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United States Department of Agriculture

Agricultural Research Service

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

Location: Sustainable Perennial Crops Laboratory

2013 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 2013, progress was made in the development of an in house SNP genotyping method. A rapid, reliable, and low-cost method for cacao genotyping was developed in collaboration with Fluidigm Corporation, San Francisco, CA. This SNP genotyping method is ideal for cacao because the specific target amplification (STA) protocol can efficiently deal with the high level of polyphenolic compounds or other PCR inhibitory compounds in cacao leaves. Genomic DNA samples extracted from leaves of different qualities were tested and the results were all successful with outstanding data quality. The robust and simple genotyping tool is highly useful and the system is routinely used now for molecular characterization of cacao germplasm. Progress was also made in assessing genetic diversity in wild cacao populations from Peru. The Peruvian Amazon harbors the highest genetic diversity of cacao. In FY 2013, the wild trees collected in the last four years were analyzed using SNP markers. Spatial pattern of diversity distribution was analyzed based on SNP fingerprinting data and geographic coordinates. The resultant information significantly improves our understanding about the spatial distribution of cacao genetic diversity in the Amazon, which revealed diversity gaps where future collecting expeditions need to be taken.

4. Accomplishments

Last Modified: 2/23/2016
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