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Agro-morphological and structural diversity of rice germplasm revealed by SSR markers in Benin Republic

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Abstract

Background

In developing countries, rice is a staple food and cash crop for the people. In Benin Republic, paddy rice production has increased over time. Accordingly, local varieties were replaced by improved varieties, leading unfortunatley to a loss of the diversity of Beninese rice germplasm.

Methods and results

The investigation focused on the structure and genetic diversity of 72 rice accessions collected throughout 22 villages using 13 quantitative traits and 17 SSR markers. The descriptive analysis of the 13 quantitative parameters showed a significant difference among the accessions, with a grouping in three clusters. Group I (16.66% of samples) was composed of accessions with long, wide and thick grains alongside with four controls TOG5681, TOG5307, Azucena and Moroberekan. Group II (7% of samples) contained accessions with late vegetative cycle. Group III contained most of the accessions (76.39% of the samples), including accessions such as the CG14 and Nipponbare control lines, and almost all the improved varieties. The molecular analysis revealed a significant diversity (mean number of alleles: 4.47 with polymorphism information content of 0.633). Population structure based on molecular markers showed three primary populations with a mixture of phenotypic groupings at ΔK, K = 3.

Conclusion

This study showed that Beninese rice germplasm was divided into two structures: phenotypically similar cultivars but genotypically distinct (homonyms), and phenotypically different cultivars but genotypically similar (synonyms). Some local cultivars such Bagou19, Bagou20 and Koud44 can be used for large scale production due to their agronomics and molecular traits. The molecular structure obtained in this investigation might be used for future conservation and breeding programs.

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Acknowledgements

Authors express their gratitude to rice growers from different villages in Benin for contributing in sample collection.

Funding

This study was funded by the French Institute for Sustainable Development (IRD) through the JEAI-GRAB « Genetic Resources & Agronomic Biodiversity in Benin » grant.

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Authors and Affiliations

  1. Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Ingénierie et Mathématiques (UNSTIM), Université Nationale des Sciences, BP 14, Technologies, Dassa-Zoumé, Bénin

    Paulin Sedah, Lambert Gustave Djedatin, Laura Yêyinou Estelle Loko, Chalemagne Dossou Seblodo Judes Gbemavo, Joelle Toffa, Cyrille Tchakpa & Eben-Ezer Baba Kayodé Ewedje

  2. Institut National des Recherches Agricoles du Bénin (INRAB), Cotonou, 01 B P 884, Bénin

    Azize Orobiyi

  3. DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F-34 394, France

    Francois Sabot

  4. Jeune Equipe Associée à l’Institut de Recherche pour le Développement (JEAI-GRAB), Montpellier Cedex 5, France

    Paulin Sedah, Lambert Gustave Djedatin, Laura Yêyinou Estelle Loko, Chalemagne Dossou Seblodo Judes Gbemavo, Azize Orobiyi, Joelle Toffa, Cyrille Tchakpa, Eben-Ezer Baba Kayodé Ewedje & Francois Sabot

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  1. Paulin Sedah
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  2. Lambert Gustave Djedatin
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  3. Laura Yêyinou Estelle Loko
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Contributions

All authors contributed to the study conception and design. Sample collection and Field study were achived by P.S., A.O., C.T. and J.T. Material preparation, molecular work and data collection were performed by P.S., L.G.D., E-E.E., Y.L.E.L. and F.S. Data analysis were carried out by C.D.S.J.G. and P.S. The first draft of the manuscript was written by P.S. and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Paulin Sedah.

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Sedah, P., Djedatin, L.G., Loko, L.Y.E. et al. Agro-morphological and structural diversity of rice germplasm revealed by SSR markers in Benin Republic. Mol Biol Rep 50, 10207–10217 (2023). https://doi.org/10.1007/s11033-023-08874-8

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