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Analysis of population structure and genetic diversity reveals gene flow and geographic patterns in cultivated rice (O. sativa and O. glaberrima) in West Africa

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Abstract

To fully exploit the diversity in African rice germplasm and to broaden the gene pool reliable information on the population genetic diversity and phenotypic characteristics is a prerequisite. In this paper, the population structure and genetic diversity of 42 cultivated African rice (Oryza spp.) accessions originating from West Africa (Benin, Mali and Nigeria, Liberia etc.) were investigated using 20 simple sequence repeats (SSR) and 77 amplified fragment length polymorphisms (AFLP). Additionally, field trials were set up to gain insight into phenotypic characteristics that differentiate the genetic populations among rice accessions. The analysis revealed considerably high polymorphisms for SSR markers (PIC mean = 0.78) in the germplasm studied. A significant association was found between AFLP markers and geographic origin of rice accessions (R = 0.72). Germplasm structure showed that Oryza sativa accessions were not totally isolated from Oryza glaberrima accessions. The results allowed identification of five O. glaberrima accessions which grouped together with O. sativa accessions, sharing common alleles of 18 loci out of the 20 SSR markers analyzed. Population structure analysis revealed existence of a gene flow between O. sativa and O. glaberrima rice accessions which can be used to combine several interesting traits in breeding programs. Further studies are needed to clarify the contributions of this gene flow to valuable traits such as abiotic and biotic stresses including disease resistance.

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Acknowledgements

Funding of this Research work by the Monsanto’s Beachell-Borlaug International Scholars Program (MBBIS) and the Flemish Fund for Scientific Research (BOF) with support of AfricaRice. Special thanks to the AfricaRice genebank for providing seed and the related information.

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Author notes

  1. Drissa Silue

    Present address: AfricaRice Center, 01, B.P.O. 2551, Bouake 01, Côte d’Ivoire

Authors and Affiliations

  1. Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium

    Octaviano Igor Yelome, Kris Audenaert, Sofie Landschoot, Wouter Vanhove, Patrick Van Damme & Geert Haesaert

  2. Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Université d’Abomey, Abomey-Calavi, Benin

    Alexandre Dansi

  3. AfricaRice Center, 01, B.P.O. 2031, Cotonou, Benin

    Drissa Silue

  4. Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague 6 – Suchdol, Czech Republic

    Patrick Van Damme

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  1. Octaviano Igor Yelome
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Contributions

OIY carried out the field works, the genotyping, data analysis and drafted the manuscript. KA participated in project design, genotyping, data analysis and revised the manuscript. SL participated in statistical analysis of data and revised the manuscript. DS, AD, WV, PVD, and GH participated in project design, data analysis and revised the manuscript.

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Correspondence to Sofie Landschoot.

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Yelome, O.I., Audenaert, K., Landschoot, S. et al. Analysis of population structure and genetic diversity reveals gene flow and geographic patterns in cultivated rice (O. sativa and O. glaberrima) in West Africa. Euphytica 214, 215 (2018). https://doi.org/10.1007/s10681-018-2285-1

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