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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT OF AN INTERNATIONAL MARKER ASSISTED SELECTION PROGRAM FOR CACAO Title: Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L

Authors
item Aikpokpodion, P -
item Kolesnikova-Allen, M -
item Adetimirin, V -
item Guiltinan, M -
item Eskes, A -
item Motamayor, J -
item Schnell Ii, Raymond

Submitted to: SILVAE GENETICA
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 20, 2008
Publication Date: December 5, 2010
Citation: Aikpokpodion, P.O., Kolesnikova-Allen, M., Adetimirin, V.0., Guiltinan, M.J., Eskes, A.B., Motamayor, J.C., Schnell Ii, R.J. 2010. Population structure and molecular characterization of Nigerian field genebank collections of cacao, Theobroma cacao L. SILVAE GENETICA. 59(6):273-285.

Interpretive Summary: West Africa produces 70% of the world’s cacao crop and Nigeria currently ranks fourth globally in cocoa production. Cocoa bean exports represent ~65% of the total agricultural exports from Nigeria and several hundred thousand families depend on this cash crop for their livelihood. Cacao breeding and selection for improved cultivars began in Nigeria in 1931 and since then a series of additional germplasm introductions have been made and several hundred clones and accessions now exist in the Nigerian field collection. To use the germplasm in a rational and efficient manner one must understand the nature and amount of genetic diversity as well as the relationships among various accessions. One of the most efficient ways to accomplish this is with molecular markers. In this study 13 microsatellite molecular markers were used to estimate genetic diversity among 242 cacao clones in the germplasm bank of the Cocoa Research Institute of Nigeria (CRIN). These clones could be divided into 11 populations based on the history of the material. Bayesian model clustering methods were used to test the 11 populations and this number was reduced to six base populations with members of the other five populations being hybrids between these six basic groups. When comparing the introduced populations to the local selections it was determined that parents upper Amazon clones from the Nanay, Parinari and Iquitos Mixed Calabacillo were the main ancestral progenitors along with the Amelonado and Trinitario populations originally introduced into West Africa . The main conclusion from this study was that only a small proportion of the genetic diversity in the Upper Amazon groups has been used in local cultivar development in Nigeria and that this genetic variation can be exploited in variety development. This study revealed the need for guided exploitation of useful diversity in Scavina and IMC populations for the development of cultivars and to address production problems of black pod and cacao swollen shoot virus diseases.

Technical Abstract: Over the last 130 years since cacao introduction into Nigeria, genetic variability in cacao cultivated which has increased as a result of further introduction and breeding activities, remain largely unknown. To determine the genetic diversity and population structure of cacao populations, 13 cacao microsatellite loci were used to genotype 600 samples collected from all three cocoa growing ecological zones covering the parent, genebank and farmers’ populations. A total of 288 alleles were detected and estimated gene diversity was appreciably high with expected heterozygosity, He = 0.748, 0.762 and 0.725 in parent, genebank and farmers’ population, respectively. Inbreeding coefficient, Fis = 0.336, 0.210 and 0.229 in parent, genebank and farmers’ population, respectively, indicating significant deficiency of heterozygotes. Gene diversity was highest in 1944 Posnette’s introduced T-clones, followed by Upper Amazon parents and lowest in local Amelonado landraces parent population. Pairwise comparison of Fst(theta) was highest between Upper Amazon and local Amelonado landraces parent population (0.1692) and lowest between 1967 Trinidad Introduction and F2 Amazon hybrids (0.0045). Neighbour-joining tree dendrogram revealed a distinct separation of farmers’ population from parental and genebank populations and three clearly defined groups were identified. A newly identified group, “West African Amazon”, which apparently evolved as a result of farmers’ practice from a melting pot of introduced cacao populations, the popular “F3-Amazon cocoa” and “West African Amelonado”. Overall, it appears that the current level of genetic diversity available in Nigeria is high enough but needs to be more evenly distributed, through a more effective planting material delivery system to reduce impact of farmers’ practice on further reduction of genetic diversity, particularly in the south-eastern part at the border with Cameroon. Allele frequency distribution showed no evidence of recent genetic bottleneck or deviation from mutation-drift equilibrium. However, the highly significant deficiency of heterozygosity provided evidence of historical population expansion, Founder effect and non-random mating. Until now, no information is available on the mutation models in population genetics study of cacao. Three mutation models were tested and the complementary assumption of Infinite allele model (IAM) and two-phase mutation (TPM) was found sufficient for correct estimation of genetic parameters.

Last Modified: 10/21/2014