Genetic diversity in shea tree (Vitellaria paradoxa subspecies nilotica) ethno-varieties in Uganda assessed with microsatellite markers

Abstract

Shea trees (Vitellariaparadoxa C. F. Gaertn.) are classified locally into several folk or ethno-varieties by farmers in Uganda. It is, however, not clear whether this folk classification is supported by genetic differentiation between ethno-varieties. Genetically linked traits from folk classification are useful in conservation and breeding programmes. A total of 118 individual shea trees constituting 28 ethno-varieties sampled from three farming systems of Uganda were analysed using microsatellite markers. The number of alleles amplified per microsatellite locus ranged from 6 to 13 with an average of 9.5, with a total of 106 alleles identified. Observed (H_o) and expected heterozygosity (H_e) per locus ranged from 0.366 to 0.934 and 0.580 to 0.840, respectively. Mean H_o and H_e values for all loci across all ethno-varieties were 0.633 and 0.727, respectively. Analysis of molecular variance indicated that most of the variation (86.28%) occurred within individual trees; 11.25% was found among individual trees within ethno-varieties while 2.47% was found among ethno-varieties. The in-breeding index (f = 0.130), fixation index (θ_P = 0.025), gene flow value (N_m = 6.56) and cluster analysis show that all shea tree ethno-varieties were a single out-crossing population with very low genetic differentiation and high gene flow. The low differentiation in shea tree ethno-varieties was most likely due to the utilization of non-genetic traits in folk classification. However, while ethno-variety genetic structure was very weak, overall spatial population structure indicated the presence of three populations (West Nile, Northern and Teso). The West Nile population was more distantly related to the other two most likely due to isolation barriers such as the Rift Valley, Lake Albert and River Nile.

Keywords::

• farming system
• genetic variation
• gene flow
• heterozygosity
• folk classification
• population structure
• SSR fingerprinting

Acknowledgements

We are very grateful to the farmers in the shea parklands of Uganda for their support and cooperation during fieldwork. We are also greatly indebted to the field assistants (Richard Amuge, Henry Asindua, Joel Buyinza, Jaspher Okello, Joseph Okello, Slim Abok Openythoo, Paul Okiror and Samuel Oyuko) for all their efforts during fieldwork and language translation. We are grateful for the technical assistance of the staff of the genetic improvement unit of CIRAD and the genotyping platform of the Montpellier Languedoc-Roussillon Genopole located in the UMR PIA of CIRAD.

Additional information

Funding

Funding for this work was obtained from Makerere University School of Graduate Studies – Carnegie Corporation Competitive Research grant. Additional funding was provided by the European Union INCO – CT project no. 032037 (Innovative Tools and Techniques for Sustainable Use of the Shea Tree in Sudano – Sahelian zone – INNOVKAR) and the World Agroforestry Centre, Nairobi through the SII/World Agroforestry Project: ‘Advancing Agroforestry Research and Development through Training and Education’.