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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #424482

Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

2016 Annual Report


Objectives
The goal of this project is to improve the management efficiency of and facilitate the use of germplasm of tropical tree crops, primarily Theobroma cacao. The specific objectives are: Objective 1: Elucidate geospatial patterns of genetic diversity in cacao and other tropical tree crops, and incorporate that information into the project website, cacao and other tropical crop databases, and/or GRIN-Global. Sub-objective 1.A. Identify traditional varieties in farmers’ fields and characterize wild populations in non-U.S. national cacao collections. Sub-objective 1.B. Assess geospatial distribution of genetic diversity in the primary gene pool of T. cacao. Objective 2: Apply the preceding genetic information to strategically acquire new accessions of cacao and other tropical tree crops to fill gaps in genebank collections, and to support in situ, dynamic conservation of selected taxa. Objective 3: Evaluate cacao genetic resources for host-plant resistance to priority diseases, in conjunction with domestic and international collaborators. The first two objectives function together to identify and analyze the existing diversity within the primary cacao gene pool. This identifies diversity gaps that need to be filled by collecting from the remaining wild populations. This permits in-depth analysis of origin, dispersal, and population dynamics to be conducted. The third objective, to initiate evaluations of key agronomic traits, is based on the information about genetic diversity and germplasm revealed in the other two objectives, as well as in previous projects. Germplasm accessions harboring favorable genes/alleles that can contribute to new genetic variation of agronomic traits will be identified. These same objectives are applicable to other tropical tree crops. These priority crops are in the process of being identified in conjunction with ARS tropical tree crop curators and similar research goals will be initiated as necessary.


Approach
The project will first elucidate geospatial patterns of genetic diversity in the primary gene pool of T. cacao using research tools of genomics, spatial genetics and bioinformatics. Cacao germplasm that have been collected and maintained in various ex-situ genebanks will be characterized using single nucleotide polymorphism (SNP) markers. The generated SNP data, together with those previously obtained from the two international genebanks and other non-U.S. national collections, will be compiled and used for assessment of genetic diversity within and among collections. Completion of this work will allow ARS to have a clear understanding about the scope of existing wild germplasm and traditional varieties maintained in the non-U.S. national collections. It will also enable mapping of the geographical distribution of traditional varieties of T. cacao in the Americas using tools of spatial genetics. Second, diversity gaps in ex situ collections will be identified and filled through new collection expeditions, with emphasis on increasing representation from the geographical center of diversity. Based on the existing information, ARS collecting expeditions will focus on the Peruvian Amazon bordered by Brazil and Colombia, including Ríos Ucayali, Putumayo, Yavari, and their tributaries. In addition, landraces and traditional varieties which have a distinct genetic profile, specific regional distribution, and fine flavor, will be identified to support in situ/on-farm conservation. Resulting information will serve as a scientific baseline to support rational decision-making for future germplasm conservation and utilization. Finally, in collaboration with the curators of international and national collections, cacao germplasm will be evaluated for key agronomic traits, primarily disease resistance. Quantitative trait loci mapping, based on field evaluation, SNP genotyping, and genome-wide association mapping will be applied to discover new sources of resistance to major diseases. Approaches established and utilized in cacao will be applied to other tropical tree crops of major economic importance as they are identified and as conservation procedures are established.


