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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #443779

Research Project: Evaluation of Cacao Germplasm for Enhanced Agronomic Traits in the International Cocao Genebank, Trinidad

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21000-303-015-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: May 31, 2023
End Date: May 31, 2028

This project will address the critical need in understanding functional diversity in cacao germplasm and identify likely sources of disease resistance, new genes or alleles for breeders. So far, the efforts in characterization and evaluation of germplasm have received much less attention than germplasm maintenance. Most of the phenotyping in this collection has been limited in morphological descriptors. Only a small fraction of the germplasm held in the international collections has been evaluated for major agronomic traits and disease resistance. Within the genebank holdings, there remains a significant amount of untapped wild germplasm, which may harbor new sources of variations in resistance to diseases and pests, for environmental adaptation, and for processing quality. Through this project, we would like to evaluate the major agronomic traits, such as yield components and diseases resistance in untapped wild populations and analyze the susceptible and resistance mechanisms in a specific set of clones. With improved phenotyping results and high through-put genotyping using next generation sequencing and functional gene markers, we can better understand and document the functional diversity in this collection. Results of this project will contribute to more efficient management and better use of cacao germplasm for varietal development through the identification of new sources and higher levels of resistance to cacao diseases and other important agricultural traits. The new disease resistance genes identified can be used by cacao breeders to improve breeding programs. The objectives of the agreement directly relate to specific project objectives in the NP301 project “Characterizing and Evaluating the Genetic Diversity and Horticultural Value of Genetic Resources for Cacao and Other Tropical Tree Crops Economically Important to the United States’.

Genetic diversity and phenotypic trait analysis of the International Cocoa Genebank, Trinidad (ICG,T). A subset of 200-300 cacao germplasm accessions held in CRU/ UWI (approximately 10% of the entire collection) comprising different wild cacao populations will be selected. The criteria to assemble this working collection will be based on (i) confirmed genetic identity through previous DNA fingerprinting, ii) geographic origin and genotypic diversity, and (iii) historical importance of the accessions. Phenotyping will be carried out in the International Cocoa Genebank, Trinidad. Within plot (intra-clone) mislabeling will be identified using 40-50 SNPs. Phenotypic traits related to yield components and diseases resistance will be evaluated, including number of pods, pod index, bean number, bean size, bean weight, butter fat content, and field resistance to witches’ broom disease and black pod. Previously recorded data on morphological variations, (Bekele et al., 2006) will be combined with new observations. Where duplicated trees in different environments are available, phenotypic data will be recorded from different environments. Technology of next generation sequencing and candidate gene markers will be used to genotype these wild populations. Population structure patterns will be investigated using the Bayesian clustering method implemented in the STRUCTURE program. Both single marker models and haplotype-based tests will be applied for all SNP–trait combinations. Marker data will be compared with trait values by three statistical methods. Patterns of linkage disequilibrium (LD) among SNPs that are significantly associated with the same trait will be assessed using the maximum-likelihood approach implanted in GENETICS.