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Analysis of genetic diversity in farmers’ rice varieties in Sierra Leone using morphological and AFLP® markers

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Abstract

The objective of the current research was to investigate the status of rice genetic resources in post-war Sierra Leone using both morphological and amplified fragment length polymorphism (AFLP) data. Specifically, we aimed at investigating farmers’ rice genetic resources for homogeneity and differentiation, and at examining the genetic identity of similarly named varieties, including varieties within Sierra Leone, and between Sierra Leone and Guinea. This research was also motivated by the assumption that genetic erosion might have occurred as a result of the civil war. To determine the level of diversity and genetic relationships among farmers’ varieties of rice recently collected in Sierra Leone, two methods were used using subsets of the collected samples: (1) Using morphological data, 74 samples of 29 different varieties were analysed to investigate the relationship between (a) varieties grown in two districts in Sierra Leone, and (b) the two main cultivated species, Oryza sativa and Oryza glaberrima. A dendrogram largely clustered the varieties according to region and to the species to which the varieties belonged. (2) Using AFLP data, three separate investigations were conducted: (a) 33 samples of 10 varieties were investigated to evaluate diversity within and between varieties. The results indicated that the rice varieties possess different levels of intra-variety variation, whereas inter-variety diversity was high enough to distinguish one variety from the other. In particular, an AMOVA analysis revealed that 38 % of the total variation occurred within varieties, and 62 % between varieties. (b) 37 samples of 18 different varieties were investigated to determine the consistency of naming of varieties by farmers. The results showed that there was consistency in the naming by farmers of traditional varieties, but inconsistency in the naming of newly acquired varieties and cultivars. (c) 12 samples were investigated to check the identity of varieties carrying identical names collected in two separate regions, Sierra Leone and the neighbouring country of Guinea. The results indicated no close genetic relationships between the varieties found in Sierra Leone and Guinea despite similarities in the names given to these varieties by farmers, indicating the influence of different cultivation practices in the two countries.

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Acknowledgments

The field work described in this paper was carried out at the Rice Research Station (RRS) in Sierra Leone, and the AFLP analyses were conducted at Wageningen University and Research Centre in the Netherlands. The authors wish to thank the field technicians at the RRS, particularly Edward Munu for the field work, and Ria Vrielink of the Biosystematics Department in Wageningen for the AFLP work. We also thank the Centre for Genetic Resources, the Netherlands, the Biosystematics Group and the Dutch Organization for Scientific Investigation (NWO) for the financial contributions to the research.

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Authors and Affiliations

  1. Centre for Genetic Resources, Wageningen, The Netherlands

    Robert Chakanda, Rob van Treuren & Bert Visser

  2. Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands

    Robert Chakanda, Rob van Treuren & Bert Visser

  3. Biosystematics Group, Wageningen University and Research Centre, Wageningen, The Netherlands

    Ronald van den Berg

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  1. Robert Chakanda
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  2. Rob van Treuren
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  3. Bert Visser
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  4. Ronald van den Berg
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Correspondence to Ronald van den Berg.

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Chakanda, R., van Treuren, R., Visser, B. et al. Analysis of genetic diversity in farmers’ rice varieties in Sierra Leone using morphological and AFLP® markers. Genet Resour Crop Evol 60, 1237–1250 (2013). https://doi.org/10.1007/s10722-012-9914-7

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