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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #434577

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

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21000-281-001-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2018
End Date: Aug 31, 2023

This project will address the critical need in understanding genetic diversity of Agrosavia’s cacao collection using SNP fingerprinting, identify and eliminate mislabeled accessions, assess diversity gaps in the collection and analyze genetic diversity of on-farm and wild cacao populations. The cacao germplasm collection established at Agrosavia is composed of accessions collected from within Colombia as well as those introduced from international collections. However, the collection has limited information on identity and diversity of the resources contained therein. A clear knowledge of how much genetic diversity, mislabeling and redundancy exist in the collection is unknown. Mislabeled trees hamper the effectiveness of germplasm evaluation and utilization. By taking this foundational step, Agrosavia, with the support of ARS, will preserve Colombia’s invaluable cacao genetic resources. This project will also assess the common diseases of cacao and determine genetic diversity of these pathogens, which has been largely unknown and therefore, farmers’ efforts to control these diseases are nonspecific and are the same across the country. Results of this project will contribute to more efficient management and better use of cacao germplasm for varietal development through the improved accuracy and efficiency in genebank management and breeding and identification of new sources and higher levels of resistance to cacao diseases and other important horticultural traits. The project will also fill the knowledge gap of genetic diversity of major fungal cacao pathogens within Colombia. Fungal pathogens severely reduce the yield potential of cacao and a complete understanding of the diversity of pathogen populations will greatly improve disease resistant breeding programs in Colombia and across South America.

A total of 6000 - 8,000 leaf samples, representing 700 cacao accessions in Agrosavia’s cacao collection will be sent to Sustainable Perennial Crops Laboratory (SPCL), USDA ARS, BARC in Beltsville, Maryland. DNA will be extracted and checked for concentration and quality at SPCL and submitted to LGC Genomics for SNP genotyping. Off-types will be identified and pedigree records will be verified. Moreover, the scope of genetic diversity in the Agrosavia cacao collection will be analyzed and diversity gaps will be detected. The unique genotypes from Agrosavia gene bank will be identified and high-resolution genotyping will be performed using genotype-by-sequencing techniques (GBS). The objective would be to associate SNP markers with agronomy traits of interest, in particular resistance or tolerance to diseases. The association mapping will generate needed information for marker assisted germplasm evaluation thus accelerate the cacao breeding program in Agrosavia. Based on the result of molecular characterization, representativeness of genetic diversity in Agrosavia's collection will be assessed. Gap filling collecting expeditions will be taken to strategically collecting new accessions from natural populations and farmer fields. This collaborative project also aims at generating knowledge about the diversity of pathogens affecting cacao in Colombia. Disease cacao trees from across different regions of Colombia will be sampled and the sample sent to Agrosavia facilitates to purify the causal organism. If permits can be obtained, then these samples will be sent to USDA-SPCL for analysis. If permits cannot be obtained, then DNA from each sample will be extracted at Agrosavia and the DNA sent to SPCL for analysis. SNP analysis will be conducted as described above for the cacao accessions. The improved knowledge on genetic diversity of the pathogens will enhance the effectiveness of diseases-control measures which are nonspecific and varies across the country. Disease management practices work better when they are tailored to the specific pathogens known to affect the crops in a particular region, and when based on the diversity of the pathogen.