Location: Sustainable Perennial Crops Laboratory
Project Number: 8042-21000-281-000-D
Project Type: In-House Appropriated
Start Date: Mar 14, 2018
End Date: Mar 13, 2023
Objective 1: With NPGS and international cooperators, elucidate the geospatial patterns of genetic diversity for the primary gene pool of cacao; strategically acquire cacao genetic resources to fill gaps in NPGS and other genebank collections; and incorporate genetic diversity data into this project’s website, international cacao genetic resources databases, and GRIN-Global. [NP301, C2, PS2A; C4, PS4] Sub-Objective 1A: Elucidate geospatial patterns of genetic diversity for the primary gene pool of cacao. Sub-Objective 1B: Assess whether the genetic diversity in ex situ collections is representative of cacao’s primary gene pool. Fill genetic gaps in those collections by strategically collecting new accessions from natural populations and farmer fields. Sub-Objective 1C: Incorporate genetic diversity data into the project’s website, international cacao genetic resources databases and GRIN-Global. Objective 2: With domestic and international cooperators, characterize and evaluate cacao genetic resources for tolerance to abiotic stresses, for adaptation to growth under different environments and horticultural management regimens, and for other priority horticultural traits. [NP301, C2, PS2A; C1, PS1A] Sub-Objective 2A: Evaluate cacao germplasm for tolerance of soil moisture deficits to identify tolerant clones for breeding drought-tolerant varieties. Sub-Objective 2B: Evaluate cacao germplasm for accumulation and translocation of heavy metals, such as cadmium; assess nutrient use efficiency in different environments to identify superior clones for breeding varieties with high nutrient use efficiency and low concentration of toxic heavy metals. Objective 3: Develop and apply genomic tools for improving the efficiency and effectiveness of managing and utilizing genetic resources of other priority tropical crops, such as tea, guava, longan, rambutan, pitaya, star fruit, mangosteen, peach palm and macadamia nut. [NP301, C2, PS2A] With support from this budgetary increase, more effective coffee genetic resource evaluation, and characterization methods will be developed and applied, focusing on germplasm to be incorporated into the new USDA/ARS coffee genetic resource collection.
Firstly, the project will elucidate geospatial patterns of genetic diversity in the primary gene pool of Theobroma cacao using genomics, spatial genetics and bioinformatics. Wild cacao trees originated from Colombia, Peru, Ecuador, Bolivia, Brazil and French Guiana will be genotyped using Next Generation Sequencing. The NGS data, in conjunction with GIS and ecological information, will be analyzed to reveal distribution of Theobroma cacao in the Amazon. The resulting information will serve as a scientific baseline to support rational decision-making for future germplasm conservation and utilization. Diversity gaps in ex situ collections will be identified and filled through new collection expeditions to increase representation from the geographical centers of diversity and collect landraces and traditional varieties to support in situ/on-farm conservation. In collaboration with USDA’s GRIN-Global team and international partners, this project will also improve the genetic integrity of the genebank holdings and allow us to significantly improve the accuracy of information in the public databases. Secondly, this project will evaluate cacao germplasm for tolerance to key abiotic stresses and horticultural traits, with the emphasis on drought tolerance and lower uptake and transport of Cd to improve the productivity and quality of cacao beans. Research will be conducted with research institutes and universities in Peru, Brazil, Puerto Rico and Ecuador. Cacao genetic resources will be characterized and evaluated in different agricultural ecologies in the Americas for tolerance to abiotic stresses. Field studies will be implemented with drought-tolerant genotypes identified to assess their growth performance and yield potentials under different cacao growing regions of South America. Interntional germplasm will be evaluated to identify genotypes that are tolerant to toxic levels of Cd. New parental genotypes with superior ability to establish under abiotic stresses and superior tolerance to drought and low uptake of soil Cd conditions, will be incorporated in breeding programs. A third objective is to assess the diversity of other less studied tropical fruit and nut species. Genomic tools will be developed for improving the efficiency and effectiveness of managing and utilizing genetic resources of tropical fruits and nuts, such as tea, coffee, guava, longan, rambutan, pitaya, star fruit, mangosteen, peach palm and macadamia. SNP markers will be developed through data mining and/or NGS technology for these species. These putative SNP markers will be validated and evaluated for suitability in germplasm identification and genetic diversity assessment. High quality SNPs will be selected to form a genotyping panel for each species, which will be applied for SNP fingerpritting of germplasm of tropical specialty crops maintained USDA tropical fruits and nuts germplasm collections in Hilo, Hawaii and Mayagüez, Puerto Rico.