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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #440808

Research Project: Molecular Characterization and Diversity Analysis of Colombian Cacao Genebank Collections and Cacao Pathogens from Colombia

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21000-303-008-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2021
End Date: Aug 1, 2026

The Colombian Amazon is within the center of origin and center of genetic diversity for cacao (the source of chocolate). Understanding the genetic diversity of cacao and its pathogens in Colombia is important for germplasm conservation and disease control. This project will address the genetic diversity of Agrosavia’s cacao collection by identifying and eliminating mislabeled accessions and by assessing diversity gaps in the Colombian cacao collection. Furthermore, this project will analyze the genetic diversity of on-farm and wild cacao populations from various regions of Colombia. A clear knowledge of how much genetic diversity, mislabeling and redundancy that exists in this South American collection is unknown. By taking this foundational step, Agrosavia, with the support of ARS, will improve the preservation of cacao genetic resources in Colombia. This project will also assess the common diseases of cacao in Colombia and determine the genetic diversity of these pathogens, which is largely unknown and therefore, negatively impacting farmers’ efforts to control these diseases. Results of this project will contribute to more efficient management and better use of cacao germplasm for varietal development through efficiency genebank management and breeding. Identification of pathogen genetic diversity will improve the search for new sources of resistance and improve disease control measures for these cacao diseases. This collaborative agreement supports several ARS research projects and the U.S. chocolate industry by promoting a safe and stable supply of fine quality raw material from Colombia. Additionally, this agreement supports the research needs of the USAID/FAS Cacao for Peace Initiative which promotes cacao as a mechanism of peace in Colombia.

Leaf samples from cacao accessions in Agrosavia’s cacao collection and from farmer’s fields will be sent to Sustainable Perennial Crops Laboratory (SPCL), USDA ARS, BARC in Beltsville, Maryland. DNA will be extracted and submitted to LGC Genomics for genotyping. Off-types will be identified, and pedigree records will be verified. Moreover, the scope of genetic diversity in Agrosavia’s cacao collection will be analyzed and diversity gaps will be detected. Unique genotypes from Agrosavia’s collection will be identified and high-resolution genotyping will be performed. Based on this information, gap filling collecting expeditions will be taken to strategically collect new accessions from natural populations and farmer’s fields to augment Agrosavia’s cacao collection. This collaborative project also aims to analysis the diversity of pathogens affecting cacao in Colombia. Diseased cacao trees from across different regions of Colombia will be sampled and the samples sent to Agrosavia’s facilitates to purify the causal organisms. Through Colombian and Aphis permits these samples will be sent to USDA-SPCL for analysis. Genetic analysis will be conducted, and new genotypes of specific pathogens will be further studied via genomic and transcriptomic analysis. Genetic diversity and gene functional analysis of these pathogens will enhance the development and effectiveness of diseases-control measures in Colombia.