Progress Report
In FY 2016, progress was made in identification of a cacao landrace “Piura Porcelana” in Peru. In collaboration with Tropical Crop Institute (ICT), Peru, we analyzed 200 farmer varieties from the provinces of Piura, Cajamarca and Amazonas in Peru, using Single Nucleic Polymorphism markers (SNP) and compared their SNP profiles with the Ecuadorian germplasm collection and wild cacao trees collected from Santiago and Pastaza rivers. Our results, which are relevant to objectives 1A and 2, show that “Piura Porcelana” is a landrace indigenous to Northern Peru and Southern Ecuador. It shares same genetic profile as the ancient “Nacional” cacao in Ecuador. Its unique light bean color and fine nutty flavor offers an opportunity in high-end international cocoa market. This landrace has been collected and transplanted in the ICT cacao germplasm collection. This information will be used by cacao researchers to improve their understanding about on-going domestication and facilitate on-farm conservation of landraces and traditional varieties in the primary gene pool. Progress was made in the application of SNP markers to fingerprint Nigerian cacao germplasm. In collaboration with Nigerian Cacao Research Institute, International Institute of Tropical Agriculture and World Cocoa Foundation, a total of 1840 trees maintained in eight breeders clone collections and seed gardens in Nigeria. These results help us meet the project objective 1A and provide an overall assessment regarding the effect of clone mislabeling in the Nigerian cacao research program. The level of mislabeling observed reinforces the need to accurately identify parental clones before their use in seed gardens. Nigeria is the 4th largest cacao producer in the world and germplasm mislabeling has been a major problem hindering the progress in cacao breeding and seeds production. These research results provide a strong basis for improving the efficiency in cacao germplasm management and variety development process, as well as mobilizing available certified, improved varieties of cacao to farmers in Nigeria. Scientists, plant breeders and farmers across West Africa will use this information. Progress was made in assessing the on-farm genetic diversity in Sulawesi, Indonesia as part of objective 1A. Indonesia is the third largest cacao-producing country in the world. In collaboration with the Indonesian Cocoa and Coffee Research Institute and Bogor Agricultural University, we assessed genetic diversity and parentage of farmer selections of cacao in southern Sulawesi, Indonesia. Our results show that the current on-farm genetic diversity in Sulawesi is low. Only a small number of germplasm groups contributed to these farmer selections. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials is one of the conclusions. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. This information will be used by cacao researchers to improve their breeding strategy for germplasm enhancement in Indonesia. Progress was made in analyzing functional diversity in different cacao populations (objective 3). In collaboration with cacao research program in Pennsylvania State University, we comparatively analyzed sequence polymorphism of three defense genes for wild and cultivated populations from three geographical regions in South America. The analysis identified 15 SNPS causing nine non-synonymous and six synonymous mutations. Intra-population nucleotide diversity differed significantly among regions, showing a pattern compatible with cacao’s dispersal history from its center of diversity in Upper Amazon. Two defense genes showed signatures of natural selection, indicating that both demography and natural selections impacted the allelic diversity of these defense genes in cacao. This is the first study showing the geographical distribution of putative defense gene diversity in cacao. This information will be used by researchers to select candidate genes for association mapping of disease resistances and facilitate the use of cacao germplasm in breeding. Progress was made in addressing objective 3 by developing research tools for germplasm evaluation in cacao. In collaboration with Cacao Research Center, the University of West Indies, Trinidad, we identified putative molecular markers linked with agronomic and quality traits in cacao, including pod size, pod weight, bean number and butterfat content, and resistance to black pod and witches’ broom diseases in cacao. The association analysis was conducted on 483 cacao accessions held in the International Cocoa Genebank, Trinidad. Five SSR markers and six SNP markers were associated with the studied traits. This pilot study provided new insight about the experimental design for association QTL mapping in cacao. This information will be used by researchers to select candidate genes for association mapping of disease resistances and facilitate the use of cacao germplasm in breeding. Progress was made in application of single nucleotide polymorphism (SNP) genotyping method for genotyping of processed tea, in reference to both objectives 1 and 2. The market for specialty tea has been rapidly expanding due to the increased revenues and profits brought to growers and industry. Analytical technologies are needed for protection and value enhancement of high-quality tea brands, which in return will support the on-farm conservation of the genetic diversity of these teas. Using a nanofluidic array to identify variant SNP sequences, we tested genetic identities of 14 processed commercial tea products. Based on the profiles of 60 SNP markers, the genetic identity of each tea sample was unambiguously identified. This new method worked well on green, oolong, and black teas, and can handle a large number of samples in a short period of time. It is robust and cost-effective, thus showing high potential for practical application in the value chain of the tea industry.


Accomplishments
1. Identification of mislabeling in Nigerian cacao germplasm collection. Large scale genotyping was applied to identify mislabeling in cacao germplasm in Nigeria. Nigeria is the 4th largest cacao producer in the world and germplasm mislabeling has been a major problem hindering the progress in cacao breeding and seeds production. ARS scientists in Beltsville, Maryland, in collaboration with Nigerian Cacao Research Institute, International Institute of Tropical Agriculture and World Cocoa Foundation, maintained a total of 1840 trees in eight collections and seed gardens in Nigeria were genotyped. The results provide an overall assessment of clone mislabeling in Nigerian’s cacao research program and reinforces the need to accurately identify parental clones before using themin seed gardens. This accomplishment significantly improved accuracy and efficiency in cacao germplasm management in Nigeria.

2. Genetic characterization of the “Piura Porcelana” Landrace cacao from Northern Peru. “Piura Porcelana” is a farmer’s variety of cacao from northern Peru. In collaboration with Tropical Crop Institute (ICT), Peru, ARS scientists in Beltsville, Maryalnd analyzed the genetic diversity in this variety using Single Nucleic Polymorphism (SNP) markers. Our results confirmed that ‘Piura Porcelana' is a landrace indigenous to Northern Peru and Southern Ecuador. This landrace has a unique flavor which offers an opportunity in high-end international cacao markets. This landrace has been collected and transplanted in the ICT cacao germplasm collection. This accomplishment filled a diversity gap in the cacao germplasm collection and supports on-farm conservation of cacao genetic diversity.


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Review Publications
Zhou, L., Matsumoto Brower, T.K., Tan, H., Meinhardt, L.W., Mischke, B.S., Wang, B., Zhang, D. 2015. Developing Single Nucleotide Polymorphism (SNP) markers for the identification of pineapple (Ananas comosus) germplasm. Horticulture Research. 2:15056.
Zhou, L., Vega, F.E., Tan, H., Ramirez Lluch, A., Meinhardt, L.W., Fang, W., Mischke, B.S., Irish, B.M., Zhang, D. 2016. Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm. Tropical Plant Biology. 9:82-95.
Dinarti, D., Susilo, A.W., Meinhardt, L.W., Ji, K., Motilal, L., Mischke, B.S., Zhang, D. 2015. Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers. Journal of Breeding Science. 65:438-446.
Fang, W., Meinhardt, L.W., Tan, H., Zhou, L., Wang, X., Mischke, B.S., Zhang, D. 2016. Identification of the varietal origin of loose leaf tea based on analysis of a single leaf by SNP nanofluidic array. Journal of Agricultural and Food Chemistry. doi: 10.1016/j.cj.2016.02.001.
Zhang, D., Motilar, L. 2016. Origin, dispersal and current global distribution of cacao genetic diversity. In: Bailey, B. A., Meinhardt, L.W., editors, Cacao Diseases: A history of old enemies and new encounters. Switzerland: Springer. 3-31.