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Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker

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Abstract

Knowledge of genebank and on-farm genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L., representing eight groups covering parental populations in West Africa, genebank, and farmers’ populations in Nigeria. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. The largest genetic diversity was found in the Upper Amazon parent population (H nb  = 0.730), followed by the 1944 Posnette’s Introduction (H nb  = 0.704), and was lowest in the Local parent population (H nb  = 0.471). Gene diversity was appreciably high in the farmers’ populations (H nb  = 0.563–0.624); however, the effective number of alleles was lower than that found in the genebank’s Posnette’s population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (F is  = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (F is  = −0.341). The presence of inbreeding in the Local parent populations and substructure (Wahlund effect) in the Upper Amazon were suggested for the deficiency of heterozygotes observed. Non-significant genetic differentiation observed between the genebank’s and farmers’ populations indicated significant impact of national breeding programs on varieties grown in farmers’ plantations. From this study, we showed that appreciable genetic diversity was present in on-farm and field genebank collections of cacao that can be exploited for crop improvement in West Africa. Suggestions for future conservation of on-farm genetic diversity and local landraces are further discussed.

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Acknowledgement

This study was carried out within the framework of Sustainable Tree Crops Program (STCP) project sponsored by the United States Agency for International Development (USAID), United States Department of Agriculture (USDA), and Mars Incorporated on the Assessment of Genetic Diversity in West African Cocoa Collections. The excellent field and laboratory assistance of Messrs. Raji LO, Efunla MS, Sunday Taiwo and useful suggestions from Drs. Ranjana Bhattarcharjee, Rob Lockwood (UK) and Eric Rosinquest (USDA), Kolawole Badaru (now Late) are gratefully acknowledged. We also thank the first two anonymous reviewers for their very useful comments.

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Authors and Affiliations

  1. Plant Breeding Division, Cocoa Research Institute of Nigeria PMB, 5244, Ibadan, Nigeria

    Peter O. Aikpokpodion

  2. Central Biotechnology Laboratory, International Institute of Tropical Agriculture PMB, 5320, Ibadan, Nigeria

    Peter O. Aikpokpodion, Ivan Ingelbrecht & Maria Kolesnikova-Allen

  3. Mars Incorporated Subtropical Horticulture Research Station, USDA/ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA

    Juan C. Motamayor

  4. Department of Agronomy, University of Ibadan, Ibadan, Nigeria

    Victor O. Adetimirin

  5. Plant Breeding Division, Cocoa Research Institute of Ghana, New Tafo, Ghana

    Yaw Adu-Ampomah

  6. Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 5, France

    Albertus B. Eskes

  7. Subtropical Horticulture Research Station, USDA/ARS, 13601 Old Cutler Road, Miami, FL, 33158, USA

    Raymond J. Schnell

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  1. Peter O. Aikpokpodion
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  8. Maria Kolesnikova-Allen
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Correspondence to Peter O. Aikpokpodion.

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Communicated by E. Dirlewanger

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Aikpokpodion, P.O., Motamayor, J.C., Adetimirin, V.O. et al. Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker. Tree Genetics & Genomes 5, 699–711 (2009). https://doi.org/10.1007/s11295-009-0221-1

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