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Complex origin of Trinitario-type Theobroma cacao (Malvaceae) from Trinidad and Tobago revealed using plastid genomics

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Abstract

Trinidad and Tobago has a long history of producing high-quality cacao (Theobroma cacao L.). Cacao genotypes in Trinidad and Tobago are of a highly distinctive kind, the so-called “Trinitario” cultivar group, widely considered to be of elite quality. The origin of Trinitario cacao is unclear, although it is generally considered to be of hybrid origin. We used massive parallel sequencing to identify polymorphic plastidic single nucleotide polymorphisms (cpSNPs) and polymorphic plastidic simple sequence repeats (cpSSRs) in order to determine the origin of the Trinitario cultivar group by comparing patterns of polymorphism to a reference set of ten completely sequenced chloroplast genomes (nine T. cacao and one outgroup, T. grandiflorum (Willd. ex Spreng.) Schum). Only three cpSNP haplotypes were present in the Trinitario cultivars sampled, each highly distinctive and corresponding to reference genotypes for the Criollo (CRI), Upper Amazon Forastero (UAF) and Lower Amazon Forastero (LAF) varietal groups. These three cpSNP haplotypes likely represent the founding lineages of cacao to Trinidad and Tobago. The cpSSRs were more variable with eight haplotypes, but these clustered into three groups corresponding to the three cpSNP haplotypes. The most common haplotype found in farms of Trinidad and Tobago was LAF, followed by UAF and then CRI. We conclude that the Trinitario cultivar group is of complex hybrid origin and has derived from at least three original introduction events.

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Acknowledgements

We thank the World Bank for a Development Marketplace grant awarded to QC, HD and Johannes Engels and coordinated by Bioversity International. The Staff of Cocoa Research, Centeno, Trinidad is highly acknowledged for identifying and collecting leaves from the farmers’ cacao trees, sometimes under very challenging conditions. We thank Chris Grassa for analytical assistance, and Brian Irish (USDA, ARS) and Kyle Wallick (USBG) for providing leaf samples. Stephen Pinney (USDA, ARS) and Kasey Gordon (CRU) are thanked for assistance with DNA extractions. Jon Armstrong and Jarret Glasscock (Cofactor Genomics, St. Louis) provided valuable sequencing assistance. We also gratefully acknowledge the laboratory support from an NSERC (Canada) discovery grant to Quentin Cronk.

Data Archiving Statement

Short-read sequences generated by the Illumina GA-II platform to assemble the T. cacao chloroplast genome have been deposited in the NIH Sequence Read Archive (SRA). The SRA accession number is SRA048198. The whole chloroplast genome sequences of the nine T. cacao genotypes and one T. grandiflorum genotype were deposited in GenBank. The accession numbers for these sequences are JQ228379-JQ228389. The DNA sequences used to obtain the ten SNPs were deposited in GenBank as well. The GenBank accession numbers for the first SNP primer pair are JX413598–JX413691; and the GenBank accession number for the second primer pair are JX413692–JX413781. The GenBank accession numbers for the SSR primers are JF979116–JF979124.

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Authors and Affiliations

  1. Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada

    Ji Yong Yang, Moira Scascitelli, Saemundur Sveinsson, Nolan C. Kane, Hannes Dempewolf & Quentin C. B. Cronk

  2. Cocoa Research Unit, The University of the West Indies, St. Augustine, Trinidad, West Indies, Republic of Trinidad and Tobago

    Lambert A. Motilal

  3. Biodiversity International, 00057, Maccarese, Rome, Italy

    Johannes M. M. Engels

  4. SPCL, USDA-ARS, Building 001 BARC-West, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA

    Dapeng Zhang

  5. Ministry of Agriculture, Food Production Land, and Marine Resources Affairs, Central Experiment Station, Centeno, Via Arima P.O., West Indies, Republic of Trinidad and Tobago

    Kamaldeo Maharaj

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  1. Ji Yong Yang
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  2. Moira Scascitelli
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  3. Lambert A. Motilal
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  4. Saemundur Sveinsson
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  5. Johannes M. M. Engels
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  7. Hannes Dempewolf
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  8. Dapeng Zhang
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  9. Kamaldeo Maharaj
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  10. Quentin C. B. Cronk
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Correspondence to Ji Yong Yang.

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Communicated by R. Sederoff

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Yang, J.Y., Scascitelli, M., Motilal, L.A. et al. Complex origin of Trinitario-type Theobroma cacao (Malvaceae) from Trinidad and Tobago revealed using plastid genomics. Tree Genetics & Genomes 9, 829–840 (2013). https://doi.org/10.1007/s11295-013-0601-4

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