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Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

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Abstract

Cacao is an economically important commodity in Jamaica. Knowledge of the genetic diversity of Jamaican cacao germplasm is essential for their conservation and management. In spite of cacao’s economic importance in Jamaica, the crop is under studied, therefore limiting sound decisions toward improving productivity. Assessment of germplasm and on-farm genetic diversity is required to assist selecting superior genotypes to propagate and distribute across the island, as well as to use them as parental clones in breeding programs. Using 94 single nucleotide polymorphism (SNP) markers, 140 Jamaican cacao samples from two germplasm collections and a farmer’s estate along with 150 reference samples were analyzed. The principal coordinate analysis demonstrated that the majority of the Jamaican cacao selections were hybrids derived from five original germplasm groups, including Criollo, Amelonado and three Upper Amazon Forastero groups. Among the Upper Amazon groups, the Bayesian clustering analysis revealed that the Parinari (PA) ancestral lineage contributed the most (29.9%) to the Jamaican cacao germplasm. The germplasm collections showed greater diversity in terms of ancestral contributions compared to the farmer’s estate. However, the genetic differentiation between the three collecting sites was small (Fst = 0.036), indicating that samples collected from the three sites were derived from a common pool of germplasm. The current study supports the historical records and clarified the ancestry of Jamaican cacao. Although the majority of the cacao genetic groups were observed in the Jamaican cacao collections, several diversity gaps were found in both germplasm collections and in the farmer’s estate, especially germplasm with disease resistance to cacao frosty pod rot that was recently found in Jamaica.

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Abbreviations

cDNA:

Complementary DNA

DNA:

Deoxyribonucleic acid

EST:

Expressed sequence tag

PCR:

Polymerase chain reaction

SNP:

Single nucleotide polymorphism

TARS:

Tropical Agriculture Research Station

USDA ARS:

United States Department of Agriculture, Agricultural Research Service

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Acknowledgements

We would like to give special thanks to Stephen Pinney (USDA-ARS) and Lin Zhou (Nanjing Agricultural University, China) for assistance with SNP genotyping using the nanofluidic array system. We also thank Sue Mischke (USDA-ARS) for editing the manuscript. References by USDA to a company and/or product are only for the purposes of information and do not imply approval or recommendation of the product to the exclusion of others that may also be suitable. This project was supported in part by grants from The University of the West Indies, Mona Campus Research and Publications Committee and Inter-American Development Bank Multilateral Investment Fund (IDB MIF) through the Jamaica Cocoa Farmers’ Association (JCFA). Special thanks to Mr. Desmond Jadusingh owner of Bachelor’s Hall Estate who graciously accommodated the research on his farm.

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Authors and Affiliations

  1. Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, Mona Campus, Kingston 7, Jamaica

    Aliza A. Lindo, Dwight E. Robinson & Paula F. Tennant

  2. The Biotechnology Centre, 2 St. John’s Close, The University of the West Indies, Mona Campus, Kingston 7, Jamaica

    Paula F. Tennant

  3. USDA/ARS, Beltsville Agricultural Research Center, NEA, BARC, SPCL, 10300 Baltimore Avenue, Bldg. 001, Rm. 223, BARC-W, Beltsville, MD, 20705, USA

    Lyndel W. Meinhardt & Dapeng Zhang

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  1. Aliza A. Lindo
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Correspondence to Dapeng Zhang.

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Lindo, A.A., Robinson, D.E., Tennant, P.F. et al. Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers. Tropical Plant Biol. 11, 93–106 (2018). https://doi.org/10.1007/s12042-018-9203-5

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