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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #345749

Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

Title: Genetic identity and diversity of Nigerian cacao genebank collections verified by Single Nucleotide polymorphisms (SNPs): A guide to field genebank management and utilization

Author
item Olasupo, Festus - Cocoa Research Institute Of Nigeria
item Adewale, Daniel - University Of Nigeria
item Aikpokpodion, Peter - Cocoa Research Institute Of Nigeria
item Muyiwa, Anna - Cocoa Research Institute Of Nigeria
item Bhattacharjee, Ranjana - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - Nigeria
item Gutierrez, Osman
item Motamayor, Juan Carlos - Mars, Inc
item Schnell, Raymond - Mars, Inc
item Ebai, Sona - Cocoa Research Institute Of Ghana
item Zhang, Dapeng

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2018
Publication Date: 3/21/2018
Citation: Olasupo, F., Adewale, D., Aikpokpodion, P., Muyiwa, A., Bhattacharjee, R., Gutierrez, O.A., Motamayor, J., Schnell, R., Ebai, S., Zhang, D. 2018. Genetic identity and diversity of Nigerian cacao genebank collections verified by Single Nucleotide polymorphisms (SNPs): A guide to field genebank management and utilization. Tree Genetics and Genomes. https://doi.org/10.1007/s11295-018-1244-2.
DOI: https://doi.org/10.1007/s11295-018-1244-2

Interpretive Summary: Nigeria is the fourth largest cacao producer in the world; however poor field performance and low quality of hybrid cacao in Nigeria is the result of the mislabeling of parental clones in the field genebank collection. Using Single Nucleotide Polymorphism (SNP) markers to assess the genetic integrity in Nigeria cacao germplasm, we verified 1457 cacao trees sampled from seven major field genebank plots in Nigeria. High rates of mislabeling (up to 78%) were revealed for introduced international cacao germplasm and for West African local selections. The problem of mislabeling has been attributed to errors from the sources of introduction, pre-planting labeling errors and rootstocks overtaking budded scions due to poor field management. The resultant information also showed that only a small proportion of the available genetic resources in Nigeria have been utilized for variety development. This study significantly improved accuracy and efficiency of cacao identification for genebank management, and for mobilizing improved varieties to cacao farmers in Nigeria. This information will be used by the cocoa industry, researchers, extension staff and farmers to improve cacao production and cacao breeding in Nigeria.

Technical Abstract: Nigeria is the fourth largest cacao producer in the world. Field performance and quality of cacao hybrid families is largely dependent on the genetic integrity of parental clones obtained from field genebank collections. However, information on the impact of mislabeling on seed garden output and germplasm management in Nigeria is lacking. Using 63 single nucleotide polymorphism (SNP) markers, we fingerprinted 1457 cacao trees sampled from seven major field genebank plots in Nigeria to assess the genetic integrity in Nigerian cacao germplasm. The procedure of multilocus matching with known reference clones revealed up to 78% mislabeling in recently introduced international cacao germplasm. High rates of mislabeling were also revealed in the West African local selections and breeding lines, using Bayesian assignment test. The problem of mislabeling has been attributed to errors from the sources of introduction, pre-planting labeling errors and rootstocks overtaking budded scions due to poor field management. Analysis of genetic diversity revealed an acceptable representation of the available cacao germplasm groups in Nigerian field genebanks, including Iquitos Mixed Calabacillo (IMC), Refractario (Nacional hybrid), Nanay, Parinari, Scavina, Criollo, Amelonado and Trinitario. This indicates that the genetic base of Nigeria cacao germplasm has been significantly widened through germplasm introductions. However, only a small proportion of the available genetic resources in the genebank have been utilized for variety development. This study proved the utility of SNP markers for cleaning-up the genebanks and reducing off-types; thereby, they provide a strong basis for improving the accuracy and efficiency in cacao genebank management and breeding, as well as for mobilizing improved varieties to cacao farmers in Nigeria.