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The development of a novel SNP genotyping assay to differentiate cacao clones

Jocelyn De Wever (UGent) , Helena Everaert (UGent) , Frauke Coppieters (UGent) , Hayley Rottiers (UGent) , Koen Dewettinck (UGent) , Steve Lefever (UGent) and Kathy Messens (UGent)
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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.
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Multidisciplinary

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Chicago
De Wever, Jocelyn, Helena Everaert, Frauke Coppieters, Hayley Rottiers, Koen Dewettinck, Steve Lefever, and Kathy Messens. 2019. “The Development of a Novel SNP Genotyping Assay to Differentiate Cacao Clones.” Scientific Reports 9.
APA
De Wever, J., Everaert, H., Coppieters, F., Rottiers, H., Dewettinck, K., Lefever, S., & Messens, K. (2019). The development of a novel SNP genotyping assay to differentiate cacao clones. SCIENTIFIC REPORTS, 9.
Vancouver
1.
De Wever J, Everaert H, Coppieters F, Rottiers H, Dewettinck K, Lefever S, et al. The development of a novel SNP genotyping assay to differentiate cacao clones. SCIENTIFIC REPORTS. 2019;9.
MLA
De Wever, Jocelyn et al. “The Development of a Novel SNP Genotyping Assay to Differentiate Cacao Clones.” SCIENTIFIC REPORTS 9 (2019): n. pag. Print.
@article{8622447,
  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.},
  articleno    = {9512},
  author       = {De Wever, Jocelyn and Everaert, Helena and Coppieters, Frauke and Rottiers, Hayley and Dewettinck, Koen and Lefever, Steve and Messens, Kathy},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keywords     = {Multidisciplinary},
  language     = {eng},
  pages        = {10},
  title        = {The development of a novel SNP genotyping assay to differentiate cacao clones},
  url          = {http://dx.doi.org/10.1038/s41598-019-45884-8},
  volume       = {9},
  year         = {2019},
}

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