  • Weedy Form