Abstract

In this study, a double-mismatch allele-specific (DMAS) qPCR SNP genotyping method has been designed, tested and validated specifically for cacao, using 65 well annotated international cacao reference accessions retrieved from the Center for Forestry Research and Technology Transfer (CEFORTT) and the International Cocoa Quarantine Centre (ICQC). In total, 42 DMAS-qPCR SNP genotyping assays have been validated, with a 98.05% overall efficiency in calling the correct genotype. In addition, the test allowed for the identification of 15.38% off-types and two duplicates, highlighting the problem of mislabeling in cacao collections and the need for conclusive genotyping assays. The developed method showed on average a high genetic diversity (He = 0.416) and information index (I = 0.601), making it applicable to assess intra-population variation. Furthermore, only the 13 most informative markers were needed to achieve maximum differentiation. This simple, effective method provides robust and accurate genotypic data which allows for more efficient resource management (e.g. tackling mislabeling, conserving valuable genetic material, parentage analysis, genetic diversity studies), thus contributing to an increased knowledge on the genetic background of cacao worldwide. Notably, the described method can easily be integrated in other laboratories for a wide range of objectives and organisms.

Details

Title
The development of a novel SNP genotyping assay to differentiate cacao clones
Author
De Wever, Jocelyn 1   VIAFID ORCID Logo  ; Everaert, Helena 2 ; Coppieters, Frauke 3 ; Rottiers, Hayley 2 ; Dewettinck, Koen 4 ; Lefever, Steve 5   VIAFID ORCID Logo  ; Messens, Kathy 6 

1  Research unit Molecular Biology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium 
2  Research unit Molecular Biology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Laboratory of Food Technology and Engineering (FTE), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 
3  Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium 
4  Laboratory of Food Technology and Engineering (FTE), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 
5  Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium 
6  Research unit Molecular Biology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium 
Pages
1-10
Publication year
2019
Publication date
Jul 2019
Publisher
Nature Publishing Group
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41598-019-45884-8
ProQuest document ID
2251071942
Copyright
© 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.