Selecting SNP markers reflecting population origin for cacao (Theobroma Cacao L.) germplasm identification

Authors: Gutierrez, Osman; Martinez, Kathleen; Zhang, Dapeng; LIVINGSTONE, DONALD - Mars, Inc; TURNBULL, CHRIS - University Of Reading; MOTAMAYOR, JUAN - Mars, Inc

Submitted to: Beverage Plant Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2021
Publication Date: 12/27/2021
Citation: Gutierrez, O.A., Martinez, K.A., Zhang, D., Livingstone, D.S., Turnbull, C.J., Motamayor, J.C. 2021. Selecting SNP markers reflecting population origin for cacao (Theobroma Cacao L.) germplasm identification. Beverage Plant Research. 1: Article 15. https://doi.org/10.48130/BPR-2021-0015.
DOI: https://doi.org/10.48130/BPR-2021-0015

Interpretive Summary: Cacao (Theobroma cacao L.) is a worldwide, valuable tropical crop that produces the raw material used in the manufacturing of chocolate. Mislabeling cacao accessions have been a recurring problem in cacao germplasm collections around the world. Molecular markers have been widely used to address this problem; however, reference genotypes representing each of the genetic groups are urgently needed. In addition, a set of core molecular markers that can separate the established genetic groups and identify the level of admixture in cacao accessions is also needed. Four hundred and twenty cacao leaf samples, representing all of the 10 genetic groups, were collected from different germplasm collections and from locations in the center of origin and domestication of cacao. Genetic characterization of the samples was done using 1,060 single nucleotide polymorphism (SNP) molecular markers. Results indicated a core set panel of 219 SNP markers that would be effective for germplasm identification and selection of reference genotypes. These results were also highly correlated with previously obtained outcomes using simple sequence repeats markers. The resulting SNP panel and the chosen reference germplasm are appropriate for cacao germplasm preservation, identification as well as their application in breeding programs.

Technical Abstract: Cacao is one of the most economically important agricultural commodities in the world, providing the principal ingredient for the global chocolate industry. Accurate genotype identification is essential for effective conservation and utilization of cacao germplasm. Here, we report the screening of 956 candidate SNPs, pre-selected from the 6 and 15K Theobroma cacao SNP Arrays using targeted Genotyping-by-Sequencing on 451 cacao germplasm accessions, representing 10 known genetic groups from the tropical Americas. Based on call rate (No call rate < 10%), Minor Allele Frequency (MAF > 0.15) and Linkage Disequilibrium (LD = 0.5), a total of 219 SNPs were selected. The efficacy of these SNP markers for population classification was compared with the previous SSR-based analysis in cacao. The population assignment results of the retained 420 cacao accessions was highly comparable with the SSR study. The matrix of genetic distance between SSR and SNP markers is highly correlated (r = 0.718; P< 0.001). These results demonstrated the consistency in using the present SNP markers for cacao germplasm identification. This is our pilot project for the development of SNP markers reflecting population origin for cacao germplasm identification. These SNP markers and the selected reference germplasm for different populations are suitable for use in cacao germplasm management and crop improvement, including genotype identification, seed gardens and nursery accreditation, and cocoa authentication. Effort is being continued with the emphasis on selecting SNP markers for the detection of sub-population structures in the primary gene pool of T. cacao.