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Title: The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

Author
item PADI, FRANCIS - Cocoa Research Institute Of Ghana
item OFORI, ATTA - Cocoa Research Institute Of Ghana
item TAKRAMA, JEMMY - Cocoa Research Institute Of Ghana
item DJAN, ESTER - Cocoa Research Institute Of Ghana
item OPOKU, STEPHEN - Cocoa Research Institute Of Ghana
item BHATTACHARJEE, RANJANA - International Institute Of Tropical Agriculture (IITA)
item MOTAMAYOR, JUAN CARLOS - Mars, Inc
item Zhang, Dapeng

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2015
Publication Date: 4/26/2015
Citation: Padi, F.K., Ofori, A., Takrama, J., Djan, E., Opoku, S.Y., Bhattacharjee, R., Motamayor, J., Zhang, D. 2015. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao. Tree Genetics and Genomes. DOI:10.1007/s11295-015-0875-9.

Interpretive Summary: West Africa produces approximately 70 % of the world’s cacao beans, yet research into the genetic improvement of this crop has lagged behind other major industrial crops. Cacao breeding and production of planting materials were seriously affected by problem of mislabeling in breeding stocks, seed gardens and clone nurseries. Improving cacao productivity through better planting material is one of the objectives to support sustainable productivity growth and improved food security on diversified cacao farms in West Africa. Using the new generation of DNA fingerprinting technology, we examined examine the genetic identity and parentage in 2551 trees maintained in six seed gardens, breeders clone collection and farmers’ fields in Ghana. The results of the present study provide an overall assessment about the effect of clone mislabeling on the efficiency of variety recommendations in cacao and reinforce the need to accurately identify contamination in hybrid progenies. The results provide a strong basis for improving the efficiency in cacao germplasm management and variety development process, as well as mobilizing available certified, improved varieties to cacao farmers in West Africa. Scientists, plant breeders and farmers across west Africa will use this information.

Technical Abstract: Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process.