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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

2014 Annual Report


1a. Objectives (from AD-416):
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.


1b. Approach (from AD-416):
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.


3. Progress Report:
In FY 2014, progress was made in the development of a single nucleotide polymorphism (SNP) genotyping method for a single fermented cacao bean, thus enabling accurate and robust varietal authenticate of cacao. This is the first time that varietal identification on the basis of a single cacao bean has been accomplished. This method greatly enhances the chocolate industry's capacity to authentication cacao sources. Production and marketing of specialty high-value cocoa provides socioeconomic opportunities for growers, the chocolate industry and especially for consumers. From the conservation perspective, the higher farm-gate revenues from this premium market provides strong economic incentives for demand-driven, in situ/on-farm conservation of cacao genetic diversity. Progress was also made in understanding on–farm genetic diversity in Southeast Asia. SNP markers were used to analyze the genetic background of superior cacao clones selected from farmers’ fields in Aceh, Indonesia. The study revealed that the Aceh farmer selections were largely hybrids between two Upper Amazon Forastero and Trinitario type varieties. It shows that only a small fraction of available cacao genetic diversity from Upper Amazon has been incorporated into farmers’ fields. The narrow genetic background was likely due to limited access to diverse planting materials by local farmers. Increasing the range of parental clones in breeding programs and seed gardens is needed. The results provide scientific baseline information to support cacao rehabilitation in Aceh, Indonesia. In 2014, we used SNP markers to assist the analysis of genotype variation of tolerance to cocoa pod borer (CPB) in Indonesia. CPB is a serious pest of cacao (and rambutan) in Southeast Asia, causing significant yield loss and quality deterioration. A large difference was observed among cacao clones in terms of tolerance to CPB. However, whether this difference can be explored in breeding has not been studied. We estimated heritability of tolerance to CPB in cacao germplasm based on CPB tolerance data repeatedly recorded over five years in Indonesia. Our result shows CPB tolerance has a low heritability, mainly due to the large clone x year interaction. These results provide scientific baseline information for cacao germplasm utilization in Indonesia. Progress was made on the identification of traditional cacao germplasm. Farmer varieties from traditional cacao farms in Madagascar were analyzed using microsatellite DNA markers. The analysis identified three traditional varieties, including Criollo, Amelonado and Trinitario. These are very different from cacao cultivated on the African continent, which has had a significant admixture of Upper Amazon cacao germplasm since the 1950s. The present study showed that Madagascar is distinctive in that all three traditional cacao varieties are still maintained on-farm for cocoa production. Production and marketing of these traditional varieties can provide economic incentives for on-farm conservation of this threatened cacao genetic diversity. Progress was also made in development of SNP markers for tea (Camellia sinensis) germplasm management. Apart from water, tea is the world’s most consumed beverage, representing a $40 billion-a-year global industry. We designed a set of single nucleotide polymorphism (SNP) markers based on the expressed sequence tag (EST) database, and validate these SNP markers in a diverse group of tea varieties, including both fresh and processed commercial loose-leaf teas. This method provides a powerful tool for variety authentication and quality control for the tea industry. This tool is also highly useful for the management of tea genetic resources and breeding, where accurate and efficient genotype identification is essential.


4. Accomplishments
1. Varietal authentication of cacao bean based on single nucleotide polymorphism (SNP) genotyping. A method for assessing varietal authenticity of cacao bean was developed in 2014. This method can verify the genetic identity of a single fermented cacao bean and enabled accurate and robust varietal authentication of cacao. This is the first time that varietal identification on the basis on a single cacao bean has been accomplished. This method greatly enhances the chocolate industry's capacity to authenticate their various sources of cacao. Production and marketing of specialty high-value cocoa provides socioeconomic opportunities for growers, the chocolate industry and especially for consumers. From the conservation perspective, the higher farm-gate revenues from this premium market provides strong economic incentives for demand-driven, in situ/on-farm conservation of cacao genetic diversity.

2. Development of single nucleotide polymorphism (SNP) markers for tea (Camellia sinensis) germplasm management. Apart from water, tea is the world’s most widely consumed beverage. We designed a set of single nucleotide polymorphism (SNP) markers based on the expressed sequence tag (EST) database, and we validated these SNP markers on a diverse group of tea varieties, including both fresh and processed commercial loose-leaf teas. The validation led to the designation of a SNP genotyping panel that can effectively establish DNA fingerprints for all tested tea varieties. This method provides a powerful tool for variety authentication and quality control for the tea industry. This tool is also highly useful for the management of tea genetic resources and breeding, where accurate and efficient genotype identification is essential.


Review Publications
Sitther, V., Zhang, D., Harris, D., Zee, F.T., Yadav, A., Meinhardt, L.W., Dhekney, S. 2014. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-014-0078-5.

Fang, W., Meinhardt, L.W., Mischke, B.S., Bellato, C., Motilal, L., Zhang, D. 2013. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authenticity and traceability. Journal of Agricultural and Food Chemistry. 62:481-487.

Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Umaharan, P. 2013. Microsatellite-aided detection of genetic redundancy improves management of the International Cocoa Genebank, Trinidad. Tree Genetics and Genomes. 9:1395-1411.

Motilal, L., Zhang, D., Umaharanl, P., Boccara, M., Mischke, B.S., Sankar, A., Meinhardt, L.W. 2012. Elucidating genetic identities of cacao germplam in an international cacao collection using molecular markers. Plant Genetic Resources: Characterization and Utilization. 10(3):232-241.

Ji, K., Takrama, J., Meinhardt, L.W., Mischke, B.S., Opoku, S., Padi, F., Zhang, D. 2014. Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers. African Journal of Biotechnology. 13(21):2127-2136.

Zhou, L., Xu, H., Mischke, B.S., Meinhardt, L.W., Zhang, D., Fang, W. 2014. Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress. Horticulture Research. doi:10.1038/hortres.2014.29.